File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 89682ms, 88.09% of 101809ms total Dropped 1099 nodes (cum <= 509.05ms) flat flat% sum% cum cum% 0 0% 0% 101576ms 99.77% __libc_start_call_main 0 0% 0% 101576ms 99.77% __libc_start_main_impl 0 0% 0% 101576ms 99.77% _start 0 0% 0% 101553ms 99.75% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 101553ms 99.75% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 101553ms 99.75% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 101553ms 99.75% main 0 0% 0% 101517ms 99.71% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 101517ms 99.71% CxxTest::TestRunner::runTest (inline) 0 0% 0% 101517ms 99.71% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0029% 0.0029% 101510ms 99.71% AbstractCellBasedSimulation::Solve 10ms 0.0098% 0.013% 53021ms 52.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.014% 0.027% 49636ms 48.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 71ms 0.07% 0.096% 48251ms 47.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 312ms 0.31% 0.4% 37236ms 36.57% NagaiHondaForce::AddForceContribution 0 0% 0.4% 35547ms 34.92% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.002% 0.4% 21114ms 20.74% VertexBasedCellPopulation::Update 0 0% 0.4% 20982ms 20.61% MutableVertexMesh::ReMesh 81ms 0.08% 0.48% 17314ms 17.01% Cell::ReadyToDivide 8681ms 8.53% 9.01% 16694ms 16.40% Cylindrical2dVertexMesh::GetVectorFromAtoB 32ms 0.031% 9.04% 16149ms 15.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 87ms 0.085% 9.13% 15394ms 15.12% NagaiHondaForce::GetAdhesionParameter 60ms 0.059% 9.19% 13864ms 13.62% SimpleWntCellCycleModel::UpdateCellCyclePhase 792ms 0.78% 9.96% 13046ms 12.81% std::__new_allocator::allocate (inline) 405ms 0.4% 10.36% 12866ms 12.64% boost::numeric::ublas::c_vector::c_vector (partial-inline) 77ms 0.076% 10.44% 12737ms 12.51% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.44% 12518ms 12.30% std::allocator_traits::allocate (inline) 0 0% 10.44% 12261ms 12.04% std::_Rb_tree::_M_create_node (inline) 889ms 0.87% 11.31% 12244ms 12.03% operator new 0 0% 11.31% 11883ms 11.67% std::_Rb_tree::_M_get_node (inline) 244ms 0.24% 11.55% 11459ms 11.26% boost::numeric::ublas::vector_assign (inline) 3790ms 3.72% 15.27% 11007ms 10.81% __GI___libc_malloc 88ms 0.086% 15.36% 10644ms 10.45% VertexBasedCellPopulation::GetDampingConstant 46ms 0.045% 15.41% 10583ms 10.39% AbstractTargetAreaModifier::UpdateTargetAreas 0 0% 15.41% 10573ms 10.39% std::_Rb_tree::_Alloc_node::operator() (inline) 39ms 0.038% 15.44% 10495ms 10.31% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 99ms 0.097% 15.54% 10388ms 10.20% AbstractCellProperty::IsSubType (inline) 2758ms 2.71% 18.25% 10309ms 10.13% __dynamic_cast 7ms 0.0069% 18.26% 10153ms 9.97% AbstractCellBasedSimulation::DoCellBirth 141ms 0.14% 18.40% 9404ms 9.24% MutableVertexMesh::CheckForIntersections 1009ms 0.99% 19.39% 8929ms 8.77% std::_Rb_tree::_M_erase 0 0% 19.39% 8905ms 8.75% std::_Rb_tree::_M_drop_node (inline) 354ms 0.35% 19.73% 8429ms 8.28% std::_Rb_tree::~_Rb_tree (inline) 523ms 0.51% 20.25% 8420ms 8.27% std::map::operator[] (partial-inline) 2325ms 2.28% 22.53% 8254ms 8.11% boost::numeric::ublas::indexing_vector_assign 117ms 0.11% 22.65% 8119ms 7.97% std::__new_allocator::deallocate (inline) 0 0% 22.65% 8093ms 7.95% std::allocator_traits::deallocate (inline) 0 0% 22.65% 8021ms 7.88% std::_Rb_tree::_M_put_node (inline) 0 0% 22.65% 8016ms 7.87% std::set::~set (inline) 67ms 0.066% 22.71% 7922ms 7.78% Cell::GetMutationState 2012ms 1.98% 24.69% 7844ms 7.70% __GI___libc_free 43ms 0.042% 24.73% 7830ms 7.69% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.73% 7661ms 7.52% std::set::insert (inline) 13ms 0.013% 24.74% 7611ms 7.48% MutableVertexMesh::RemoveDeletedNodesAndElements 571ms 0.56% 25.30% 7328ms 7.20% VertexMesh::GetCentroidOfElement 423ms 0.42% 25.72% 7229ms 7.10% VertexMesh::GetNextEdgeGradientOfElementAtNode 835ms 0.82% 26.54% 7073ms 6.95% std::_Rb_tree::_M_insert_ (inline) 534ms 0.52% 27.06% 6995ms 6.87% VertexMesh::ElementIncludesPoint 112ms 0.11% 27.17% 6706ms 6.59% std::_Rb_tree::_Rb_tree (partial-inline) 613ms 0.6% 27.78% 6416ms 6.30% std::_Rb_tree::_M_copy (inline) 9ms 0.0088% 27.79% 6287ms 6.18% std::set::set (inline) 6113ms 6.00% 33.79% 6113ms 6.00% boost::numeric::ublas::c_vector::operator() 6097ms 5.99% 39.78% 6097ms 5.99% __strcmp_evex 2286ms 2.25% 42.02% 5964ms 5.86% std::_Rb_tree::_M_lower_bound (inline) 137ms 0.13% 42.16% 5951ms 5.85% SimpleWntCellCycleModel::GetWntLevel 60ms 0.059% 42.22% 5923ms 5.82% std::set_intersection (inline) 188ms 0.18% 42.40% 5863ms 5.76% std::__set_intersection 5003ms 4.91% 47.32% 5771ms 5.67% _int_free 122ms 0.12% 47.44% 5703ms 5.60% WntConcentration::GetWntLevel 756ms 0.74% 48.18% 5618ms 5.52% std::_Rb_tree::_M_clone_node (inline) 871ms 0.86% 49.03% 5596ms 5.50% AbstractMesh::GetDistanceBetweenNodes 30ms 0.029% 49.06% 5435ms 5.34% MutableVertexMesh::RemoveDeletedNodes 4390ms 4.31% 53.38% 5304ms 5.21% _int_malloc 50ms 0.049% 53.42% 5255ms 5.16% EdgeHelper::RemoveDeletedEdges 0 0% 53.42% 5097ms 5.01% std::_Rb_tree::lower_bound (inline) 0 0% 53.42% 5097ms 5.01% std::map::lower_bound (inline) 573ms 0.56% 53.99% 5073ms 4.98% boost::numeric::ublas::c_vector::operator[] (inline) 18ms 0.018% 54.01% 5003ms 4.91% EdgeHelper::UpdateEdgesMapKey 2303ms 2.26% 56.27% 4890ms 4.80% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.27% 4642ms 4.56% std::insert_iterator::operator= (inline) 126ms 0.12% 56.39% 4580ms 4.50% MutableElement::ResetIndex 87ms 0.085% 56.48% 4511ms 4.43% AbstractCellPopulation::GetCellUsingLocationIndex 36ms 0.035% 56.51% 4402ms 4.32% Cell::GetCellProliferativeType 0 0% 56.51% 4353ms 4.28% std::_Rb_tree::_M_insert_unique_ (inline) 3ms 0.0029% 56.51% 4274ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 4209ms 4.13% 60.65% 4209ms 4.13% boost::numeric::ublas::same_impl_ex 137ms 0.13% 60.78% 3454ms 3.39% AbstractCellProperty::IsType (inline) 3ms 0.0029% 60.79% 3308ms 3.25% std::_Rb_tree::_M_insert_unique 119ms 0.12% 60.90% 3295ms 3.24% Cell::SetCellProliferativeType 3283ms 3.22% 64.13% 3283ms 3.22% [libchaste_cell_based.so] 57ms 0.056% 64.18% 3253ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3151ms 3.10% 67.28% 3151ms 3.10% std::_Rb_tree::_S_right (inline) 793ms 0.78% 68.06% 2999ms 2.95% AbstractElement::GetNodeLocation 105ms 0.1% 68.16% 2836ms 2.79% boost::detail::shared_count::~shared_count (inline) 0 0% 68.16% 2836ms 2.79% boost::shared_ptr::~shared_ptr (inline) 33ms 0.032% 68.19% 2747ms 2.70% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.0079% 68.20% 2695ms 2.65% AbstractCellPopulation::Iterator::operator++ (inline) 229ms 0.22% 68.43% 2682ms 2.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 2643ms 2.60% 71.02% 2670ms 2.62% boost::detail::sp_counted_base::release 54ms 0.053% 71.08% 2581ms 2.54% std::_Rb_tree::erase 15ms 0.015% 71.09% 2501ms 2.46% Cell::GetCellData 159ms 0.16% 71.25% 2475ms 2.43% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.25% 2361ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 46ms 0.045% 71.29% 2351ms 2.31% CellPropertyCollection::HasProperty 1ms 0.00098% 71.29% 2332ms 2.29% AbstractCellPopulation::WriteResultsToFiles 0 0% 71.29% 2295ms 2.25% Cell::HasCellProperty (inline) 491ms 0.48% 71.77% 2245ms 2.21% AbstractCellProperty::IsSame 52ms 0.051% 71.83% 2228ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.83% 2211ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 270ms 0.27% 72.09% 2183ms 2.14% std::_Rb_tree_const_iterator::operator++ (inline) 2106ms 2.07% 74.16% 2106ms 2.07% [libchaste_mesh.so] 25ms 0.025% 74.18% 2019ms 1.98% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 246ms 0.24% 74.43% 1980ms 1.94% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 74.43% 1916ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 6ms 0.0059% 74.43% 1905ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 142ms 0.14% 74.57% 1857ms 1.82% CellPropertyCollection::AddProperty 281ms 0.28% 74.85% 1846ms 1.81% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 196ms 0.19% 75.04% 1754ms 1.72% std::type_info::operator== (inline) 0 0% 75.04% 1724ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 99ms 0.097% 75.14% 1714ms 1.68% VertexMesh::GetVolumeOfElement 0 0% 75.14% 1688ms 1.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.0029% 75.14% 1684ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.14% 1684ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 67ms 0.066% 75.21% 1635ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.00098% 75.21% 1538ms 1.51% tcache_get (inline) 1537ms 1.51% 76.72% 1537ms 1.51% tcache_get_n (inline) 62ms 0.061% 76.78% 1495ms 1.47% MutableVertexMesh::CheckForSwapsFromShortEdges 3ms 0.0029% 76.78% 1475ms 1.45% OffLatticeSimulation::ApplyBoundaries 69ms 0.068% 76.85% 1417ms 1.39% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 76.85% 1394ms 1.37% boost::numeric::ublas::vector_binary::operator() (inline) 75ms 0.074% 76.92% 1382ms 1.36% VertexMesh::GetSurfaceAreaOfElement 1306ms 1.28% 78.20% 1306ms 1.28% std::_Rb_tree_increment 31ms 0.03% 78.23% 1288ms 1.27% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 802ms 0.79% 79.02% 1279ms 1.26% std::_Rb_tree::equal_range (inline) 42ms 0.041% 79.06% 1266ms 1.24% Node::RemoveElement 0 0% 79.06% 1224ms 1.20% std::set::erase (inline) 41ms 0.04% 79.10% 1185ms 1.16% Edge::AddElement 13ms 0.013% 79.12% 1176ms 1.16% MutableElement::RegisterWithEdges (inline) 56ms 0.055% 79.17% 1171ms 1.15% CellPropertyRegistry::Get 139ms 0.14% 79.31% 1149ms 1.13% boost::numeric::ublas::vector_reference::operator() (inline) 9ms 0.0088% 79.32% 1086ms 1.07% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.32% 1082ms 1.06% CellPropertyCollection::~CellPropertyCollection (inline) 1054ms 1.04% 80.35% 1054ms 1.04% [libstdc++.so.6.0.33] 1044ms 1.03% 81.38% 1044ms 1.03% std::_Rb_tree_insert_and_rebalance 169ms 0.17% 81.54% 1043ms 1.02% boost::numeric::ublas::detail::equals 1008ms 0.99% 82.53% 1008ms 0.99% Node::rGetLocation 18ms 0.018% 82.55% 981ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.55% 954ms 0.94% boost::numeric::ublas::norm_2 (inline) 97ms 0.095% 82.65% 925ms 0.91% std::_Rb_tree::find (inline) 396ms 0.39% 83.04% 924ms 0.91% boost::numeric::ublas::vector_norm_2::apply 0 0% 83.04% 889ms 0.87% std::__new_allocator::destroy (inline) 0 0% 83.04% 889ms 0.87% std::allocator_traits::destroy (inline) 1ms 0.00098% 83.04% 887ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 83.04% 885ms 0.87% std::_Rb_tree::_M_destroy_node (inline) 866ms 0.85% 83.89% 866ms 0.85% tcache_put (inline) 0 0% 83.89% 857ms 0.84% std::_Rb_tree::clear (inline) 0 0% 83.89% 840ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.00098% 83.89% 840ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 134ms 0.13% 84.02% 839ms 0.82% std::swap_ranges (inline) 58ms 0.057% 84.08% 837ms 0.82% std::less::operator() (inline) 0 0% 84.08% 836ms 0.82% std::map::clear (inline) 0 0% 84.08% 796ms 0.78% std::map::find (inline) 634ms 0.62% 84.70% 791ms 0.78% CellPropertyCollection::GetProperty 598ms 0.59% 85.29% 779ms 0.77% std::operator< (inline) 45ms 0.044% 85.33% 751ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.33% 743ms 0.73% boost::numeric::ublas::norm_inf (inline) 257ms 0.25% 85.58% 743ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.58% 705ms 0.69% std::iter_swap (inline) 705ms 0.69% 86.28% 705ms 0.69% std::swap (inline) 693ms 0.68% 86.96% 693ms 0.68% std::vector::size (inline) 0 0% 86.96% 686ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.023% 86.98% 686ms 0.67% std::_Rb_tree::_M_insert_node (inline) 67ms 0.066% 87.05% 678ms 0.67% MutableElement::GetNodeLocalIndex 294ms 0.29% 87.33% 675ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 24ms 0.024% 87.36% 652ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 2ms 0.002% 87.36% 646ms 0.63% vtkPolygon::New 0 0% 87.36% 644ms 0.63% vtkPolygon::vtkPolygon 1ms 0.00098% 87.36% 632ms 0.62% std::_Vector_base::_M_allocate (inline) 89ms 0.087% 87.45% 628ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 27ms 0.027% 87.47% 626ms 0.61% MutableElement::RegisterWithNodes (inline) 42ms 0.041% 87.52% 586ms 0.58% Node::AddElement 578ms 0.57% 88.08% 578ms 0.57% Node::GetIndex 5ms 0.0049% 88.09% 533ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.09% 533ms 0.52% boost::numeric::ublas::vector::vector (inline)