File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97365ms, 88.96% of 109454ms total Dropped 1053 nodes (cum <= 547.27ms) flat flat% sum% cum cum% 0 0% 0% 108970ms 99.56% __libc_start_call_main 0 0% 0% 108970ms 99.56% __libc_start_main_impl 0 0% 0% 108970ms 99.56% _start 0 0% 0% 108951ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108951ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108951ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108951ms 99.54% main 0 0% 0% 108914ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108914ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108914ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 108907ms 99.50% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.014% 56441ms 51.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 24ms 0.022% 0.036% 53291ms 48.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 113ms 0.1% 0.14% 52165ms 47.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 319ms 0.29% 0.43% 39917ms 36.47% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.43% 39389ms 35.99% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.43% 24317ms 22.22% VertexBasedCellPopulation::Update 0 0% 0.43% 24193ms 22.10% MutableVertexMesh::ReMesh 14532ms 13.28% 13.71% 22892ms 20.91% Cylindrical2dVertexMesh::GetVectorFromAtoB 82ms 0.075% 13.78% 17664ms 16.14% Cell::ReadyToDivide 69ms 0.063% 13.85% 16412ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 319ms 0.29% 14.14% 14901ms 13.61% NagaiHondaForce::GetAdhesionParameter 121ms 0.11% 14.25% 14271ms 13.04% CellPropertyCollection::GetPropertiesType (inline) 113ms 0.1% 14.35% 13934ms 12.73% SimpleWntCellCycleModel::UpdateCellCyclePhase 436ms 0.4% 14.75% 13930ms 12.73% boost::numeric::ublas::c_vector::c_vector (partial-inline) 327ms 0.3% 15.05% 12368ms 11.30% boost::numeric::ublas::vector_assign (inline) 128ms 0.12% 15.17% 11995ms 10.96% MutableVertexMesh::CheckForIntersections 3607ms 3.30% 18.46% 11841ms 10.82% __dynamic_cast 81ms 0.074% 18.54% 11822ms 10.80% VertexBasedCellPopulation::GetDampingConstant 87ms 0.079% 18.62% 11781ms 10.76% AbstractCellProperty::IsSubType (inline) 109ms 0.1% 18.72% 10746ms 9.82% AbstractTargetAreaModifier::UpdateTargetAreas 54ms 0.049% 18.76% 10609ms 9.69% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.026% 18.79% 10415ms 9.52% AbstractCellBasedSimulation::DoCellBirth 1339ms 1.22% 20.01% 10322ms 9.43% std::__new_allocator::allocate (inline) 0 0% 20.01% 9856ms 9.00% std::allocator_traits::allocate (inline) 0 0% 20.01% 9847ms 9.00% std::_Rb_tree::_M_create_node (inline) 2713ms 2.48% 22.49% 9266ms 8.47% boost::numeric::ublas::indexing_vector_assign 0 0% 22.49% 9208ms 8.41% std::_Rb_tree::_M_get_node (inline) 1406ms 1.28% 23.78% 9203ms 8.41% std::_Rb_tree::_M_erase 84ms 0.077% 23.85% 9120ms 8.33% Cell::GetMutationState 890ms 0.81% 24.67% 9086ms 8.30% operator new 375ms 0.34% 25.01% 8949ms 8.18% VertexMesh::GetNextEdgeGradientOfElementAtNode 767ms 0.7% 25.71% 8883ms 8.12% VertexMesh::ElementIncludesPoint 23ms 0.021% 25.73% 8852ms 8.09% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.73% 8591ms 7.85% std::_Rb_tree::_Alloc_node::operator() (inline) 203ms 0.19% 25.92% 8360ms 7.64% std::_Rb_tree::~_Rb_tree (inline) 477ms 0.44% 26.35% 8339ms 7.62% VertexMesh::GetCentroidOfElement 0 0% 26.35% 8093ms 7.39% std::_Rb_tree::_M_drop_node (inline) 3109ms 2.84% 29.19% 8030ms 7.34% __GI___libc_malloc 0 0% 29.19% 7894ms 7.21% std::set::~set (inline) 270ms 0.25% 29.44% 7885ms 7.20% std::__new_allocator::deallocate (inline) 0 0% 29.44% 7846ms 7.17% std::allocator_traits::deallocate (inline) 423ms 0.39% 29.83% 7830ms 7.15% std::map::operator[] (partial-inline) 0 0% 29.83% 7784ms 7.11% std::_Rb_tree::_M_put_node (inline) 27ms 0.025% 29.85% 7701ms 7.04% MutableVertexMesh::RemoveDeletedNodesAndElements 3050ms 2.79% 32.64% 7660ms 7.00% __GI___libc_free 1480ms 1.35% 33.99% 7068ms 6.46% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 114ms 0.1% 34.09% 7033ms 6.43% std::_Rb_tree::_Rb_tree (partial-inline) 646ms 0.59% 34.68% 6694ms 6.12% std::_Rb_tree::_M_copy (inline) 6690ms 6.11% 40.80% 6690ms 6.11% __strcmp_avx2 13ms 0.012% 40.81% 6603ms 6.03% std::set::set (inline) 102ms 0.093% 40.90% 6291ms 5.75% SimpleWntCellCycleModel::GetWntLevel 2469ms 2.26% 43.16% 6208ms 5.67% std::_Rb_tree::_M_lower_bound (inline) 100ms 0.091% 43.25% 6111ms 5.58% WntConcentration::GetWntLevel 6029ms 5.51% 48.76% 6029ms 5.51% boost::numeric::ublas::c_vector::operator() 775ms 0.71% 49.47% 5751ms 5.25% std::_Rb_tree::_M_clone_node (inline) 2685ms 2.45% 51.92% 5679ms 5.19% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.022% 51.94% 5560ms 5.08% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.94% 5463ms 4.99% std::set::insert (inline) 37ms 0.034% 51.97% 5400ms 4.93% EdgeHelper::RemoveDeletedEdges 35ms 0.032% 52.01% 5127ms 4.68% EdgeHelper::UpdateEdgesMapKey 0 0% 52.01% 5101ms 4.66% std::_Rb_tree::lower_bound (inline) 0 0% 52.01% 5101ms 4.66% std::map::lower_bound (inline) 1547ms 1.41% 53.42% 4933ms 4.51% boost::numeric::ublas::c_vector::operator[] (inline) 181ms 0.17% 53.59% 4710ms 4.30% MutableElement::ResetIndex 1ms 0.00091% 53.59% 4649ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 514ms 0.47% 54.06% 4649ms 4.25% std::_Rb_tree::_M_insert_ (inline) 4293ms 3.92% 57.98% 4604ms 4.21% _int_free 47ms 0.043% 58.02% 4375ms 4.00% std::set_intersection (inline) 238ms 0.22% 58.24% 4328ms 3.95% std::__set_intersection 111ms 0.1% 58.34% 4222ms 3.86% AbstractCellPopulation::GetCellUsingLocationIndex 3963ms 3.62% 61.96% 3963ms 3.62% boost::numeric::ublas::same_impl_ex 74ms 0.068% 62.03% 3954ms 3.61% AbstractCellProperty::IsType (inline) 42ms 0.038% 62.07% 3940ms 3.60% Cell::GetCellProliferativeType 8ms 0.0073% 62.07% 3599ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.07% 3265ms 2.98% std::insert_iterator::operator= (inline) 831ms 0.76% 62.83% 3253ms 2.97% AbstractElement::GetNodeLocation 2387ms 2.18% 65.01% 3243ms 2.96% _int_malloc 3111ms 2.84% 67.86% 3111ms 2.84% std::_Rb_tree::_S_right (inline) 34ms 0.031% 67.89% 3052ms 2.79% Cell::SetCellProliferativeType 42ms 0.038% 67.93% 3011ms 2.75% std::_Rb_tree::erase 8ms 0.0073% 67.93% 2841ms 2.60% std::_Rb_tree::_M_insert_unique_ (inline) 70ms 0.064% 68.00% 2807ms 2.56% CellPropertyCollection::HasProperty 795ms 0.73% 68.72% 2804ms 2.56% AbstractCellProperty::IsSame 384ms 0.35% 69.07% 2796ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 618ms 0.56% 69.64% 2705ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.64% 2699ms 2.47% Cell::HasCellProperty (inline) 3ms 0.0027% 69.64% 2622ms 2.40% std::_Rb_tree::_M_insert_unique 0 0% 69.64% 2582ms 2.36% boost::numeric::ublas::c_vector::operator-= (inline) 26ms 0.024% 69.66% 2562ms 2.34% Cell::GetCellData 209ms 0.19% 69.86% 2449ms 2.24% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.86% 2421ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 103ms 0.094% 69.95% 2388ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.95% 2320ms 2.12% AbstractCellPopulation::WriteResultsToFiles 41ms 0.037% 69.99% 2255ms 2.06% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0046% 69.99% 2218ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 2214ms 2.02% 72.01% 2214ms 2.02% std::_Rb_tree_increment 216ms 0.2% 72.21% 2203ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 103ms 0.094% 72.31% 2197ms 2.01% VertexMesh::GetVolumeOfElement 1417ms 1.29% 73.60% 2047ms 1.87% std::_Rb_tree::equal_range (inline) 499ms 0.46% 74.06% 2009ms 1.84% std::type_info::operator== (inline) 0 0% 74.06% 1903ms 1.74% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.06% 1894ms 1.73% VertexBasedCellPopulation::WriteCellVtkResultsToFile 57ms 0.052% 74.11% 1852ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 74.11% 1832ms 1.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.11% 1832ms 1.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 21ms 0.019% 74.13% 1725ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.13% 1698ms 1.55% VertexMeshWriter::WriteVtkUsingMesh 51ms 0.047% 74.18% 1640ms 1.50% Node::RemoveElement 23ms 0.021% 74.20% 1606ms 1.47% std::set::erase (inline) 24ms 0.022% 74.22% 1600ms 1.46% VertexMesh::GetSurfaceAreaOfElement 163ms 0.15% 74.37% 1570ms 1.43% CellPropertyCollection::AddProperty 26ms 0.024% 74.39% 1550ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 91ms 0.083% 74.48% 1532ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.48% 1482ms 1.35% tcache_get (inline) 1482ms 1.35% 75.83% 1482ms 1.35% tcache_get_n (inline) 155ms 0.14% 75.97% 1439ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.97% 1312ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 63ms 0.058% 76.03% 1305ms 1.19% std::less::operator() (inline) 0 0% 76.03% 1256ms 1.15% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1044ms 0.95% 76.98% 1242ms 1.13% std::operator< (inline) 1225ms 1.12% 78.10% 1225ms 1.12% Node::rGetLocation 1ms 0.00091% 78.10% 1217ms 1.11% OffLatticeSimulation::ApplyBoundaries 16ms 0.015% 78.12% 1170ms 1.07% CellPropertyRegistry::Get 0 0% 78.12% 1148ms 1.05% boost::numeric::ublas::norm_2 (inline) 0 0% 78.12% 1147ms 1.05% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 78.12% 1147ms 1.05% boost::numeric::ublas::c_vector::swap (inline) 1142ms 1.04% 79.16% 1142ms 1.04% std::_Rb_tree_insert_and_rebalance 75ms 0.069% 79.23% 1142ms 1.04% std::swap_ranges (inline) 489ms 0.45% 79.68% 1139ms 1.04% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1105ms 1.01% 80.69% 1105ms 1.01% [libchaste_cell_based.so] 110ms 0.1% 80.79% 1104ms 1.01% std::_Rb_tree::find (inline) 67ms 0.061% 80.85% 1100ms 1.00% std::_Rb_tree::_M_erase_aux (partial-inline) 1069ms 0.98% 81.83% 1069ms 0.98% std::swap (inline) 0 0% 81.83% 1067ms 0.97% std::iter_swap (inline) 0 0% 81.83% 1049ms 0.96% std::_Rb_tree::clear (inline) 15ms 0.014% 81.84% 1036ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 81.84% 1030ms 0.94% std::map::clear (inline) 138ms 0.13% 81.97% 1004ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.97% 1004ms 0.92% boost::shared_ptr::~shared_ptr (inline) 3ms 0.0027% 81.97% 995ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 965ms 0.88% 82.85% 965ms 0.88% std::vector::size (inline) 369ms 0.34% 83.19% 957ms 0.87% Edge::GetMapIndex 1ms 0.00091% 83.19% 911ms 0.83% std::map::find (inline) 9ms 0.0082% 83.20% 897ms 0.82% boost::numeric::ublas::detail::expression_type_check (inline) 895ms 0.82% 84.02% 895ms 0.82% [libchaste_mesh.so] 146ms 0.13% 84.15% 872ms 0.8% boost::numeric::ublas::detail::equals 0 0% 84.15% 849ms 0.78% VertexMeshWriter::MakeVtkMesh 835ms 0.76% 84.91% 840ms 0.77% boost::detail::sp_counted_base::release 120ms 0.11% 85.02% 812ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 93ms 0.085% 85.11% 780ms 0.71% MutableElement::GetNodeLocalIndex 773ms 0.71% 85.81% 773ms 0.71% Node::GetIndex 136ms 0.12% 85.94% 773ms 0.71% boost::shared_ptr::shared_ptr (inline) 21ms 0.019% 85.96% 765ms 0.7% MutableElement::RegisterWithEdges (inline) 25ms 0.023% 85.98% 755ms 0.69% Edge::AddElement 0 0% 85.98% 691ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.00% 691ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.00% 684ms 0.62% boost::numeric::ublas::norm_inf (inline) 336ms 0.31% 86.30% 684ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.30% 678ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 106ms 0.097% 86.40% 676ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.40% 676ms 0.62% std::allocator_traits::construct (inline) 406ms 0.37% 86.77% 670ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.77% 646ms 0.59% std::_Vector_base::_M_allocate (inline) 0 0% 86.77% 639ms 0.58% std::_Rb_tree::_M_construct_node (inline) 607ms 0.55% 87.33% 637ms 0.58% boost::detail::shared_count::shared_count (inline) 0 0% 87.33% 617ms 0.56% vtkPolygon::New 1ms 0.00091% 87.33% 617ms 0.56% vtkPolygon::vtkPolygon 37ms 0.034% 87.36% 616ms 0.56% MutableElement::RegisterWithNodes (inline) 588ms 0.54% 87.90% 588ms 0.54% boost::shared_ptr::operator-> (inline) 26ms 0.024% 87.92% 582ms 0.53% Node::AddElement 571ms 0.52% 88.44% 571ms 0.52% [libstdc++.so.6.0.33] 7ms 0.0064% 88.45% 556ms 0.51% std::vector::_M_default_append (inline) 0 0% 88.45% 552ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 552ms 0.5% 88.96% 552ms 0.5% operator delete