File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96657ms, 88.17% of 109621ms total Dropped 1104 nodes (cum <= 548.11ms) flat flat% sum% cum cum% 0 0% 0% 109160ms 99.58% __libc_start_call_main 0 0% 0% 109160ms 99.58% __libc_start_main_impl 0 0% 0% 109160ms 99.58% _start 0 0% 0% 109141ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109141ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109141ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109141ms 99.56% main 0 0% 0% 109106ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109106ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109106ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109099ms 99.52% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.016% 56723ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.026% 53462ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 109ms 0.099% 0.12% 52359ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 400ms 0.36% 0.49% 40342ms 36.80% NagaiHondaForce::AddForceContribution 0 0% 0.49% 39415ms 35.96% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.49% 24470ms 22.32% VertexBasedCellPopulation::Update 2ms 0.0018% 0.49% 24338ms 22.20% MutableVertexMesh::ReMesh 14689ms 13.40% 13.89% 23302ms 21.26% Cylindrical2dVertexMesh::GetVectorFromAtoB 71ms 0.065% 13.96% 17523ms 15.99% Cell::ReadyToDivide 63ms 0.057% 14.02% 16380ms 14.94% AbstractPhaseBasedCellCycleModel::ReadyToDivide 378ms 0.34% 14.36% 15147ms 13.82% NagaiHondaForce::GetAdhesionParameter 117ms 0.11% 14.47% 14073ms 12.84% CellPropertyCollection::GetPropertiesType (inline) 417ms 0.38% 14.85% 14047ms 12.81% boost::numeric::ublas::c_vector::c_vector (partial-inline) 115ms 0.1% 14.95% 13995ms 12.77% SimpleWntCellCycleModel::UpdateCellCyclePhase 402ms 0.37% 15.32% 12474ms 11.38% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.44% 12080ms 11.02% MutableVertexMesh::CheckForIntersections 3510ms 3.20% 18.64% 11803ms 10.77% __dynamic_cast 78ms 0.071% 18.72% 11723ms 10.69% AbstractCellProperty::IsSubType (inline) 75ms 0.068% 18.78% 11523ms 10.51% VertexBasedCellPopulation::GetDampingConstant 95ms 0.087% 18.87% 10481ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 1301ms 1.19% 20.06% 10370ms 9.46% std::__new_allocator::allocate (inline) 51ms 0.047% 20.10% 10363ms 9.45% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 36ms 0.033% 20.14% 10258ms 9.36% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.14% 9852ms 8.99% std::allocator_traits::allocate (inline) 0 0% 20.14% 9843ms 8.98% std::_Rb_tree::_M_create_node (inline) 2666ms 2.43% 22.57% 9188ms 8.38% boost::numeric::ublas::indexing_vector_assign 0 0% 22.57% 9180ms 8.37% std::_Rb_tree::_M_get_node (inline) 1434ms 1.31% 23.88% 9166ms 8.36% std::_Rb_tree::_M_erase 824ms 0.75% 24.63% 9162ms 8.36% operator new 79ms 0.072% 24.70% 8993ms 8.20% Cell::GetMutationState 831ms 0.76% 25.46% 8979ms 8.19% VertexMesh::ElementIncludesPoint 322ms 0.29% 25.75% 8967ms 8.18% VertexMesh::GetNextEdgeGradientOfElementAtNode 29ms 0.026% 25.78% 8930ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.78% 8742ms 7.97% std::_Rb_tree::_Alloc_node::operator() (inline) 520ms 0.47% 26.25% 8418ms 7.68% VertexMesh::GetCentroidOfElement 195ms 0.18% 26.43% 8251ms 7.53% std::_Rb_tree::~_Rb_tree (inline) 3446ms 3.14% 29.57% 8155ms 7.44% __GI___libc_malloc 0 0% 29.57% 8065ms 7.36% std::_Rb_tree::_M_drop_node (inline) 267ms 0.24% 29.82% 7803ms 7.12% std::__new_allocator::deallocate (inline) 0 0% 29.82% 7772ms 7.09% std::allocator_traits::deallocate (inline) 0 0% 29.82% 7770ms 7.09% std::set::~set (inline) 19ms 0.017% 29.84% 7727ms 7.05% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.84% 7724ms 7.05% std::_Rb_tree::_M_put_node (inline) 3019ms 2.75% 32.59% 7567ms 6.90% __GI___libc_free 490ms 0.45% 33.04% 7412ms 6.76% std::map::operator[] (partial-inline) 165ms 0.15% 33.19% 7343ms 6.70% std::_Rb_tree::_Rb_tree (partial-inline) 1497ms 1.37% 34.55% 7292ms 6.65% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 673ms 0.61% 35.17% 6900ms 6.29% std::_Rb_tree::_M_copy (inline) 11ms 0.01% 35.18% 6865ms 6.26% std::set::set (inline) 6627ms 6.05% 41.22% 6627ms 6.05% __strcmp_avx2 100ms 0.091% 41.31% 6391ms 5.83% SimpleWntCellCycleModel::GetWntLevel 152ms 0.14% 41.45% 6213ms 5.67% WntConcentration::GetWntLevel 6120ms 5.58% 47.03% 6120ms 5.58% boost::numeric::ublas::c_vector::operator() 743ms 0.68% 47.71% 5936ms 5.42% std::_Rb_tree::_M_clone_node (inline) 2323ms 2.12% 49.83% 5895ms 5.38% std::_Rb_tree::_M_lower_bound (inline) 2647ms 2.41% 52.25% 5552ms 5.06% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.026% 52.27% 5522ms 5.04% MutableVertexMesh::RemoveDeletedNodes 0 0% 52.27% 5487ms 5.01% std::set::insert (inline) 31ms 0.028% 52.30% 5352ms 4.88% EdgeHelper::RemoveDeletedEdges 42ms 0.038% 52.34% 5047ms 4.60% EdgeHelper::UpdateEdgesMapKey 1569ms 1.43% 53.77% 4990ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.77% 4750ms 4.33% std::_Rb_tree::lower_bound (inline) 0 0% 53.77% 4750ms 4.33% std::map::lower_bound (inline) 225ms 0.21% 53.98% 4747ms 4.33% MutableElement::ResetIndex 2ms 0.0018% 53.98% 4678ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 573ms 0.52% 54.50% 4637ms 4.23% std::_Rb_tree::_M_insert_ (inline) 4248ms 3.88% 58.37% 4530ms 4.13% _int_free 59ms 0.054% 58.43% 4485ms 4.09% std::set_intersection (inline) 304ms 0.28% 58.71% 4426ms 4.04% std::__set_intersection 115ms 0.1% 58.81% 4123ms 3.76% AbstractCellPopulation::GetCellUsingLocationIndex 42ms 0.038% 58.85% 4007ms 3.66% Cell::GetCellProliferativeType 3993ms 3.64% 62.49% 3993ms 3.64% boost::numeric::ublas::same_impl_ex 3ms 0.0027% 62.49% 3615ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 76ms 0.069% 62.56% 3572ms 3.26% AbstractCellProperty::IsType (inline) 0 0% 62.56% 3264ms 2.98% std::insert_iterator::operator= (inline) 50ms 0.046% 62.61% 3184ms 2.90% Cell::SetCellProliferativeType 780ms 0.71% 63.32% 3149ms 2.87% AbstractElement::GetNodeLocation 2243ms 2.05% 65.37% 3092ms 2.82% _int_malloc 3005ms 2.74% 68.11% 3005ms 2.74% std::_Rb_tree::_S_right (inline) 28ms 0.026% 68.13% 2998ms 2.73% std::_Rb_tree::erase 0 0% 68.13% 2948ms 2.69% std::_Rb_tree::_M_insert_unique_ (inline) 634ms 0.58% 68.71% 2820ms 2.57% boost::numeric::ublas::vector_binary::size (inline) 242ms 0.22% 68.93% 2712ms 2.47% VertexMesh::GetAreaGradientOfElementAtNode 442ms 0.4% 69.34% 2576ms 2.35% std::_Rb_tree_const_iterator::operator++ (inline) 746ms 0.68% 70.02% 2572ms 2.35% AbstractCellProperty::IsSame 1ms 0.00091% 70.02% 2539ms 2.32% std::_Rb_tree::_M_insert_unique 43ms 0.039% 70.06% 2506ms 2.29% CellPropertyCollection::HasProperty 0 0% 70.06% 2446ms 2.23% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.06% 2412ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.06% 2401ms 2.19% Cell::HasCellProperty (inline) 24ms 0.022% 70.08% 2398ms 2.19% Cell::GetCellData 139ms 0.13% 70.21% 2303ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 70.21% 2281ms 2.08% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.19% 70.40% 2272ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 94ms 0.086% 70.48% 2239ms 2.04% VertexMesh::GetVolumeOfElement 0 0% 70.48% 2236ms 2.04% boost::numeric::ublas::c_vector::operator-= (inline) 44ms 0.04% 70.52% 2123ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 1415ms 1.29% 71.81% 2040ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 71.81% 2000ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0036% 71.82% 1992ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1953ms 1.78% 73.60% 1953ms 1.78% std::_Rb_tree_increment 1ms 0.00091% 73.60% 1917ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.60% 1917ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 71ms 0.065% 73.66% 1910ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 481ms 0.44% 74.10% 1826ms 1.67% std::type_info::operator== (inline) 0 0% 74.10% 1786ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 38ms 0.035% 74.14% 1725ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 17ms 0.016% 74.15% 1616ms 1.47% VertexMesh::GetSurfaceAreaOfElement 46ms 0.042% 74.19% 1604ms 1.46% Node::RemoveElement 23ms 0.021% 74.22% 1578ms 1.44% std::set::erase (inline) 181ms 0.17% 74.38% 1530ms 1.40% CellPropertyCollection::AddProperty 78ms 0.071% 74.45% 1500ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 72ms 0.066% 74.52% 1498ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 31ms 0.028% 74.55% 1492ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.55% 1402ms 1.28% tcache_get (inline) 1402ms 1.28% 75.82% 1402ms 1.28% tcache_get_n (inline) 0 0% 75.82% 1317ms 1.20% OffLatticeSimulation::ApplyBoundaries 0 0% 75.82% 1260ms 1.15% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.82% 1252ms 1.14% boost::numeric::ublas::norm_2 (inline) 545ms 0.5% 76.32% 1246ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 63ms 0.057% 76.38% 1242ms 1.13% std::less::operator() (inline) 982ms 0.9% 77.28% 1179ms 1.08% std::operator< (inline) 98ms 0.089% 77.36% 1149ms 1.05% std::_Rb_tree::find (inline) 1144ms 1.04% 78.41% 1144ms 1.04% Node::rGetLocation 0 0% 78.41% 1113ms 1.02% std::_Rb_tree::clear (inline) 1107ms 1.01% 79.42% 1107ms 1.01% std::_Rb_tree_insert_and_rebalance 92ms 0.084% 79.50% 1105ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 23ms 0.021% 79.52% 1102ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.52% 1101ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.52% 1086ms 0.99% std::map::clear (inline) 1041ms 0.95% 80.47% 1041ms 0.95% [libchaste_cell_based.so] 1041ms 0.95% 81.42% 1041ms 0.95% std::vector::size (inline) 25ms 0.023% 81.45% 1027ms 0.94% CellPropertyRegistry::Get 158ms 0.14% 81.59% 1019ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 81.59% 1019ms 0.93% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0073% 81.60% 1017ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 964ms 0.88% 82.48% 964ms 0.88% [libchaste_mesh.so] 411ms 0.37% 82.85% 941ms 0.86% Edge::GetMapIndex 0 0% 82.85% 931ms 0.85% std::map::find (inline) 0 0% 82.85% 913ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0036% 82.85% 913ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.068% 82.92% 909ms 0.83% std::swap_ranges (inline) 28ms 0.026% 82.95% 892ms 0.81% boost::numeric::ublas::detail::expression_type_check (inline) 146ms 0.13% 83.08% 856ms 0.78% boost::numeric::ublas::detail::equals 2ms 0.0018% 83.08% 854ms 0.78% VertexMeshWriter::MakeVtkMesh 837ms 0.76% 83.85% 837ms 0.76% std::swap (inline) 118ms 0.11% 83.95% 834ms 0.76% MutableElement::GetNodeLocalIndex 0 0% 83.95% 834ms 0.76% std::iter_swap (inline) 829ms 0.76% 84.71% 832ms 0.76% boost::detail::sp_counted_base::release 185ms 0.17% 84.88% 797ms 0.73% boost::shared_ptr::shared_ptr (inline) 102ms 0.093% 84.97% 782ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 20ms 0.018% 84.99% 769ms 0.7% MutableElement::RegisterWithEdges (inline) 19ms 0.017% 85.01% 766ms 0.7% Edge::AddElement 446ms 0.41% 85.42% 737ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 724ms 0.66% 86.08% 724ms 0.66% Node::GetIndex 114ms 0.1% 86.18% 713ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.18% 713ms 0.65% std::allocator_traits::construct (inline) 0 0% 86.18% 695ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.18% 677ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.20% 677ms 0.62% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0018% 86.21% 673ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.21% 665ms 0.61% boost::numeric::ublas::norm_inf (inline) 343ms 0.31% 86.52% 665ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.52% 663ms 0.6% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.52% 619ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 568ms 0.52% 87.04% 610ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 87.04% 609ms 0.56% vtkPolygon::New 0 0% 87.04% 608ms 0.55% vtkPolygon::vtkPolygon 603ms 0.55% 87.59% 603ms 0.55% operator delete 32ms 0.029% 87.62% 602ms 0.55% MutableElement::RegisterWithNodes (inline) 578ms 0.53% 88.14% 578ms 0.53% [libstdc++.so.6.0.33] 26ms 0.024% 88.17% 561ms 0.51% Node::AddElement 7ms 0.0064% 88.17% 550ms 0.5% std::vector::_M_default_append (inline)