File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 104580ms, 88.30% of 118440ms total Dropped 1122 nodes (cum <= 592.20ms) flat flat% sum% cum cum% 0 0% 0% 118178ms 99.78% __libc_start_call_main 0 0% 0% 118178ms 99.78% __libc_start_main_impl 0 0% 0% 118178ms 99.78% _start 0 0% 0% 118160ms 99.76% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 118160ms 99.76% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 118160ms 99.76% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 118160ms 99.76% main 0 0% 0% 118123ms 99.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 118123ms 99.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 118123ms 99.73% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0034% 0.0034% 118115ms 99.73% AbstractCellBasedSimulation::Solve 12ms 0.01% 0.014% 62293ms 52.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 29ms 0.024% 0.038% 58297ms 49.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 151ms 0.13% 0.17% 56859ms 48.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 587ms 0.5% 0.66% 44867ms 37.88% NagaiHondaForce::AddForceContribution 1ms 0.00084% 0.66% 40484ms 34.18% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.0059% 0.67% 23887ms 20.17% VertexBasedCellPopulation::Update 1ms 0.00084% 0.67% 23760ms 20.06% MutableVertexMesh::ReMesh 100ms 0.084% 0.75% 20414ms 17.24% Cell::ReadyToDivide 10003ms 8.45% 9.20% 20074ms 16.95% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.081% 9.28% 19148ms 16.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 400ms 0.34% 9.62% 17571ms 14.84% boost::numeric::ublas::c_vector::c_vector (partial-inline) 82ms 0.069% 9.69% 17027ms 14.38% NagaiHondaForce::GetAdhesionParameter 148ms 0.12% 9.81% 16484ms 13.92% SimpleWntCellCycleModel::UpdateCellCyclePhase 553ms 0.47% 10.28% 15789ms 13.33% boost::numeric::ublas::vector_assign (inline) 1122ms 0.95% 11.23% 14659ms 12.38% std::__new_allocator::allocate (inline) 53ms 0.045% 11.27% 14576ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.27% 13959ms 11.79% std::allocator_traits::allocate (inline) 0 0% 11.27% 13634ms 11.51% std::_Rb_tree::_M_create_node (inline) 827ms 0.7% 11.97% 13505ms 11.40% operator new 0 0% 11.97% 13142ms 11.10% std::_Rb_tree::_M_get_node (inline) 67ms 0.057% 12.03% 12606ms 10.64% AbstractTargetAreaModifier::UpdateTargetAreas 35ms 0.03% 12.06% 12487ms 10.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 4289ms 3.62% 15.68% 12089ms 10.21% __GI___libc_malloc 162ms 0.14% 15.81% 11884ms 10.03% AbstractCellProperty::IsSubType (inline) 0 0% 15.81% 11883ms 10.03% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.0059% 15.82% 11875ms 10.03% AbstractCellBasedSimulation::DoCellBirth 3841ms 3.24% 19.06% 11801ms 9.96% __dynamic_cast 85ms 0.072% 19.13% 11462ms 9.68% VertexBasedCellPopulation::GetDampingConstant 2832ms 2.39% 21.52% 11425ms 9.65% boost::numeric::ublas::indexing_vector_assign 156ms 0.13% 21.66% 10586ms 8.94% MutableVertexMesh::CheckForIntersections 0 0% 21.66% 9747ms 8.23% std::_Rb_tree::_M_drop_node (inline) 1242ms 1.05% 22.71% 9721ms 8.21% std::_Rb_tree::_M_erase 642ms 0.54% 23.25% 9622ms 8.12% VertexMesh::GetNextEdgeGradientOfElementAtNode 90ms 0.076% 23.32% 9303ms 7.85% VertexBasedCellPopulation::GetLocationOfCellCentre 20ms 0.017% 23.34% 9082ms 7.67% MutableVertexMesh::RemoveDeletedNodesAndElements 366ms 0.31% 23.65% 8939ms 7.55% std::__new_allocator::deallocate (inline) 0 0% 23.65% 8932ms 7.54% std::allocator_traits::deallocate (inline) 350ms 0.3% 23.94% 8890ms 7.51% std::_Rb_tree::~_Rb_tree (inline) 42ms 0.035% 23.98% 8878ms 7.50% Cell::GetMutationState 747ms 0.63% 24.61% 8864ms 7.48% VertexMesh::GetCentroidOfElement 0 0% 24.61% 8809ms 7.44% std::_Rb_tree::_M_put_node (inline) 2125ms 1.79% 26.40% 8770ms 7.40% __GI___libc_free 111ms 0.094% 26.50% 8576ms 7.24% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 26.50% 8465ms 7.15% std::set::~set (inline) 695ms 0.59% 27.09% 8318ms 7.02% std::_Rb_tree::_M_copy (inline) 648ms 0.55% 27.63% 8315ms 7.02% std::map::operator[] (partial-inline) 580ms 0.49% 28.12% 7970ms 6.73% VertexMesh::ElementIncludesPoint 0 0% 28.12% 7743ms 6.54% std::set::insert (inline) 16ms 0.014% 28.14% 7691ms 6.49% std::set::set (inline) 7380ms 6.23% 34.37% 7380ms 6.23% boost::numeric::ublas::c_vector::operator() 986ms 0.83% 35.20% 7357ms 6.21% std::_Rb_tree::_M_clone_node (inline) 223ms 0.19% 35.39% 7259ms 6.13% SimpleWntCellCycleModel::GetWntLevel 888ms 0.75% 36.14% 6886ms 5.81% std::_Rb_tree::_M_insert_ (inline) 152ms 0.13% 36.27% 6882ms 5.81% WntConcentration::GetWntLevel 5750ms 4.85% 41.12% 6402ms 5.41% _int_free 1041ms 0.88% 42.00% 6056ms 5.11% AbstractMesh::GetDistanceBetweenNodes 40ms 0.034% 42.03% 6032ms 5.09% std::set_intersection (inline) 182ms 0.15% 42.19% 5992ms 5.06% std::__set_intersection 5991ms 5.06% 47.25% 5991ms 5.06% __strcmp_evex 220ms 0.19% 47.43% 5762ms 4.86% MutableElement::ResetIndex 2128ms 1.80% 49.23% 5752ms 4.86% std::_Rb_tree::_M_lower_bound (inline) 29ms 0.024% 49.25% 5735ms 4.84% MutableVertexMesh::RemoveDeletedNodes 4430ms 3.74% 52.99% 5648ms 4.77% _int_malloc 2481ms 2.09% 55.09% 5581ms 4.71% __cxxabiv1::__si_class_type_info::__do_dyncast 95ms 0.08% 55.17% 5552ms 4.69% EdgeHelper::RemoveDeletedEdges 982ms 0.83% 56.00% 5408ms 4.57% boost::numeric::ublas::c_vector::operator[] (inline) 22ms 0.019% 56.01% 5214ms 4.40% EdgeHelper::UpdateEdgesMapKey 4923ms 4.16% 60.17% 4923ms 4.16% boost::numeric::ublas::same_impl_ex 0 0% 60.17% 4875ms 4.12% std::_Rb_tree::lower_bound (inline) 0 0% 60.17% 4875ms 4.12% std::map::lower_bound (inline) 0 0% 60.17% 4792ms 4.05% std::insert_iterator::operator= (inline) 96ms 0.081% 60.25% 4749ms 4.01% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 60.25% 4712ms 3.98% AbstractCellBasedSimulation::DoCellRemoval (inline) 33ms 0.028% 60.28% 4608ms 3.89% Cell::GetCellProliferativeType 0 0% 60.28% 4555ms 3.85% std::_Rb_tree::_M_insert_unique_ (inline) 182ms 0.15% 60.43% 4175ms 3.52% AbstractCellProperty::IsType (inline) 904ms 0.76% 61.20% 3780ms 3.19% AbstractElement::GetNodeLocation 156ms 0.13% 61.33% 3731ms 3.15% Cell::SetCellProliferativeType 61ms 0.052% 61.38% 3727ms 3.15% std::_Rb_tree::erase 45ms 0.038% 61.42% 3529ms 2.98% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 834ms 0.7% 62.12% 3321ms 2.80% boost::numeric::ublas::vector_binary::size (inline) 3312ms 2.80% 64.92% 3312ms 2.80% [libchaste_cell_based.so] 2ms 0.0017% 64.92% 3188ms 2.69% std::_Rb_tree::_M_insert_unique (inline) 3164ms 2.67% 67.59% 3164ms 2.67% std::_Rb_tree::_S_right (inline) 0 0% 67.59% 3136ms 2.65% boost::numeric::ublas::c_vector::assign (inline) 387ms 0.33% 67.92% 3088ms 2.61% std::_Rb_tree_const_iterator::operator++ (inline) 19ms 0.016% 67.93% 3036ms 2.56% Cell::GetCellData 157ms 0.13% 68.07% 2869ms 2.42% boost::detail::shared_count::~shared_count (inline) 0 0% 68.07% 2869ms 2.42% boost::shared_ptr::~shared_ptr (inline) 5ms 0.0042% 68.07% 2783ms 2.35% AbstractCellPopulation::Iterator::operator++ (inline) 227ms 0.19% 68.26% 2779ms 2.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 35ms 0.03% 68.29% 2750ms 2.32% CellPropertyCollection::HasProperty 38ms 0.032% 68.32% 2740ms 2.31% std::_Rb_tree::_M_emplace_hint_unique 0 0% 68.32% 2699ms 2.28% Cell::HasCellProperty (inline) 0 0% 68.32% 2686ms 2.27% AbstractCellPopulation::WriteResultsToFiles 325ms 0.27% 68.60% 2666ms 2.25% VertexMesh::GetAreaGradientOfElementAtNode 2607ms 2.20% 70.80% 2644ms 2.23% boost::detail::sp_counted_base::release 685ms 0.58% 71.38% 2574ms 2.17% AbstractCellProperty::IsSame 0 0% 71.38% 2523ms 2.13% boost::numeric::ublas::c_vector::operator-= (inline) 61ms 0.052% 71.43% 2517ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2361ms 1.99% 73.42% 2361ms 1.99% [libchaste_mesh.so] 0 0% 73.42% 2214ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0025% 73.43% 2196ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 28ms 0.024% 73.45% 2123ms 1.79% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1247ms 1.05% 74.50% 2055ms 1.74% std::_Rb_tree::equal_range (inline) 116ms 0.098% 74.60% 2024ms 1.71% VertexMesh::GetVolumeOfElement 1ms 0.00084% 74.60% 2017ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 1998ms 1.69% 76.29% 1998ms 1.69% std::_Rb_tree_increment 547ms 0.46% 76.75% 1889ms 1.59% std::type_info::operator== (inline) 252ms 0.21% 76.96% 1881ms 1.59% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 93ms 0.079% 77.04% 1865ms 1.57% std::_Rb_tree::_M_erase_aux (partial-inline) 1ms 0.00084% 77.04% 1842ms 1.56% tcache_get (inline) 1841ms 1.55% 78.60% 1841ms 1.55% tcache_get_n (inline) 148ms 0.12% 78.72% 1784ms 1.51% CellPropertyCollection::AddProperty 0 0% 78.72% 1751ms 1.48% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.72% 1739ms 1.47% boost::numeric::ublas::vector_binary::operator() (inline) 10ms 0.0084% 78.73% 1732ms 1.46% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.73% 1732ms 1.46% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 175ms 0.15% 78.88% 1706ms 1.44% boost::numeric::ublas::vector_reference::operator() (inline) 95ms 0.08% 78.96% 1592ms 1.34% MutableVertexMesh::CheckForSwapsFromShortEdges 79ms 0.067% 79.02% 1579ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 97ms 0.082% 79.11% 1497ms 1.26% VertexMesh::GetSurfaceAreaOfElement 0 0% 79.11% 1476ms 1.25% OffLatticeSimulation::ApplyBoundaries 34ms 0.029% 79.14% 1472ms 1.24% Node::RemoveElement 9ms 0.0076% 79.14% 1438ms 1.21% std::set::erase (inline) 1403ms 1.18% 80.33% 1403ms 1.18% [libstdc++.so.6.0.33] 45ms 0.038% 80.37% 1339ms 1.13% CellPropertyRegistry::Get 44ms 0.037% 80.40% 1307ms 1.10% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.00084% 80.40% 1193ms 1.01% std::_Rb_tree::clear (inline) 1182ms 1% 81.40% 1182ms 1% Node::rGetLocation 0 0% 81.40% 1167ms 0.99% std::map::clear (inline) 10ms 0.0084% 81.41% 1149ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 42ms 0.035% 81.45% 1108ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 12ms 0.01% 81.46% 1080ms 0.91% MutableElement::RegisterWithEdges (inline) 17ms 0.014% 81.47% 1071ms 0.9% Edge::AddElement 5ms 0.0042% 81.47% 1052ms 0.89% VertexMeshWriter::MakeVtkMesh 266ms 0.22% 81.70% 1043ms 0.88% boost::numeric::ublas::detail::equals 0 0% 81.70% 1032ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.70% 988ms 0.83% boost::numeric::ublas::norm_2 (inline) 238ms 0.2% 81.90% 967ms 0.82% boost::numeric::ublas::vector_norm_2::apply 967ms 0.82% 82.72% 967ms 0.82% std::_Rb_tree_insert_and_rebalance 0 0% 82.72% 944ms 0.8% std::__new_allocator::destroy (inline) 0 0% 82.72% 944ms 0.8% std::allocator_traits::destroy (inline) 0 0% 82.72% 939ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.72% 937ms 0.79% std::map::map (inline) 102ms 0.086% 82.80% 928ms 0.78% std::_Rb_tree::find (inline) 49ms 0.041% 82.84% 881ms 0.74% std::less::operator() (inline) 504ms 0.43% 83.27% 870ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 641ms 0.54% 83.81% 832ms 0.7% std::operator< (inline) 123ms 0.1% 83.91% 824ms 0.7% MutableElement::GetNodeLocalIndex 0 0% 83.91% 806ms 0.68% std::_Vector_base::_M_allocate (inline) 98ms 0.083% 84.00% 796ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.00% 795ms 0.67% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0068% 84.00% 795ms 0.67% boost::numeric::ublas::c_vector::swap (inline) 115ms 0.097% 84.10% 787ms 0.66% std::swap_ranges (inline) 0 0% 84.10% 783ms 0.66% vtkPolygon::New 2ms 0.0017% 84.10% 783ms 0.66% vtkPolygon::vtkPolygon 777ms 0.66% 84.76% 777ms 0.66% std::vector::size (inline) 0 0% 84.76% 772ms 0.65% std::map::find (inline) 46ms 0.039% 84.80% 746ms 0.63% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 84.80% 746ms 0.63% boost::numeric::ublas::vector::vector (inline) 0 0% 84.80% 744ms 0.63% boost::numeric::ublas::norm_inf (inline) 368ms 0.31% 85.11% 744ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 25ms 0.021% 85.13% 729ms 0.62% AbstractNumericalMethod::DetectStepSizeExceptions 570ms 0.48% 85.61% 718ms 0.61% CellPropertyCollection::GetProperty 713ms 0.6% 86.21% 713ms 0.6% tcache_put (inline) 0 0% 86.21% 672ms 0.57% std::iter_swap (inline) 672ms 0.57% 86.78% 672ms 0.57% std::swap (inline) 663ms 0.56% 87.34% 663ms 0.56% Node::GetIndex 2ms 0.0017% 87.34% 649ms 0.55% std::vector::_M_default_append (inline) 94ms 0.079% 87.42% 648ms 0.55% VertexBasedCellPopulation::CheckForStepSizeException 25ms 0.021% 87.44% 647ms 0.55% MutableElement::RegisterWithNodes (inline) 84ms 0.071% 87.51% 644ms 0.54% std::_Rb_tree::_M_upper_bound (inline) 536ms 0.45% 87.97% 631ms 0.53% malloc_consolidate 38ms 0.032% 88.00% 622ms 0.53% Node::AddElement 0 0% 88.00% 622ms 0.53% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.019% 88.02% 622ms 0.53% std::_Rb_tree::_M_insert_node (inline) 0 0% 88.02% 618ms 0.52% vtkCell::vtkCell 334ms 0.28% 88.30% 617ms 0.52% Edge::GetMapIndex