File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98285ms, 88.14% of 111513ms total Dropped 1133 nodes (cum <= 557.57ms) flat flat% sum% cum cum% 0 0% 0% 111159ms 99.68% __libc_start_call_main 0 0% 0% 111159ms 99.68% __libc_start_main_impl 0 0% 0% 111159ms 99.68% _start 0 0% 0% 111137ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 111137ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 111137ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 111137ms 99.66% main 0 0% 0% 111089ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 111089ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 111089ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 111081ms 99.61% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.022% 57810ms 51.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.015% 0.038% 54339ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 167ms 0.15% 0.19% 52812ms 47.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 332ms 0.3% 0.49% 40093ms 35.95% NagaiHondaForce::AddForceContribution 0 0% 0.49% 39803ms 35.69% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0045% 0.49% 24595ms 22.06% VertexBasedCellPopulation::Update 1ms 0.0009% 0.49% 24433ms 21.91% MutableVertexMesh::ReMesh 14470ms 12.98% 13.47% 23144ms 20.75% Cylindrical2dVertexMesh::GetVectorFromAtoB 99ms 0.089% 13.56% 17878ms 16.03% Cell::ReadyToDivide 81ms 0.073% 13.63% 16516ms 14.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 144ms 0.13% 13.76% 14479ms 12.98% CellPropertyCollection::GetPropertiesType (inline) 338ms 0.3% 14.06% 14437ms 12.95% NagaiHondaForce::GetAdhesionParameter 161ms 0.14% 14.20% 14077ms 12.62% SimpleWntCellCycleModel::UpdateCellCyclePhase 448ms 0.4% 14.61% 13962ms 12.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 284ms 0.25% 14.86% 12442ms 11.16% boost::numeric::ublas::vector_assign (inline) 3701ms 3.32% 18.18% 12211ms 10.95% __dynamic_cast 74ms 0.066% 18.25% 12111ms 10.86% VertexBasedCellPopulation::GetDampingConstant 39ms 0.035% 18.28% 12084ms 10.84% AbstractCellProperty::IsSubType (inline) 143ms 0.13% 18.41% 11890ms 10.66% MutableVertexMesh::CheckForIntersections 68ms 0.061% 18.47% 10919ms 9.79% AbstractTargetAreaModifier::UpdateTargetAreas 41ms 0.037% 18.51% 10807ms 9.69% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 19ms 0.017% 18.52% 10391ms 9.32% AbstractCellBasedSimulation::DoCellBirth 1437ms 1.29% 19.81% 10169ms 9.12% std::__new_allocator::allocate (inline) 0 0% 19.81% 9611ms 8.62% std::allocator_traits::allocate (inline) 0 0% 19.81% 9589ms 8.60% std::_Rb_tree::_M_create_node (inline) 2912ms 2.61% 22.42% 9561ms 8.57% boost::numeric::ublas::indexing_vector_assign 418ms 0.37% 22.80% 9496ms 8.52% VertexMesh::GetNextEdgeGradientOfElementAtNode 84ms 0.075% 22.87% 9074ms 8.14% Cell::GetMutationState 1253ms 1.12% 24.00% 9060ms 8.12% std::_Rb_tree::_M_erase 779ms 0.7% 24.70% 8800ms 7.89% operator new 0 0% 24.70% 8798ms 7.89% std::_Rb_tree::_M_get_node (inline) 809ms 0.73% 25.42% 8743ms 7.84% VertexMesh::ElementIncludesPoint 20ms 0.018% 25.44% 8680ms 7.78% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.44% 8407ms 7.54% std::_Rb_tree::_Alloc_node::operator() (inline) 18ms 0.016% 25.46% 8226ms 7.38% MutableVertexMesh::RemoveDeletedNodesAndElements 453ms 0.41% 25.86% 8211ms 7.36% VertexMesh::GetCentroidOfElement 236ms 0.21% 26.07% 8170ms 7.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.07% 8135ms 7.30% std::_Rb_tree::_M_drop_node (inline) 210ms 0.19% 26.26% 7924ms 7.11% std::__new_allocator::deallocate (inline) 0 0% 26.26% 7916ms 7.10% std::allocator_traits::deallocate (inline) 500ms 0.45% 26.71% 7910ms 7.09% std::map::operator[] (partial-inline) 0 0% 26.71% 7832ms 7.02% std::_Rb_tree::_M_put_node (inline) 2876ms 2.58% 29.29% 7815ms 7.01% __GI___libc_malloc 0 0% 29.29% 7732ms 6.93% std::set::~set (inline) 2452ms 2.20% 31.49% 7468ms 6.70% __GI___libc_free 1608ms 1.44% 32.93% 7453ms 6.68% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 170ms 0.15% 33.08% 7279ms 6.53% std::_Rb_tree::_Rb_tree (partial-inline) 752ms 0.67% 33.76% 6837ms 6.13% std::_Rb_tree::_M_copy (inline) 6790ms 6.09% 39.85% 6790ms 6.09% __strcmp_avx2 32ms 0.029% 39.88% 6790ms 6.09% std::set::set (inline) 2584ms 2.32% 42.19% 6302ms 5.65% std::_Rb_tree::_M_lower_bound (inline) 130ms 0.12% 42.31% 6277ms 5.63% SimpleWntCellCycleModel::GetWntLevel 6135ms 5.50% 47.81% 6135ms 5.50% boost::numeric::ublas::c_vector::operator() 185ms 0.17% 47.98% 6064ms 5.44% WntConcentration::GetWntLevel 3014ms 2.70% 50.68% 5885ms 5.28% __cxxabiv1::__si_class_type_info::__do_dyncast 813ms 0.73% 51.41% 5845ms 5.24% std::_Rb_tree::_M_clone_node (inline) 26ms 0.023% 51.43% 5535ms 4.96% MutableVertexMesh::RemoveDeletedNodes 44ms 0.039% 51.47% 5315ms 4.77% EdgeHelper::RemoveDeletedEdges 1925ms 1.73% 53.20% 5312ms 4.76% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.20% 5292ms 4.75% std::set::insert (inline) 0 0% 53.20% 5179ms 4.64% std::_Rb_tree::lower_bound (inline) 0 0% 53.20% 5179ms 4.64% std::map::lower_bound (inline) 212ms 0.19% 53.39% 5080ms 4.56% MutableElement::ResetIndex 4539ms 4.07% 57.46% 4997ms 4.48% _int_free 36ms 0.032% 57.49% 4945ms 4.43% EdgeHelper::UpdateEdgesMapKey 0 0% 57.49% 4803ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 146ms 0.13% 57.62% 4591ms 4.12% AbstractCellPopulation::GetCellUsingLocationIndex 521ms 0.47% 58.09% 4432ms 3.97% std::_Rb_tree::_M_insert_ (inline) 142ms 0.13% 58.22% 4218ms 3.78% std::set_intersection (inline) 42ms 0.038% 58.25% 4136ms 3.71% Cell::GetCellProliferativeType 211ms 0.19% 58.44% 4076ms 3.66% std::__set_intersection 40ms 0.036% 58.48% 3939ms 3.53% AbstractCellProperty::IsType (inline) 3868ms 3.47% 61.95% 3868ms 3.47% boost::numeric::ublas::same_impl_ex 7ms 0.0063% 61.95% 3531ms 3.17% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 71ms 0.064% 62.02% 3324ms 2.98% std::_Rb_tree::erase 2216ms 1.99% 64.00% 3291ms 2.95% _int_malloc 3177ms 2.85% 66.85% 3177ms 2.85% std::_Rb_tree::_S_right (inline) 988ms 0.89% 67.74% 3169ms 2.84% AbstractElement::GetNodeLocation 38ms 0.034% 67.77% 3151ms 2.83% Cell::SetCellProliferativeType 0 0% 67.77% 3122ms 2.80% std::insert_iterator::operator= (inline) 744ms 0.67% 68.44% 2797ms 2.51% AbstractCellProperty::IsSame 33ms 0.03% 68.47% 2785ms 2.50% CellPropertyCollection::HasProperty 264ms 0.24% 68.71% 2710ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.71% 2703ms 2.42% Cell::HasCellProperty (inline) 7ms 0.0063% 68.71% 2702ms 2.42% std::_Rb_tree::_M_insert_unique_ (inline) 642ms 0.58% 69.29% 2682ms 2.41% boost::numeric::ublas::vector_binary::size (inline) 17ms 0.015% 69.30% 2651ms 2.38% Cell::GetCellData 0 0% 69.30% 2606ms 2.34% boost::numeric::ublas::c_vector::assign (inline) 208ms 0.19% 69.49% 2590ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0018% 69.49% 2590ms 2.32% std::_Rb_tree::_M_insert_unique 0 0% 69.49% 2527ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.49% 2502ms 2.24% AbstractCellPopulation::WriteResultsToFiles 45ms 0.04% 69.53% 2340ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 72ms 0.065% 69.60% 2286ms 2.05% VertexMesh::GetVolumeOfElement 6ms 0.0054% 69.60% 2238ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 182ms 0.16% 69.77% 2225ms 2.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 1428ms 1.28% 71.05% 2216ms 1.99% std::_Rb_tree::equal_range (inline) 41ms 0.037% 71.08% 2170ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2164ms 1.94% 73.02% 2164ms 1.94% std::_Rb_tree_increment 4ms 0.0036% 73.03% 2077ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.03% 2077ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 490ms 0.44% 73.47% 2053ms 1.84% std::type_info::operator== (inline) 0 0% 73.47% 2036ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 73.47% 2022ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 62ms 0.056% 73.52% 1853ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 73.53% 1823ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.023% 73.55% 1752ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 37ms 0.033% 73.58% 1598ms 1.43% VertexMesh::GetSurfaceAreaOfElement 22ms 0.02% 73.60% 1597ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 55ms 0.049% 73.65% 1590ms 1.43% Node::RemoveElement 86ms 0.077% 73.73% 1553ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 13ms 0.012% 73.74% 1542ms 1.38% std::set::erase (inline) 142ms 0.13% 73.87% 1521ms 1.36% CellPropertyCollection::AddProperty 0 0% 73.87% 1463ms 1.31% tcache_get (inline) 1463ms 1.31% 75.18% 1463ms 1.31% tcache_get_n (inline) 2ms 0.0018% 75.18% 1429ms 1.28% OffLatticeSimulation::ApplyBoundaries 64ms 0.057% 75.24% 1395ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 1387ms 1.24% 76.48% 1387ms 1.24% [libchaste_cell_based.so] 0 0% 76.48% 1350ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 76.48% 1349ms 1.21% boost::numeric::ublas::norm_2 (inline) 574ms 0.51% 77.00% 1336ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 61ms 0.055% 77.05% 1323ms 1.19% std::less::operator() (inline) 983ms 0.88% 77.93% 1262ms 1.13% std::operator< (inline) 8ms 0.0072% 77.94% 1224ms 1.10% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 75ms 0.067% 78.01% 1218ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 21ms 0.019% 78.03% 1210ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 22ms 0.02% 78.05% 1195ms 1.07% CellPropertyRegistry::Get 0 0% 78.05% 1182ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.05% 1128ms 1.01% std::_Rb_tree::clear (inline) 0 0% 78.05% 1114ms 1% std::map::clear (inline) 106ms 0.095% 78.14% 1108ms 0.99% std::_Rb_tree::find (inline) 0 0% 78.14% 1081ms 0.97% boost::numeric::ublas::c_vector::assign_temporary (inline) 16ms 0.014% 78.16% 1081ms 0.97% boost::numeric::ublas::c_vector::swap (inline) 1076ms 0.96% 79.12% 1076ms 0.96% std::_Rb_tree_insert_and_rebalance 72ms 0.065% 79.19% 1065ms 0.96% std::swap_ranges (inline) 125ms 0.11% 79.30% 1010ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 79.30% 1010ms 0.91% boost::shared_ptr::~shared_ptr (inline) 17ms 0.015% 79.31% 1003ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.31% 993ms 0.89% std::iter_swap (inline) 993ms 0.89% 80.20% 993ms 0.89% std::swap (inline) 991ms 0.89% 81.09% 991ms 0.89% Node::rGetLocation 208ms 0.19% 81.28% 981ms 0.88% boost::numeric::ublas::detail::equals 0 0% 81.28% 966ms 0.87% std::map::find (inline) 1ms 0.0009% 81.28% 863ms 0.77% VertexMeshWriter::MakeVtkMesh 834ms 0.75% 82.03% 854ms 0.77% boost::detail::sp_counted_base::release 224ms 0.2% 82.23% 851ms 0.76% std::__new_allocator::construct (inline) 0 0% 82.23% 851ms 0.76% std::allocator_traits::construct (inline) 2ms 0.0018% 82.23% 811ms 0.73% std::_Vector_base::_M_allocate (inline) 431ms 0.39% 82.62% 807ms 0.72% Edge::GetMapIndex 87ms 0.078% 82.69% 802ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 191ms 0.17% 82.87% 792ms 0.71% boost::shared_ptr::shared_ptr (inline) 0 0% 82.87% 791ms 0.71% std::_Rb_tree::_M_construct_node (inline) 787ms 0.71% 83.57% 787ms 0.71% std::vector::size (inline) 16ms 0.014% 83.59% 786ms 0.7% MutableElement::RegisterWithEdges (inline) 25ms 0.022% 83.61% 779ms 0.7% Edge::AddElement 779ms 0.7% 84.31% 779ms 0.7% [libchaste_mesh.so] 432ms 0.39% 84.69% 769ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.69% 738ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.69% 728ms 0.65% boost::numeric::ublas::norm_inf (inline) 360ms 0.32% 85.02% 728ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 22ms 0.02% 85.04% 726ms 0.65% AbstractNumericalMethod::DetectStepSizeExceptions 726ms 0.65% 85.69% 726ms 0.65% Node::GetIndex 118ms 0.11% 85.79% 704ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.79% 700ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 123ms 0.11% 85.90% 692ms 0.62% MutableElement::GetNodeLocalIndex 6ms 0.0054% 85.91% 684ms 0.61% std::vector::_M_default_append (inline) 683ms 0.61% 86.52% 683ms 0.61% [libstdc++.so.6.0.33] 0 0% 86.52% 619ms 0.56% vtkPolygon::New 0 0% 86.52% 617ms 0.55% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.54% 617ms 0.55% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.54% 617ms 0.55% vtkPolygon::vtkPolygon 25ms 0.022% 86.56% 613ms 0.55% MutableElement::RegisterWithNodes (inline) 467ms 0.42% 86.98% 609ms 0.55% malloc_consolidate 1ms 0.0009% 86.98% 601ms 0.54% VertexElementMap::VertexElementMap 575ms 0.52% 87.50% 601ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 87.50% 600ms 0.54% std::vector::resize (inline) 27ms 0.024% 87.52% 585ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.52% 585ms 0.52% boost::numeric::ublas::vector::vector (inline) 34ms 0.03% 87.55% 584ms 0.52% Node::AddElement 94ms 0.084% 87.64% 584ms 0.52% std::_Rb_tree::_M_upper_bound (inline) 559ms 0.5% 88.14% 559ms 0.5% boost::shared_ptr::operator-> (inline)