File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96697ms, 88.50% of 109266ms total Dropped 1105 nodes (cum <= 546.33ms) flat flat% sum% cum cum% 0 0% 0% 108805ms 99.58% __libc_start_call_main 0 0% 0% 108805ms 99.58% __libc_start_main_impl 0 0% 0% 108805ms 99.58% _start 0 0% 0% 108786ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108786ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108786ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108786ms 99.56% main 0 0% 0% 108745ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108745ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108745ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 7ms 0.0064% 0.0064% 108738ms 99.52% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.017% 56268ms 51.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.038% 53011ms 48.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 132ms 0.12% 0.16% 51855ms 47.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 331ms 0.3% 0.46% 40278ms 36.86% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.46% 39646ms 36.28% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.46% 24604ms 22.52% VertexBasedCellPopulation::Update 0 0% 0.46% 24490ms 22.41% MutableVertexMesh::ReMesh 14655ms 13.41% 13.87% 23210ms 21.24% Cylindrical2dVertexMesh::GetVectorFromAtoB 130ms 0.12% 13.99% 17427ms 15.95% Cell::ReadyToDivide 78ms 0.071% 14.06% 16204ms 14.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 354ms 0.32% 14.39% 14970ms 13.70% NagaiHondaForce::GetAdhesionParameter 401ms 0.37% 14.76% 14802ms 13.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.1% 14.86% 13835ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 131ms 0.12% 14.98% 13317ms 12.19% CellPropertyCollection::GetPropertiesType (inline) 370ms 0.34% 15.32% 13268ms 12.14% boost::numeric::ublas::vector_assign (inline) 131ms 0.12% 15.44% 12153ms 11.12% MutableVertexMesh::CheckForIntersections 55ms 0.05% 15.49% 11063ms 10.12% VertexBasedCellPopulation::GetDampingConstant 3100ms 2.84% 18.33% 11021ms 10.09% __dynamic_cast 87ms 0.08% 18.40% 10906ms 9.98% AbstractCellProperty::IsSubType (inline) 83ms 0.076% 18.48% 10376ms 9.50% AbstractTargetAreaModifier::UpdateTargetAreas 19ms 0.017% 18.50% 10293ms 9.42% AbstractCellBasedSimulation::DoCellBirth 58ms 0.053% 18.55% 10277ms 9.41% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1301ms 1.19% 19.74% 9904ms 9.06% std::__new_allocator::allocate (inline) 2755ms 2.52% 22.26% 9757ms 8.93% boost::numeric::ublas::indexing_vector_assign 1502ms 1.37% 23.64% 9508ms 8.70% std::_Rb_tree::_M_erase 0 0% 23.64% 9310ms 8.52% std::allocator_traits::allocate (inline) 0 0% 23.64% 9281ms 8.49% std::_Rb_tree::_M_create_node (inline) 820ms 0.75% 24.39% 9039ms 8.27% VertexMesh::ElementIncludesPoint 328ms 0.3% 24.69% 8902ms 8.15% VertexMesh::GetNextEdgeGradientOfElementAtNode 28ms 0.026% 24.71% 8871ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 790ms 0.72% 25.44% 8706ms 7.97% operator new 0 0% 25.44% 8649ms 7.92% std::_Rb_tree::_M_get_node (inline) 200ms 0.18% 25.62% 8615ms 7.88% std::_Rb_tree::~_Rb_tree (inline) 69ms 0.063% 25.68% 8472ms 7.75% Cell::GetMutationState 0 0% 25.68% 8402ms 7.69% std::_Rb_tree::_M_drop_node (inline) 501ms 0.46% 26.14% 8308ms 7.60% VertexMesh::GetCentroidOfElement 249ms 0.23% 26.37% 8193ms 7.50% std::__new_allocator::deallocate (inline) 0 0% 26.37% 8164ms 7.47% std::allocator_traits::deallocate (inline) 0 0% 26.37% 8161ms 7.47% std::_Rb_tree::_Alloc_node::operator() (inline) 3318ms 3.04% 29.41% 8147ms 7.46% __GI___libc_free 0 0% 29.41% 8135ms 7.45% std::set::~set (inline) 0 0% 29.41% 8107ms 7.42% std::_Rb_tree::_M_put_node (inline) 17ms 0.016% 29.42% 7920ms 7.25% MutableVertexMesh::RemoveDeletedNodesAndElements 3103ms 2.84% 32.26% 7721ms 7.07% __GI___libc_malloc 452ms 0.41% 32.68% 7383ms 6.76% std::map::operator[] (partial-inline) 1402ms 1.28% 33.96% 7149ms 6.54% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 132ms 0.12% 34.08% 6698ms 6.13% std::_Rb_tree::_Rb_tree (partial-inline) 119ms 0.11% 34.19% 6395ms 5.85% SimpleWntCellCycleModel::GetWntLevel 637ms 0.58% 34.77% 6354ms 5.82% std::_Rb_tree::_M_copy (inline) 6298ms 5.76% 40.54% 6298ms 5.76% boost::numeric::ublas::c_vector::operator() 6294ms 5.76% 46.30% 6294ms 5.76% __strcmp_avx2 11ms 0.01% 46.31% 6198ms 5.67% std::set::set (inline) 183ms 0.17% 46.47% 6181ms 5.66% WntConcentration::GetWntLevel 2420ms 2.21% 48.69% 5992ms 5.48% std::_Rb_tree::_M_lower_bound (inline) 2693ms 2.46% 51.15% 5488ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 719ms 0.66% 51.81% 5415ms 4.96% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.81% 5395ms 4.94% std::set::insert (inline) 18ms 0.016% 51.83% 5352ms 4.90% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 51.86% 5187ms 4.75% EdgeHelper::RemoveDeletedEdges 230ms 0.21% 52.07% 5034ms 4.61% MutableElement::ResetIndex 38ms 0.035% 52.10% 4904ms 4.49% EdgeHelper::UpdateEdgesMapKey 1489ms 1.36% 53.47% 4866ms 4.45% boost::numeric::ublas::c_vector::operator[] (inline) 4466ms 4.09% 57.55% 4822ms 4.41% _int_free 0 0% 57.55% 4770ms 4.37% std::_Rb_tree::lower_bound (inline) 0 0% 57.55% 4770ms 4.37% std::map::lower_bound (inline) 0 0% 57.55% 4736ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 56ms 0.051% 57.61% 4696ms 4.30% std::set_intersection (inline) 281ms 0.26% 57.86% 4640ms 4.25% std::__set_intersection 517ms 0.47% 58.34% 4504ms 4.12% std::_Rb_tree::_M_insert_ (inline) 4041ms 3.70% 62.03% 4041ms 3.70% boost::numeric::ublas::same_impl_ex 96ms 0.088% 62.12% 4010ms 3.67% AbstractCellPopulation::GetCellUsingLocationIndex 43ms 0.039% 62.16% 3990ms 3.65% Cell::GetCellProliferativeType 8ms 0.0073% 62.17% 3671ms 3.36% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 58ms 0.053% 62.22% 3622ms 3.31% AbstractCellProperty::IsType (inline) 0 0% 62.22% 3316ms 3.03% std::insert_iterator::operator= (inline) 60ms 0.055% 62.28% 3219ms 2.95% Cell::SetCellProliferativeType 42ms 0.038% 62.31% 3208ms 2.94% std::_Rb_tree::erase 748ms 0.68% 63.00% 3033ms 2.78% AbstractElement::GetNodeLocation 2110ms 1.93% 64.93% 3014ms 2.76% _int_malloc 3008ms 2.75% 67.68% 3008ms 2.75% std::_Rb_tree::_S_right (inline) 4ms 0.0037% 67.69% 2933ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 617ms 0.56% 68.25% 2907ms 2.66% boost::numeric::ublas::vector_binary::size (inline) 465ms 0.43% 68.68% 2860ms 2.62% std::_Rb_tree_const_iterator::operator++ (inline) 251ms 0.23% 68.91% 2576ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 700ms 0.64% 69.55% 2563ms 2.35% AbstractCellProperty::IsSame 36ms 0.033% 69.58% 2483ms 2.27% CellPropertyCollection::HasProperty 0 0% 69.58% 2462ms 2.25% std::_Rb_tree::_M_insert_unique 0 0% 69.58% 2435ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.58% 2413ms 2.21% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00092% 69.58% 2396ms 2.19% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 69.58% 2387ms 2.18% Cell::HasCellProperty (inline) 0 0% 69.58% 2383ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 202ms 0.18% 69.77% 2358ms 2.16% AbstractCellPopulation::Iterator::IsRealCell (inline) 106ms 0.097% 69.86% 2314ms 2.12% VertexMesh::GetVolumeOfElement 27ms 0.025% 69.89% 2280ms 2.09% Cell::GetCellData 129ms 0.12% 70.01% 2270ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2202ms 2.02% 72.02% 2202ms 2.02% std::_Rb_tree_increment 47ms 0.043% 72.06% 2127ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 1427ms 1.31% 73.37% 2113ms 1.93% std::_Rb_tree::equal_range (inline) 1ms 0.00092% 73.37% 1985ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.37% 1972ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0018% 73.37% 1947ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.37% 1947ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 83ms 0.076% 73.45% 1880ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 397ms 0.36% 73.81% 1863ms 1.71% std::type_info::operator== (inline) 45ms 0.041% 73.85% 1862ms 1.70% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.85% 1783ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 31ms 0.028% 73.88% 1633ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.024% 73.91% 1629ms 1.49% VertexMesh::GetSurfaceAreaOfElement 79ms 0.072% 73.98% 1625ms 1.49% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 51ms 0.047% 74.02% 1596ms 1.46% Node::RemoveElement 23ms 0.021% 74.05% 1560ms 1.43% std::set::erase (inline) 138ms 0.13% 74.17% 1529ms 1.40% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.17% 1458ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 184ms 0.17% 74.34% 1412ms 1.29% CellPropertyCollection::AddProperty 0 0% 74.34% 1409ms 1.29% tcache_get (inline) 1409ms 1.29% 75.63% 1409ms 1.29% tcache_get_n (inline) 1ms 0.00092% 75.63% 1287ms 1.18% OffLatticeSimulation::ApplyBoundaries 77ms 0.07% 75.70% 1261ms 1.15% std::less::operator() (inline) 107ms 0.098% 75.80% 1238ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 91ms 0.083% 75.88% 1205ms 1.10% std::_Rb_tree::find (inline) 0 0% 75.88% 1202ms 1.10% boost::numeric::ublas::norm_2 (inline) 517ms 0.47% 76.36% 1188ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 949ms 0.87% 77.22% 1184ms 1.08% std::operator< (inline) 1141ms 1.04% 78.27% 1141ms 1.04% Node::rGetLocation 0 0% 78.27% 1120ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1104ms 1.01% 79.28% 1104ms 1.01% std::_Rb_tree_insert_and_rebalance 0 0% 79.28% 1096ms 1.00% std::_Rb_tree::clear (inline) 15ms 0.014% 79.29% 1090ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.29% 1074ms 0.98% std::map::clear (inline) 25ms 0.023% 79.32% 1060ms 0.97% CellPropertyRegistry::Get 1057ms 0.97% 80.28% 1057ms 0.97% [libchaste_cell_based.so] 26ms 0.024% 80.31% 1037ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 12ms 0.011% 80.32% 1016ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.32% 1006ms 0.92% std::map::find (inline) 183ms 0.17% 80.49% 1002ms 0.92% boost::numeric::ublas::detail::equals 158ms 0.14% 80.63% 972ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.63% 972ms 0.89% boost::shared_ptr::~shared_ptr (inline) 936ms 0.86% 81.49% 936ms 0.86% [libchaste_mesh.so] 404ms 0.37% 81.86% 915ms 0.84% Edge::GetMapIndex 910ms 0.83% 82.69% 910ms 0.83% std::vector::size (inline) 0 0% 82.69% 908ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 82.69% 908ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 85ms 0.078% 82.77% 902ms 0.83% std::swap_ranges (inline) 114ms 0.1% 82.88% 855ms 0.78% MutableElement::GetNodeLocalIndex 0 0% 82.88% 844ms 0.77% VertexMeshWriter::MakeVtkMesh 118ms 0.11% 82.98% 836ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 819ms 0.75% 83.73% 819ms 0.75% std::swap (inline) 0 0% 83.73% 817ms 0.75% std::iter_swap (inline) 784ms 0.72% 84.45% 794ms 0.73% boost::detail::sp_counted_base::release 27ms 0.025% 84.48% 792ms 0.72% MutableElement::RegisterWithEdges (inline) 43ms 0.039% 84.52% 787ms 0.72% Edge::AddElement 487ms 0.45% 84.96% 787ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.96% 769ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 187ms 0.17% 85.13% 769ms 0.7% boost::shared_ptr::shared_ptr (inline) 0 0% 85.13% 745ms 0.68% boost::numeric::ublas::norm_inf (inline) 365ms 0.33% 85.47% 745ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 742ms 0.68% 86.15% 742ms 0.68% Node::GetIndex 92ms 0.084% 86.23% 677ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.23% 677ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.23% 667ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 86.25% 667ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.25% 657ms 0.6% std::_Vector_base::_M_allocate (inline) 48ms 0.044% 86.30% 650ms 0.59% MutableElement::RegisterWithNodes (inline) 0 0% 86.30% 632ms 0.58% std::_Rb_tree::_M_construct_node (inline) 25ms 0.023% 86.32% 619ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.32% 619ms 0.57% boost::numeric::ublas::vector::vector (inline) 0 0% 86.32% 616ms 0.56% vtkPolygon::New 0 0% 86.32% 616ms 0.56% vtkPolygon::vtkPolygon 614ms 0.56% 86.88% 614ms 0.56% [libstdc++.so.6.0.33] 600ms 0.55% 87.43% 600ms 0.55% boost::shared_ptr::operator-> (inline) 30ms 0.027% 87.46% 596ms 0.55% Node::AddElement 0 0% 87.46% 583ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 558ms 0.51% 87.97% 582ms 0.53% boost::detail::shared_count::shared_count (inline) 564ms 0.52% 88.49% 564ms 0.52% operator delete 11ms 0.01% 88.50% 553ms 0.51% std::vector::_M_default_append (inline)