File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96455ms, 88.22% of 109330ms total Dropped 1121 nodes (cum <= 546.65ms) flat flat% sum% cum cum% 0 0% 0% 108867ms 99.58% __libc_start_call_main 0 0% 0% 108867ms 99.58% __libc_start_main_impl 0 0% 0% 108867ms 99.58% _start 0 0% 0% 108848ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108848ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108848ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108848ms 99.56% main 0 0% 0% 108810ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108810ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108810ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 108803ms 99.52% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.015% 56736ms 51.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.027% 53549ms 48.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.15% 52001ms 47.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 331ms 0.3% 0.46% 40416ms 36.97% NagaiHondaForce::AddForceContribution 0 0% 0.46% 39071ms 35.74% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.46% 24245ms 22.18% VertexBasedCellPopulation::Update 0 0% 0.46% 24124ms 22.07% MutableVertexMesh::ReMesh 14435ms 13.20% 13.66% 22851ms 20.90% Cylindrical2dVertexMesh::GetVectorFromAtoB 93ms 0.085% 13.75% 17413ms 15.93% Cell::ReadyToDivide 77ms 0.07% 13.82% 16133ms 14.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 324ms 0.3% 14.11% 15211ms 13.91% NagaiHondaForce::GetAdhesionParameter 403ms 0.37% 14.48% 14439ms 13.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 103ms 0.094% 14.58% 13718ms 12.55% SimpleWntCellCycleModel::UpdateCellCyclePhase 135ms 0.12% 14.70% 13689ms 12.52% CellPropertyCollection::GetPropertiesType (inline) 423ms 0.39% 15.09% 12917ms 11.81% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.21% 12014ms 10.99% MutableVertexMesh::CheckForIntersections 3279ms 3.00% 18.21% 11384ms 10.41% __dynamic_cast 77ms 0.07% 18.28% 11281ms 10.32% AbstractCellProperty::IsSubType (inline) 81ms 0.074% 18.35% 11095ms 10.15% VertexBasedCellPopulation::GetDampingConstant 75ms 0.069% 18.42% 10554ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 62ms 0.057% 18.48% 10457ms 9.56% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1302ms 1.19% 19.67% 10184ms 9.31% std::__new_allocator::allocate (inline) 19ms 0.017% 19.69% 10100ms 9.24% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.69% 9609ms 8.79% std::allocator_traits::allocate (inline) 0 0% 19.69% 9535ms 8.72% std::_Rb_tree::_M_create_node (inline) 2689ms 2.46% 22.15% 9480ms 8.67% boost::numeric::ublas::indexing_vector_assign 1420ms 1.30% 23.45% 9370ms 8.57% std::_Rb_tree::_M_erase 951ms 0.87% 24.32% 9014ms 8.24% operator new 772ms 0.71% 25.02% 8930ms 8.17% VertexMesh::ElementIncludesPoint 405ms 0.37% 25.39% 8916ms 8.16% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.39% 8916ms 8.16% std::_Rb_tree::_M_get_node (inline) 27ms 0.025% 25.42% 8706ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 222ms 0.2% 25.62% 8552ms 7.82% std::_Rb_tree::~_Rb_tree (inline) 83ms 0.076% 25.70% 8473ms 7.75% Cell::GetMutationState 0 0% 25.70% 8401ms 7.68% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.70% 8304ms 7.60% std::_Rb_tree::_M_drop_node (inline) 442ms 0.4% 26.10% 8221ms 7.52% VertexMesh::GetCentroidOfElement 246ms 0.23% 26.32% 8104ms 7.41% std::__new_allocator::deallocate (inline) 0 0% 26.32% 8096ms 7.41% std::set::~set (inline) 0 0% 26.32% 8062ms 7.37% std::allocator_traits::deallocate (inline) 0 0% 26.32% 7987ms 7.31% std::_Rb_tree::_M_put_node (inline) 3176ms 2.90% 29.23% 7952ms 7.27% __GI___libc_free 3221ms 2.95% 32.18% 7873ms 7.20% __GI___libc_malloc 15ms 0.014% 32.19% 7641ms 6.99% MutableVertexMesh::RemoveDeletedNodesAndElements 473ms 0.43% 32.62% 7427ms 6.79% std::map::operator[] (partial-inline) 1397ms 1.28% 33.90% 7086ms 6.48% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 147ms 0.13% 34.03% 7029ms 6.43% std::_Rb_tree::_Rb_tree (partial-inline) 653ms 0.6% 34.63% 6637ms 6.07% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.65% 6576ms 6.01% std::set::set (inline) 6533ms 5.98% 40.62% 6533ms 5.98% __strcmp_avx2 6185ms 5.66% 46.28% 6185ms 5.66% boost::numeric::ublas::c_vector::operator() 105ms 0.096% 46.38% 6164ms 5.64% SimpleWntCellCycleModel::GetWntLevel 138ms 0.13% 46.50% 5976ms 5.47% WntConcentration::GetWntLevel 2466ms 2.26% 48.76% 5754ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 733ms 0.67% 49.43% 5662ms 5.18% std::_Rb_tree::_M_clone_node (inline) 2687ms 2.46% 51.89% 5605ms 5.13% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.89% 5462ms 5.00% std::set::insert (inline) 29ms 0.027% 51.91% 5431ms 4.97% MutableVertexMesh::RemoveDeletedNodes 40ms 0.037% 51.95% 5268ms 4.82% EdgeHelper::RemoveDeletedEdges 34ms 0.031% 51.98% 5000ms 4.57% EdgeHelper::UpdateEdgesMapKey 1459ms 1.33% 53.31% 4789ms 4.38% boost::numeric::ublas::c_vector::operator[] (inline) 4455ms 4.07% 57.39% 4768ms 4.36% _int_free 209ms 0.19% 57.58% 4757ms 4.35% MutableElement::ResetIndex 4ms 0.0037% 57.58% 4716ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 57.58% 4715ms 4.31% std::_Rb_tree::lower_bound (inline) 0 0% 57.58% 4715ms 4.31% std::map::lower_bound (inline) 526ms 0.48% 58.06% 4554ms 4.17% std::_Rb_tree::_M_insert_ (inline) 57ms 0.052% 58.12% 4538ms 4.15% std::set_intersection (inline) 286ms 0.26% 58.38% 4481ms 4.10% std::__set_intersection 95ms 0.087% 58.47% 4043ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 40ms 0.037% 58.50% 4007ms 3.67% Cell::GetCellProliferativeType 3946ms 3.61% 62.11% 3946ms 3.61% boost::numeric::ublas::same_impl_ex 54ms 0.049% 62.16% 3895ms 3.56% AbstractCellProperty::IsType (inline) 16ms 0.015% 62.18% 3682ms 3.37% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.18% 3216ms 2.94% std::insert_iterator::operator= (inline) 785ms 0.72% 62.89% 3191ms 2.92% AbstractElement::GetNodeLocation 2197ms 2.01% 64.90% 3088ms 2.82% _int_malloc 43ms 0.039% 64.94% 3075ms 2.81% Cell::SetCellProliferativeType 36ms 0.033% 64.97% 2994ms 2.74% std::_Rb_tree::erase 7ms 0.0064% 64.98% 2822ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 2815ms 2.57% 67.56% 2815ms 2.57% std::_Rb_tree::_S_right (inline) 779ms 0.71% 68.27% 2804ms 2.56% AbstractCellProperty::IsSame 639ms 0.58% 68.85% 2773ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 422ms 0.39% 69.24% 2756ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.048% 69.29% 2711ms 2.48% CellPropertyCollection::HasProperty 2ms 0.0018% 69.29% 2640ms 2.41% std::_Rb_tree::_M_insert_unique 0 0% 69.29% 2611ms 2.39% Cell::HasCellProperty (inline) 254ms 0.23% 69.52% 2520ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 27ms 0.025% 69.55% 2470ms 2.26% Cell::GetCellData 0 0% 69.55% 2420ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.55% 2406ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.55% 2348ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 91ms 0.083% 69.63% 2310ms 2.11% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 86ms 0.079% 69.71% 2268ms 2.07% VertexMesh::GetVolumeOfElement 3ms 0.0027% 69.71% 2221ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 225ms 0.21% 69.92% 2201ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 34ms 0.031% 69.95% 2187ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 2163ms 1.98% 71.93% 2163ms 1.98% std::_Rb_tree_increment 1382ms 1.26% 73.19% 2036ms 1.86% std::_Rb_tree::equal_range (inline) 509ms 0.47% 73.65% 2025ms 1.85% std::type_info::operator== (inline) 0 0% 73.65% 1981ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.66% 1970ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00091% 73.66% 1948ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.66% 1948ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 82ms 0.075% 73.73% 1854ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 73.73% 1763ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.03% 73.76% 1698ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 17ms 0.016% 73.78% 1661ms 1.52% VertexMesh::GetSurfaceAreaOfElement 42ms 0.038% 73.82% 1597ms 1.46% Node::RemoveElement 129ms 0.12% 73.94% 1580ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 21ms 0.019% 73.95% 1568ms 1.43% std::set::erase (inline) 147ms 0.13% 74.09% 1559ms 1.43% CellPropertyCollection::AddProperty 41ms 0.038% 74.13% 1546ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 67ms 0.061% 74.19% 1501ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.19% 1434ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.19% 1378ms 1.26% tcache_get (inline) 1378ms 1.26% 75.45% 1378ms 1.26% tcache_get_n (inline) 1ms 0.00091% 75.45% 1288ms 1.18% OffLatticeSimulation::ApplyBoundaries 0 0% 75.45% 1254ms 1.15% boost::numeric::ublas::norm_2 (inline) 567ms 0.52% 75.97% 1251ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 72ms 0.066% 76.03% 1197ms 1.09% std::less::operator() (inline) 1188ms 1.09% 77.12% 1188ms 1.09% std::_Rb_tree_insert_and_rebalance 24ms 0.022% 77.14% 1164ms 1.06% CellPropertyRegistry::Get 1152ms 1.05% 78.20% 1152ms 1.05% Node::rGetLocation 0 0% 78.20% 1134ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 927ms 0.85% 79.04% 1125ms 1.03% std::operator< (inline) 67ms 0.061% 79.11% 1093ms 1% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.018% 79.12% 1089ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 127ms 0.12% 79.24% 1071ms 0.98% std::_Rb_tree::find (inline) 1051ms 0.96% 80.20% 1051ms 0.96% [libchaste_cell_based.so] 0 0% 80.20% 1050ms 0.96% std::_Rb_tree::clear (inline) 170ms 0.16% 80.36% 1039ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.36% 1039ms 0.95% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.36% 1032ms 0.94% std::map::clear (inline) 426ms 0.39% 80.75% 988ms 0.9% Edge::GetMapIndex 3ms 0.0027% 80.75% 987ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 978ms 0.89% 81.64% 978ms 0.89% std::vector::size (inline) 25ms 0.023% 81.67% 966ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 961ms 0.88% 82.55% 961ms 0.88% [libchaste_mesh.so] 0 0% 82.55% 939ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 82.55% 939ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 69ms 0.063% 82.61% 933ms 0.85% std::swap_ranges (inline) 163ms 0.15% 82.76% 926ms 0.85% boost::numeric::ublas::detail::equals 128ms 0.12% 82.88% 890ms 0.81% MutableElement::GetNodeLocalIndex 0 0% 82.88% 876ms 0.8% std::map::find (inline) 865ms 0.79% 83.67% 865ms 0.79% std::swap (inline) 0 0% 83.67% 864ms 0.79% std::iter_swap (inline) 845ms 0.77% 84.44% 851ms 0.78% boost::detail::sp_counted_base::release 126ms 0.12% 84.56% 845ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0018% 84.56% 842ms 0.77% VertexMeshWriter::MakeVtkMesh 836ms 0.76% 85.33% 836ms 0.76% Node::GetIndex 478ms 0.44% 85.76% 810ms 0.74% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 14ms 0.013% 85.78% 771ms 0.71% MutableElement::RegisterWithEdges (inline) 29ms 0.027% 85.80% 767ms 0.7% Edge::AddElement 141ms 0.13% 85.93% 730ms 0.67% boost::shared_ptr::shared_ptr (inline) 12ms 0.011% 85.94% 725ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 83ms 0.076% 86.02% 713ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.02% 705ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 13ms 0.012% 86.03% 705ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.03% 694ms 0.63% boost::numeric::ublas::norm_inf (inline) 384ms 0.35% 86.38% 694ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.38% 692ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.38% 691ms 0.63% std::_Vector_base::_M_allocate (inline) 107ms 0.098% 86.48% 669ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.48% 669ms 0.61% std::allocator_traits::construct (inline) 37ms 0.034% 86.51% 638ms 0.58% MutableElement::RegisterWithNodes (inline) 628ms 0.57% 87.09% 628ms 0.57% operator delete 0 0% 87.09% 620ms 0.57% vtkPolygon::New 0 0% 87.09% 619ms 0.57% std::_Rb_tree::_M_construct_node (inline) 1ms 0.00091% 87.09% 618ms 0.57% vtkPolygon::vtkPolygon 34ms 0.031% 87.12% 609ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.12% 609ms 0.56% boost::numeric::ublas::vector::vector (inline) 603ms 0.55% 87.67% 603ms 0.55% [libstdc++.so.6.0.33] 24ms 0.022% 87.69% 594ms 0.54% Node::AddElement 573ms 0.52% 88.22% 589ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 88.22% 584ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 7ms 0.0064% 88.22% 577ms 0.53% std::vector::_M_default_append (inline)