File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94600ms, 88.06% of 107422ms total Dropped 1081 nodes (cum <= 537.11ms) flat flat% sum% cum cum% 0 0% 0% 106950ms 99.56% __libc_start_call_main 0 0% 0% 106950ms 99.56% __libc_start_main_impl 0 0% 0% 106950ms 99.56% _start 0 0% 0% 106931ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106931ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106931ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106931ms 99.54% main 0 0% 0% 106892ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106892ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106892ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 106884ms 99.50% AbstractCellBasedSimulation::Solve 10ms 0.0093% 0.011% 55509ms 51.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.028% 52382ms 48.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.16% 51345ms 47.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 409ms 0.38% 0.54% 40189ms 37.41% NagaiHondaForce::AddForceContribution 0 0% 0.54% 38777ms 36.10% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0019% 0.54% 24071ms 22.41% VertexBasedCellPopulation::Update 2ms 0.0019% 0.54% 23940ms 22.29% MutableVertexMesh::ReMesh 14349ms 13.36% 13.90% 23074ms 21.48% Cylindrical2dVertexMesh::GetVectorFromAtoB 97ms 0.09% 13.99% 17202ms 16.01% Cell::ReadyToDivide 89ms 0.083% 14.07% 16016ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 299ms 0.28% 14.35% 14893ms 13.86% NagaiHondaForce::GetAdhesionParameter 408ms 0.38% 14.73% 14490ms 13.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 153ms 0.14% 14.87% 13753ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 381ms 0.35% 15.23% 12932ms 12.04% boost::numeric::ublas::vector_assign (inline) 134ms 0.12% 15.35% 12877ms 11.99% CellPropertyCollection::GetPropertiesType (inline) 120ms 0.11% 15.47% 12135ms 11.30% MutableVertexMesh::CheckForIntersections 2901ms 2.70% 18.17% 10723ms 9.98% __dynamic_cast 81ms 0.075% 18.24% 10679ms 9.94% VertexBasedCellPopulation::GetDampingConstant 86ms 0.08% 18.32% 10615ms 9.88% AbstractCellProperty::IsSubType (inline) 85ms 0.079% 18.40% 10208ms 9.50% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.057% 18.46% 10100ms 9.40% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.028% 18.49% 10096ms 9.40% AbstractCellBasedSimulation::DoCellBirth 2813ms 2.62% 21.10% 9723ms 9.05% boost::numeric::ublas::indexing_vector_assign 1223ms 1.14% 22.24% 9707ms 9.04% std::__new_allocator::allocate (inline) 1371ms 1.28% 23.52% 9397ms 8.75% std::_Rb_tree::_M_erase 0 0% 23.52% 9166ms 8.53% std::allocator_traits::allocate (inline) 0 0% 23.52% 9143ms 8.51% std::_Rb_tree::_M_create_node (inline) 366ms 0.34% 23.86% 9073ms 8.45% VertexMesh::GetNextEdgeGradientOfElementAtNode 808ms 0.75% 24.61% 9006ms 8.38% VertexMesh::ElementIncludesPoint 23ms 0.021% 24.63% 8746ms 8.14% VertexBasedCellPopulation::GetLocationOfCellCentre 213ms 0.2% 24.83% 8586ms 7.99% std::_Rb_tree::~_Rb_tree (inline) 790ms 0.74% 25.57% 8560ms 7.97% operator new 0 0% 25.57% 8487ms 7.90% std::_Rb_tree::_M_get_node (inline) 451ms 0.42% 25.99% 8335ms 7.76% VertexMesh::GetCentroidOfElement 0 0% 25.99% 8311ms 7.74% std::_Rb_tree::_M_drop_node (inline) 80ms 0.074% 26.06% 8184ms 7.62% Cell::GetMutationState 0 0% 26.06% 8127ms 7.57% std::set::~set (inline) 259ms 0.24% 26.30% 8087ms 7.53% std::__new_allocator::deallocate (inline) 0 0% 26.30% 8064ms 7.51% std::allocator_traits::deallocate (inline) 0 0% 26.30% 8049ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.30% 8018ms 7.46% std::_Rb_tree::_M_put_node (inline) 3007ms 2.80% 29.10% 7956ms 7.41% __GI___libc_free 3158ms 2.94% 32.04% 7568ms 7.05% __GI___libc_malloc 11ms 0.01% 32.05% 7458ms 6.94% MutableVertexMesh::RemoveDeletedNodesAndElements 1429ms 1.33% 33.38% 7280ms 6.78% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 495ms 0.46% 33.84% 7089ms 6.60% std::map::operator[] (partial-inline) 169ms 0.16% 34.00% 6698ms 6.24% std::_Rb_tree::_Rb_tree (partial-inline) 6392ms 5.95% 39.95% 6392ms 5.95% boost::numeric::ublas::c_vector::operator() 15ms 0.014% 39.96% 6320ms 5.88% std::set::set (inline) 110ms 0.1% 40.07% 6315ms 5.88% SimpleWntCellCycleModel::GetWntLevel 663ms 0.62% 40.68% 6282ms 5.85% std::_Rb_tree::_M_copy (inline) 6224ms 5.79% 46.48% 6224ms 5.79% __strcmp_avx2 118ms 0.11% 46.59% 6090ms 5.67% WntConcentration::GetWntLevel 2341ms 2.18% 48.77% 5531ms 5.15% std::_Rb_tree::_M_lower_bound (inline) 2659ms 2.48% 51.24% 5489ms 5.11% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.24% 5383ms 5.01% std::set::insert (inline) 732ms 0.68% 51.92% 5322ms 4.95% std::_Rb_tree::_M_clone_node (inline) 24ms 0.022% 51.95% 5268ms 4.90% MutableVertexMesh::RemoveDeletedNodes 1507ms 1.40% 53.35% 5115ms 4.76% boost::numeric::ublas::c_vector::operator[] (inline) 35ms 0.033% 53.38% 5111ms 4.76% EdgeHelper::RemoveDeletedEdges 4608ms 4.29% 57.67% 4937ms 4.60% _int_free 49ms 0.046% 57.72% 4864ms 4.53% EdgeHelper::UpdateEdgesMapKey 195ms 0.18% 57.90% 4651ms 4.33% MutableElement::ResetIndex 1ms 0.00093% 57.90% 4598ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 530ms 0.49% 58.39% 4525ms 4.21% std::_Rb_tree::_M_insert_ (inline) 40ms 0.037% 58.43% 4507ms 4.20% std::set_intersection (inline) 0 0% 58.43% 4467ms 4.16% std::_Rb_tree::lower_bound (inline) 280ms 0.26% 58.69% 4467ms 4.16% std::__set_intersection 0 0% 58.69% 4467ms 4.16% std::map::lower_bound (inline) 4114ms 3.83% 62.52% 4114ms 3.83% boost::numeric::ublas::same_impl_ex 30ms 0.028% 62.55% 3873ms 3.61% Cell::GetCellProliferativeType 114ms 0.11% 62.65% 3791ms 3.53% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.0065% 62.66% 3516ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 69ms 0.064% 62.72% 3505ms 3.26% AbstractCellProperty::IsType (inline) 0 0% 62.72% 3283ms 3.06% std::insert_iterator::operator= (inline) 59ms 0.055% 62.78% 3205ms 2.98% Cell::SetCellProliferativeType 763ms 0.71% 63.49% 3145ms 2.93% AbstractElement::GetNodeLocation 2084ms 1.94% 65.43% 2938ms 2.74% _int_malloc 652ms 0.61% 66.04% 2917ms 2.72% boost::numeric::ublas::vector_binary::size (inline) 12ms 0.011% 66.05% 2902ms 2.70% std::_Rb_tree::_M_insert_unique_ (inline) 39ms 0.036% 66.08% 2816ms 2.62% std::_Rb_tree::erase 459ms 0.43% 66.51% 2671ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 2619ms 2.44% 68.95% 2619ms 2.44% std::_Rb_tree::_S_right (inline) 0 0% 68.95% 2490ms 2.32% boost::numeric::ublas::c_vector::operator-= (inline) 1ms 0.00093% 68.95% 2481ms 2.31% std::_Rb_tree::_M_insert_unique 613ms 0.57% 69.52% 2436ms 2.27% AbstractCellProperty::IsSame 0 0% 69.52% 2435ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 50ms 0.047% 69.57% 2431ms 2.26% CellPropertyCollection::HasProperty 247ms 0.23% 69.80% 2409ms 2.24% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.80% 2365ms 2.20% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.80% 2306ms 2.15% Cell::HasCellProperty (inline) 34ms 0.032% 69.83% 2231ms 2.08% Cell::GetCellData 3ms 0.0028% 69.83% 2178ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 96ms 0.089% 69.92% 2178ms 2.03% VertexMesh::GetVolumeOfElement 112ms 0.1% 70.03% 2157ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 214ms 0.2% 70.22% 2143ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 33ms 0.031% 70.26% 2079ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 2042ms 1.90% 72.16% 2042ms 1.90% std::_Rb_tree_increment 0 0% 72.16% 1954ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00093% 72.16% 1946ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0019% 72.16% 1898ms 1.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.16% 1898ms 1.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1282ms 1.19% 73.35% 1825ms 1.70% std::_Rb_tree::equal_range (inline) 407ms 0.38% 73.73% 1823ms 1.70% std::type_info::operator== (inline) 79ms 0.074% 73.81% 1811ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.81% 1735ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.018% 73.82% 1712ms 1.59% VertexMesh::GetSurfaceAreaOfElement 25ms 0.023% 73.85% 1650ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 42ms 0.039% 73.89% 1494ms 1.39% Node::RemoveElement 33ms 0.031% 73.92% 1479ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.014% 73.93% 1465ms 1.36% std::set::erase (inline) 107ms 0.1% 74.03% 1457ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 162ms 0.15% 74.18% 1445ms 1.35% CellPropertyCollection::AddProperty 112ms 0.1% 74.28% 1386ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.28% 1337ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.28% 1288ms 1.20% OffLatticeSimulation::ApplyBoundaries 0 0% 74.28% 1283ms 1.19% tcache_get (inline) 1283ms 1.19% 75.48% 1283ms 1.19% tcache_get_n (inline) 75ms 0.07% 75.55% 1178ms 1.10% std::less::operator() (inline) 0 0% 75.55% 1173ms 1.09% boost::numeric::ublas::norm_2 (inline) 494ms 0.46% 76.01% 1162ms 1.08% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 76ms 0.071% 76.08% 1141ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 1114ms 1.04% 77.12% 1114ms 1.04% Node::rGetLocation 898ms 0.84% 77.95% 1103ms 1.03% std::operator< (inline) 0 0% 77.95% 1094ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 15ms 0.014% 77.97% 1092ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 29ms 0.027% 77.99% 1088ms 1.01% CellPropertyRegistry::Get 1083ms 1.01% 79.00% 1083ms 1.01% std::_Rb_tree_insert_and_rebalance 92ms 0.086% 79.09% 1044ms 0.97% std::_Rb_tree::find (inline) 1043ms 0.97% 80.06% 1043ms 0.97% [libchaste_cell_based.so] 10ms 0.0093% 80.07% 1039ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.07% 1027ms 0.96% std::_Rb_tree::clear (inline) 0 0% 80.07% 1007ms 0.94% std::map::clear (inline) 1005ms 0.94% 81.00% 1005ms 0.94% std::vector::size (inline) 166ms 0.15% 81.16% 992ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.16% 992ms 0.92% boost::shared_ptr::~shared_ptr (inline) 969ms 0.9% 82.06% 969ms 0.9% [libchaste_mesh.so] 23ms 0.021% 82.08% 956ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.08% 946ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0047% 82.09% 946ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 98ms 0.091% 82.18% 941ms 0.88% std::swap_ranges (inline) 154ms 0.14% 82.32% 922ms 0.86% boost::numeric::ublas::detail::equals 367ms 0.34% 82.66% 914ms 0.85% Edge::GetMapIndex 113ms 0.11% 82.77% 913ms 0.85% MutableElement::RegisterWithEdges (inline) 0 0% 82.77% 860ms 0.8% std::map::find (inline) 116ms 0.11% 82.88% 856ms 0.8% MutableElement::GetNodeLocalIndex 0 0% 82.88% 854ms 0.79% VertexMeshWriter::MakeVtkMesh 851ms 0.79% 83.67% 851ms 0.79% std::swap (inline) 0 0% 83.67% 843ms 0.78% std::iter_swap (inline) 169ms 0.16% 83.82% 826ms 0.77% boost::shared_ptr::shared_ptr (inline) 37ms 0.034% 83.86% 823ms 0.77% Edge::AddElement 797ms 0.74% 84.60% 802ms 0.75% boost::detail::sp_counted_base::release 778ms 0.72% 85.33% 778ms 0.72% Node::GetIndex 136ms 0.13% 85.45% 775ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.45% 741ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 455ms 0.42% 85.88% 735ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.88% 725ms 0.67% boost::numeric::ublas::norm_inf (inline) 364ms 0.34% 86.21% 725ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 98ms 0.091% 86.31% 708ms 0.66% std::__new_allocator::construct (inline) 0 0% 86.31% 708ms 0.66% std::allocator_traits::construct (inline) 0 0% 86.31% 675ms 0.63% std::_Vector_base::_M_allocate (inline) 633ms 0.59% 86.89% 657ms 0.61% boost::detail::shared_count::shared_count (inline) 0 0% 86.89% 656ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.89% 640ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.91% 640ms 0.6% std::_Rb_tree::_M_insert_node (inline) 597ms 0.56% 87.47% 597ms 0.56% [libstdc++.so.6.0.33] 0 0% 87.47% 595ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 33ms 0.031% 87.50% 584ms 0.54% MutableElement::RegisterWithNodes (inline) 1ms 0.00093% 87.50% 582ms 0.54% vtkPolygon::New 0 0% 87.50% 580ms 0.54% vtkPolygon::vtkPolygon 25ms 0.023% 87.52% 566ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.52% 566ms 0.53% boost::numeric::ublas::vector::vector (inline) 10ms 0.0093% 87.53% 556ms 0.52% std::vector::_M_default_append (inline) 543ms 0.51% 88.04% 543ms 0.51% operator delete 28ms 0.026% 88.06% 538ms 0.5% Node::AddElement