File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95773ms, 88.42% of 108310ms total Dropped 1104 nodes (cum <= 541.55ms) flat flat% sum% cum cum% 0 0% 0% 107864ms 99.59% __libc_start_call_main 0 0% 0% 107864ms 99.59% __libc_start_main_impl 0 0% 0% 107864ms 99.59% _start 0 0% 0% 107844ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107844ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107844ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107844ms 99.57% main 0 0% 0% 107810ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107810ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107810ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107802ms 99.53% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.02% 56047ms 51.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.039% 52978ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 94ms 0.087% 0.13% 51463ms 47.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 365ms 0.34% 0.46% 39555ms 36.52% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.46% 38851ms 35.87% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.46% 24023ms 22.18% VertexBasedCellPopulation::Update 1ms 0.00092% 0.47% 23890ms 22.06% MutableVertexMesh::ReMesh 14473ms 13.36% 13.83% 22850ms 21.10% Cylindrical2dVertexMesh::GetVectorFromAtoB 109ms 0.1% 13.93% 17429ms 16.09% Cell::ReadyToDivide 67ms 0.062% 13.99% 16149ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 339ms 0.31% 14.30% 14654ms 13.53% NagaiHondaForce::GetAdhesionParameter 429ms 0.4% 14.70% 14297ms 13.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 131ms 0.12% 14.82% 13848ms 12.79% SimpleWntCellCycleModel::UpdateCellCyclePhase 121ms 0.11% 14.93% 13451ms 12.42% CellPropertyCollection::GetPropertiesType (inline) 508ms 0.47% 15.40% 12724ms 11.75% boost::numeric::ublas::vector_assign (inline) 121ms 0.11% 15.51% 12055ms 11.13% MutableVertexMesh::CheckForIntersections 103ms 0.095% 15.61% 11509ms 10.63% VertexBasedCellPopulation::GetDampingConstant 2995ms 2.77% 18.37% 11044ms 10.20% __dynamic_cast 58ms 0.054% 18.43% 10936ms 10.10% AbstractCellProperty::IsSubType (inline) 81ms 0.075% 18.50% 10444ms 9.64% AbstractTargetAreaModifier::UpdateTargetAreas 63ms 0.058% 18.56% 10342ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 34ms 0.031% 18.59% 10237ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1269ms 1.17% 19.76% 10074ms 9.30% std::__new_allocator::allocate (inline) 0 0% 19.76% 9506ms 8.78% std::_Rb_tree::_M_create_node (inline) 0 0% 19.76% 9465ms 8.74% std::allocator_traits::allocate (inline) 1371ms 1.27% 21.03% 9319ms 8.60% std::_Rb_tree::_M_erase 2570ms 2.37% 23.40% 9253ms 8.54% boost::numeric::ublas::indexing_vector_assign 814ms 0.75% 24.15% 8998ms 8.31% VertexMesh::ElementIncludesPoint 900ms 0.83% 24.98% 8918ms 8.23% operator new 0 0% 24.98% 8876ms 8.19% std::_Rb_tree::_M_get_node (inline) 376ms 0.35% 25.33% 8748ms 8.08% VertexMesh::GetNextEdgeGradientOfElementAtNode 23ms 0.021% 25.35% 8662ms 8.00% VertexBasedCellPopulation::GetLocationOfCellCentre 299ms 0.28% 25.63% 8653ms 7.99% std::_Rb_tree::~_Rb_tree (inline) 94ms 0.087% 25.72% 8588ms 7.93% Cell::GetMutationState 0 0% 25.72% 8421ms 7.77% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.72% 8298ms 7.66% std::_Rb_tree::_M_drop_node (inline) 535ms 0.49% 26.21% 8260ms 7.63% VertexMesh::GetCentroidOfElement 0 0% 26.21% 8215ms 7.58% std::set::~set (inline) 262ms 0.24% 26.45% 8048ms 7.43% std::__new_allocator::deallocate (inline) 0 0% 26.45% 8024ms 7.41% std::allocator_traits::deallocate (inline) 0 0% 26.45% 7939ms 7.33% std::_Rb_tree::_M_put_node (inline) 3333ms 3.08% 29.53% 7811ms 7.21% __GI___libc_malloc 3214ms 2.97% 32.50% 7806ms 7.21% __GI___libc_free 22ms 0.02% 32.52% 7477ms 6.90% MutableVertexMesh::RemoveDeletedNodesAndElements 437ms 0.4% 32.92% 7363ms 6.80% std::map::operator[] (partial-inline) 1310ms 1.21% 34.13% 7127ms 6.58% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 229ms 0.21% 34.34% 6873ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 6541ms 6.04% 40.38% 6541ms 6.04% __strcmp_avx2 9ms 0.0083% 40.39% 6484ms 5.99% std::set::set (inline) 647ms 0.6% 40.99% 6409ms 5.92% std::_Rb_tree::_M_copy (inline) 94ms 0.087% 41.07% 6224ms 5.75% SimpleWntCellCycleModel::GetWntLevel 134ms 0.12% 41.20% 6060ms 5.60% WntConcentration::GetWntLevel 5979ms 5.52% 46.72% 5979ms 5.52% boost::numeric::ublas::c_vector::operator() 2615ms 2.41% 49.13% 5944ms 5.49% std::_Rb_tree::_M_lower_bound (inline) 2678ms 2.47% 51.60% 5593ms 5.16% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.60% 5525ms 5.10% std::set::insert (inline) 704ms 0.65% 52.25% 5482ms 5.06% std::_Rb_tree::_M_clone_node (inline) 30ms 0.028% 52.28% 5336ms 4.93% MutableVertexMesh::RemoveDeletedNodes 180ms 0.17% 52.45% 5170ms 4.77% EdgeHelper::RemoveDeletedEdges 35ms 0.032% 52.48% 4795ms 4.43% EdgeHelper::UpdateEdgesMapKey 0 0% 52.48% 4780ms 4.41% std::_Rb_tree::lower_bound (inline) 0 0% 52.48% 4780ms 4.41% std::map::lower_bound (inline) 1466ms 1.35% 53.83% 4769ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 570ms 0.53% 54.36% 4724ms 4.36% std::_Rb_tree::_M_insert_ (inline) 219ms 0.2% 54.56% 4590ms 4.24% MutableElement::ResetIndex 4270ms 3.94% 58.50% 4588ms 4.24% _int_free 1ms 0.00092% 58.50% 4583ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 53ms 0.049% 58.55% 4470ms 4.13% std::set_intersection (inline) 292ms 0.27% 58.82% 4417ms 4.08% std::__set_intersection 123ms 0.11% 58.94% 4285ms 3.96% AbstractCellPopulation::GetCellUsingLocationIndex 3983ms 3.68% 62.61% 3983ms 3.68% boost::numeric::ublas::same_impl_ex 37ms 0.034% 62.65% 3874ms 3.58% Cell::GetCellProliferativeType 61ms 0.056% 62.70% 3820ms 3.53% AbstractCellProperty::IsType (inline) 5ms 0.0046% 62.71% 3533ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.71% 3254ms 3.00% std::insert_iterator::operator= (inline) 797ms 0.74% 63.44% 3130ms 2.89% AbstractElement::GetNodeLocation 25ms 0.023% 63.47% 3042ms 2.81% Cell::SetCellProliferativeType 2051ms 1.89% 65.36% 2938ms 2.71% _int_malloc 36ms 0.033% 65.39% 2902ms 2.68% std::_Rb_tree::erase 3ms 0.0028% 65.40% 2893ms 2.67% std::_Rb_tree::_M_insert_unique_ (inline) 653ms 0.6% 66.00% 2846ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 2759ms 2.55% 68.55% 2759ms 2.55% std::_Rb_tree::_S_right (inline) 658ms 0.61% 69.16% 2730ms 2.52% AbstractCellProperty::IsSame 407ms 0.38% 69.53% 2663ms 2.46% std::_Rb_tree_const_iterator::operator++ (inline) 58ms 0.054% 69.58% 2642ms 2.44% CellPropertyCollection::HasProperty 1ms 0.00092% 69.59% 2632ms 2.43% std::_Rb_tree::_M_insert_unique 236ms 0.22% 69.80% 2573ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.80% 2541ms 2.35% Cell::HasCellProperty (inline) 22ms 0.02% 69.82% 2442ms 2.25% Cell::GetCellData 0 0% 69.82% 2440ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.82% 2431ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.82% 2360ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.0028% 69.83% 2293ms 2.12% AbstractCellPopulation::Iterator::operator++ (inline) 230ms 0.21% 70.04% 2279ms 2.10% AbstractCellPopulation::Iterator::IsRealCell (inline) 95ms 0.088% 70.13% 2271ms 2.10% VertexMesh::GetVolumeOfElement 82ms 0.076% 70.20% 2211ms 2.04% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 35ms 0.032% 70.23% 2102ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 2084ms 1.92% 72.16% 2084ms 1.92% std::_Rb_tree_increment 502ms 0.46% 72.62% 2072ms 1.91% std::type_info::operator== (inline) 0 0% 72.62% 1993ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.62% 1988ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 72.62% 1919ms 1.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.62% 1919ms 1.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1313ms 1.21% 73.83% 1918ms 1.77% std::_Rb_tree::equal_range (inline) 74ms 0.068% 73.90% 1834ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 73.90% 1796ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 73.92% 1795ms 1.66% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 168ms 0.16% 74.08% 1680ms 1.55% CellPropertyCollection::AddProperty 21ms 0.019% 74.10% 1636ms 1.51% VertexMesh::GetSurfaceAreaOfElement 24ms 0.022% 74.12% 1568ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.07% 74.19% 1544ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 44ms 0.041% 74.23% 1503ms 1.39% Node::RemoveElement 127ms 0.12% 74.35% 1476ms 1.36% boost::numeric::ublas::vector_reference::operator() (inline) 23ms 0.021% 74.37% 1474ms 1.36% std::set::erase (inline) 0 0% 74.37% 1368ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.37% 1353ms 1.25% tcache_get (inline) 1353ms 1.25% 75.62% 1353ms 1.25% tcache_get_n (inline) 0 0% 75.62% 1255ms 1.16% OffLatticeSimulation::ApplyBoundaries 0 0% 75.62% 1232ms 1.14% boost::numeric::ublas::norm_2 (inline) 514ms 0.47% 76.09% 1227ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 79ms 0.073% 76.16% 1211ms 1.12% std::less::operator() (inline) 1205ms 1.11% 77.28% 1205ms 1.11% [libchaste_cell_based.so] 1188ms 1.10% 78.37% 1188ms 1.10% Node::rGetLocation 22ms 0.02% 78.39% 1181ms 1.09% CellPropertyRegistry::Get 96ms 0.089% 78.48% 1146ms 1.06% std::_Rb_tree::find (inline) 934ms 0.86% 79.35% 1132ms 1.05% std::operator< (inline) 72ms 0.066% 79.41% 1127ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 1100ms 1.02% 80.43% 1100ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 80.43% 1085ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 14ms 0.013% 80.44% 1069ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 152ms 0.14% 80.58% 1034ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.58% 1034ms 0.95% boost::shared_ptr::~shared_ptr (inline) 6ms 0.0055% 80.59% 1005ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00092% 80.59% 968ms 0.89% std::_Rb_tree::clear (inline) 0 0% 80.59% 954ms 0.88% std::map::clear (inline) 952ms 0.88% 81.47% 952ms 0.88% [libchaste_mesh.so] 1ms 0.00092% 81.47% 947ms 0.87% std::map::find (inline) 24ms 0.022% 81.49% 933ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 931ms 0.86% 82.35% 931ms 0.86% std::vector::size (inline) 0 0% 82.35% 918ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 82.35% 918ms 0.85% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.07% 82.42% 913ms 0.84% std::swap_ranges (inline) 380ms 0.35% 82.77% 898ms 0.83% Edge::GetMapIndex 4ms 0.0037% 82.78% 898ms 0.83% VertexMeshWriter::MakeVtkMesh 161ms 0.15% 82.93% 897ms 0.83% boost::numeric::ublas::detail::equals 848ms 0.78% 83.71% 859ms 0.79% boost::detail::sp_counted_base::release 838ms 0.77% 84.48% 838ms 0.77% std::swap (inline) 0 0% 84.48% 837ms 0.77% std::iter_swap (inline) 0 0% 84.48% 807ms 0.75% CellPropertyCollection::~CellPropertyCollection (inline) 156ms 0.14% 84.63% 805ms 0.74% boost::shared_ptr::shared_ptr (inline) 93ms 0.086% 84.71% 802ms 0.74% MutableElement::GetNodeLocalIndex 758ms 0.7% 85.41% 758ms 0.7% Node::GetIndex 470ms 0.43% 85.85% 733ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 83ms 0.077% 85.92% 726ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 19ms 0.018% 85.94% 720ms 0.66% MutableElement::RegisterWithEdges (inline) 708ms 0.65% 86.59% 708ms 0.65% operator delete 21ms 0.019% 86.61% 705ms 0.65% Edge::AddElement 14ms 0.013% 86.63% 703ms 0.65% AbstractNumericalMethod::DetectStepSizeExceptions 111ms 0.1% 86.73% 689ms 0.64% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.73% 687ms 0.63% boost::numeric::ublas::norm_inf (inline) 373ms 0.34% 87.07% 687ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 105ms 0.097% 87.17% 685ms 0.63% std::__new_allocator::construct (inline) 0 0% 87.17% 685ms 0.63% std::allocator_traits::construct (inline) 0 0% 87.17% 680ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 32ms 0.03% 87.20% 680ms 0.63% std::_Rb_tree::_M_insert_node (inline) 628ms 0.58% 87.78% 649ms 0.6% boost::detail::shared_count::shared_count (inline) 27ms 0.025% 87.81% 636ms 0.59% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.81% 636ms 0.59% boost::numeric::ublas::vector::vector (inline) 0 0% 87.81% 630ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.81% 622ms 0.57% vtkPolygon::New 2ms 0.0018% 87.81% 621ms 0.57% vtkPolygon::vtkPolygon 29ms 0.027% 87.83% 615ms 0.57% MutableElement::RegisterWithNodes (inline) 606ms 0.56% 88.39% 606ms 0.56% [libstdc++.so.6.0.33] 0 0% 88.39% 589ms 0.54% std::_Vector_base::_M_allocate (inline) 34ms 0.031% 88.42% 580ms 0.54% Node::AddElement 0 0% 88.42% 577ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline)