File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98296ms, 87.37% of 112502ms total Dropped 1135 nodes (cum <= 562.51ms) flat flat% sum% cum cum% 0 0% 0% 112132ms 99.67% __libc_start_call_main 0 0% 0% 112132ms 99.67% __libc_start_main_impl 0 0% 0% 112132ms 99.67% _start 0 0% 0% 112109ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 112109ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 112109ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 112109ms 99.65% main 0 0% 0% 112065ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 112065ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 112065ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 112057ms 99.60% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.02% 58112ms 51.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.0098% 0.029% 54667ms 48.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 156ms 0.14% 0.17% 53569ms 47.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 297ms 0.26% 0.43% 40571ms 36.06% NagaiHondaForce::AddForceContribution 0 0% 0.43% 40356ms 35.87% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00089% 0.43% 25068ms 22.28% VertexBasedCellPopulation::Update 2ms 0.0018% 0.43% 24917ms 22.15% MutableVertexMesh::ReMesh 14791ms 13.15% 13.58% 23322ms 20.73% Cylindrical2dVertexMesh::GetVectorFromAtoB 122ms 0.11% 13.69% 17946ms 15.95% Cell::ReadyToDivide 85ms 0.076% 13.77% 16541ms 14.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 332ms 0.3% 14.06% 14574ms 12.95% NagaiHondaForce::GetAdhesionParameter 172ms 0.15% 14.21% 14232ms 12.65% SimpleWntCellCycleModel::UpdateCellCyclePhase 127ms 0.11% 14.33% 14004ms 12.45% CellPropertyCollection::GetPropertiesType (inline) 476ms 0.42% 14.75% 13587ms 12.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 104ms 0.092% 14.84% 12307ms 10.94% VertexBasedCellPopulation::GetDampingConstant 342ms 0.3% 15.15% 12049ms 10.71% boost::numeric::ublas::vector_assign (inline) 3923ms 3.49% 18.63% 11949ms 10.62% __dynamic_cast 149ms 0.13% 18.77% 11868ms 10.55% MutableVertexMesh::CheckForIntersections 50ms 0.044% 18.81% 11804ms 10.49% AbstractCellProperty::IsSubType (inline) 99ms 0.088% 18.90% 10973ms 9.75% AbstractTargetAreaModifier::UpdateTargetAreas 39ms 0.035% 18.93% 10857ms 9.65% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.022% 18.96% 10454ms 9.29% AbstractCellBasedSimulation::DoCellBirth 1543ms 1.37% 20.33% 10423ms 9.26% std::__new_allocator::allocate (inline) 0 0% 20.33% 9925ms 8.82% std::_Rb_tree::_M_create_node (inline) 0 0% 20.33% 9902ms 8.80% std::allocator_traits::allocate (inline) 371ms 0.33% 20.66% 9358ms 8.32% VertexMesh::GetNextEdgeGradientOfElementAtNode 2786ms 2.48% 23.13% 9149ms 8.13% boost::numeric::ublas::indexing_vector_assign 0 0% 23.13% 9139ms 8.12% std::_Rb_tree::_M_get_node (inline) 1332ms 1.18% 24.32% 9000ms 8.00% std::_Rb_tree::_M_erase 795ms 0.71% 25.02% 8947ms 7.95% operator new 38ms 0.034% 25.06% 8929ms 7.94% VertexBasedCellPopulation::GetLocationOfCellCentre 106ms 0.094% 25.15% 8902ms 7.91% Cell::GetMutationState 0 0% 25.15% 8779ms 7.80% std::_Rb_tree::_Alloc_node::operator() (inline) 866ms 0.77% 25.92% 8680ms 7.72% VertexMesh::ElementIncludesPoint 19ms 0.017% 25.94% 8604ms 7.65% MutableVertexMesh::RemoveDeletedNodesAndElements 442ms 0.39% 26.33% 8469ms 7.53% std::map::operator[] (partial-inline) 451ms 0.4% 26.73% 8337ms 7.41% VertexMesh::GetCentroidOfElement 0 0% 26.73% 8091ms 7.19% std::_Rb_tree::_M_drop_node (inline) 217ms 0.19% 26.92% 7974ms 7.09% std::_Rb_tree::~_Rb_tree (inline) 2840ms 2.52% 29.45% 7897ms 7.02% __GI___libc_malloc 200ms 0.18% 29.63% 7831ms 6.96% std::__new_allocator::deallocate (inline) 0 0% 29.63% 7824ms 6.95% std::allocator_traits::deallocate (inline) 0 0% 29.63% 7755ms 6.89% std::_Rb_tree::_M_put_node (inline) 170ms 0.15% 29.78% 7717ms 6.86% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.78% 7571ms 6.73% std::set::~set (inline) 2475ms 2.20% 31.98% 7325ms 6.51% __GI___libc_free 1442ms 1.28% 33.26% 7290ms 6.48% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 755ms 0.67% 33.93% 7290ms 6.48% std::_Rb_tree::_M_copy (inline) 32ms 0.028% 33.96% 7196ms 6.40% std::set::set (inline) 2813ms 2.50% 36.46% 7054ms 6.27% std::_Rb_tree::_M_lower_bound (inline) 145ms 0.13% 36.59% 6549ms 5.82% SimpleWntCellCycleModel::GetWntLevel 6512ms 5.79% 42.38% 6512ms 5.79% __strcmp_avx2 160ms 0.14% 42.52% 6307ms 5.61% WntConcentration::GetWntLevel 913ms 0.81% 43.33% 6277ms 5.58% std::_Rb_tree::_M_clone_node (inline) 6021ms 5.35% 48.68% 6021ms 5.35% boost::numeric::ublas::c_vector::operator() 19ms 0.017% 48.70% 5811ms 5.17% MutableVertexMesh::RemoveDeletedNodes 0 0% 48.70% 5774ms 5.13% std::_Rb_tree::lower_bound (inline) 0 0% 48.70% 5774ms 5.13% std::map::lower_bound (inline) 38ms 0.034% 48.73% 5620ms 5.00% EdgeHelper::RemoveDeletedEdges 2014ms 1.79% 50.52% 5355ms 4.76% boost::numeric::ublas::c_vector::operator[] (inline) 217ms 0.19% 50.72% 5340ms 4.75% MutableElement::ResetIndex 0 0% 50.72% 5315ms 4.72% std::set::insert (inline) 38ms 0.034% 50.75% 5304ms 4.71% EdgeHelper::UpdateEdgesMapKey 2825ms 2.51% 53.26% 5256ms 4.67% __cxxabiv1::__si_class_type_info::__do_dyncast 116ms 0.1% 53.36% 4875ms 4.33% AbstractCellPopulation::GetCellUsingLocationIndex 4409ms 3.92% 57.28% 4833ms 4.30% _int_free 1ms 0.00089% 57.28% 4818ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 532ms 0.47% 57.76% 4478ms 3.98% std::_Rb_tree::_M_insert_ (inline) 186ms 0.17% 57.92% 4236ms 3.77% std::set_intersection (inline) 231ms 0.21% 58.13% 4050ms 3.60% std::__set_intersection 52ms 0.046% 58.17% 3967ms 3.53% AbstractCellProperty::IsType (inline) 31ms 0.028% 58.20% 3830ms 3.40% Cell::GetCellProliferativeType 3699ms 3.29% 61.49% 3699ms 3.29% boost::numeric::ublas::same_impl_ex 3668ms 3.26% 64.75% 3668ms 3.26% std::_Rb_tree::_S_right (inline) 6ms 0.0053% 64.76% 3602ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 75ms 0.067% 64.82% 3580ms 3.18% std::_Rb_tree::erase 2389ms 2.12% 66.95% 3419ms 3.04% _int_malloc 0 0% 66.95% 3164ms 2.81% std::insert_iterator::operator= (inline) 956ms 0.85% 67.80% 3122ms 2.78% AbstractElement::GetNodeLocation 43ms 0.038% 67.83% 3085ms 2.74% Cell::SetCellProliferativeType 25ms 0.022% 67.86% 2920ms 2.60% CellPropertyCollection::HasProperty 0 0% 67.86% 2882ms 2.56% boost::numeric::ublas::c_vector::operator-= (inline) 819ms 0.73% 68.58% 2878ms 2.56% AbstractCellProperty::IsSame 0 0% 68.58% 2816ms 2.50% Cell::HasCellProperty (inline) 4ms 0.0036% 68.59% 2739ms 2.43% std::_Rb_tree::_M_insert_unique_ (inline) 39ms 0.035% 68.62% 2636ms 2.34% Cell::GetCellData 225ms 0.2% 68.82% 2606ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 619ms 0.55% 69.37% 2583ms 2.30% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.37% 2580ms 2.29% AbstractCellPopulation::WriteResultsToFiles 3ms 0.0027% 69.37% 2576ms 2.29% std::_Rb_tree::_M_insert_unique 183ms 0.16% 69.54% 2551ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.54% 2478ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 1583ms 1.41% 70.94% 2412ms 2.14% std::_Rb_tree::equal_range (inline) 5ms 0.0044% 70.95% 2409ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 218ms 0.19% 71.14% 2385ms 2.12% AbstractCellPopulation::Iterator::IsRealCell (inline) 74ms 0.066% 71.21% 2336ms 2.08% VertexMesh::GetVolumeOfElement 38ms 0.034% 71.24% 2211ms 1.97% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 47ms 0.042% 71.28% 2207ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 2187ms 1.94% 73.23% 2187ms 1.94% std::_Rb_tree_increment 0 0% 73.23% 2119ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0036% 73.23% 2104ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 528ms 0.47% 73.70% 2059ms 1.83% std::type_info::operator== (inline) 1ms 0.00089% 73.70% 2028ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.70% 2028ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.70% 1913ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 73.72% 1878ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 73ms 0.065% 73.78% 1831ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 24ms 0.021% 73.81% 1715ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 81ms 0.072% 73.88% 1688ms 1.50% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 55ms 0.049% 73.93% 1670ms 1.48% Node::RemoveElement 9ms 0.008% 73.93% 1618ms 1.44% std::set::erase (inline) 30ms 0.027% 73.96% 1607ms 1.43% VertexMesh::GetSurfaceAreaOfElement 162ms 0.14% 74.11% 1519ms 1.35% CellPropertyCollection::AddProperty 1ms 0.00089% 74.11% 1449ms 1.29% OffLatticeSimulation::ApplyBoundaries 0 0% 74.11% 1449ms 1.29% tcache_get (inline) 1449ms 1.29% 75.39% 1449ms 1.29% tcache_get_n (inline) 43ms 0.038% 75.43% 1408ms 1.25% std::less::operator() (inline) 74ms 0.066% 75.50% 1394ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.50% 1383ms 1.23% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.0098% 75.51% 1383ms 1.23% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.08% 75.59% 1372ms 1.22% std::swap_ranges (inline) 1099ms 0.98% 76.56% 1365ms 1.21% std::operator< (inline) 0 0% 76.56% 1323ms 1.18% boost::numeric::ublas::norm_2 (inline) 0 0% 76.56% 1319ms 1.17% boost::numeric::ublas::vector_binary::operator() (inline) 565ms 0.5% 77.07% 1309ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1283ms 1.14% 78.21% 1283ms 1.14% std::swap (inline) 91ms 0.081% 78.29% 1282ms 1.14% std::_Rb_tree::find (inline) 0 0% 78.29% 1282ms 1.14% std::iter_swap (inline) 1276ms 1.13% 79.42% 1276ms 1.13% [libchaste_cell_based.so] 0 0% 79.42% 1245ms 1.11% std::_Rb_tree::clear (inline) 71ms 0.063% 79.49% 1238ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.49% 1226ms 1.09% std::map::clear (inline) 22ms 0.02% 79.51% 1211ms 1.08% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 26ms 0.023% 79.53% 1180ms 1.05% CellPropertyRegistry::Get 11ms 0.0098% 79.54% 1168ms 1.04% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.54% 1146ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1123ms 1% 80.54% 1123ms 1% std::_Rb_tree_insert_and_rebalance 153ms 0.14% 80.67% 1088ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 80.67% 1088ms 0.97% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.67% 1086ms 0.97% std::map::find (inline) 981ms 0.87% 81.54% 981ms 0.87% Node::rGetLocation 13ms 0.012% 81.56% 977ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 206ms 0.18% 81.74% 957ms 0.85% boost::numeric::ublas::detail::equals 874ms 0.78% 82.52% 895ms 0.8% boost::detail::sp_counted_base::release 0 0% 82.52% 876ms 0.78% VertexMeshWriter::MakeVtkMesh 236ms 0.21% 82.73% 854ms 0.76% std::__new_allocator::construct (inline) 0 0% 82.73% 854ms 0.76% std::allocator_traits::construct (inline) 840ms 0.75% 83.47% 840ms 0.75% std::vector::size (inline) 84ms 0.075% 83.55% 835ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 440ms 0.39% 83.94% 832ms 0.74% Edge::GetMapIndex 798ms 0.71% 84.65% 798ms 0.71% [libchaste_mesh.so] 29ms 0.026% 84.67% 790ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.67% 786ms 0.7% std::_Rb_tree::_M_construct_node (inline) 25ms 0.022% 84.70% 770ms 0.68% Edge::AddElement 0 0% 84.70% 760ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00089% 84.70% 757ms 0.67% std::_Vector_base::_M_allocate (inline) 430ms 0.38% 85.08% 752ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 169ms 0.15% 85.23% 738ms 0.66% boost::shared_ptr::shared_ptr (inline) 737ms 0.66% 85.88% 737ms 0.66% [libstdc++.so.6.0.33] 0 0% 85.88% 705ms 0.63% boost::numeric::ublas::norm_inf (inline) 346ms 0.31% 86.19% 705ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.19% 696ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.19% 677ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.014% 86.21% 677ms 0.6% std::_Rb_tree::_M_insert_node (inline) 12ms 0.011% 86.22% 645ms 0.57% std::vector::_M_default_append (inline) 72ms 0.064% 86.28% 638ms 0.57% std::_Rb_tree::_M_upper_bound (inline) 0 0% 86.28% 630ms 0.56% vtkPolygon::New 0 0% 86.28% 630ms 0.56% vtkPolygon::vtkPolygon 33ms 0.029% 86.31% 623ms 0.55% MutableElement::RegisterWithNodes (inline) 116ms 0.1% 86.41% 621ms 0.55% MutableElement::GetNodeLocalIndex 506ms 0.45% 86.86% 619ms 0.55% AbstractElement::GetNodeGlobalIndex 32ms 0.028% 86.89% 593ms 0.53% Node::AddElement 0 0% 86.89% 578ms 0.51% std::map::map (inline) 542ms 0.48% 87.37% 569ms 0.51% boost::detail::shared_count::shared_count (inline)