File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97779ms, 88.94% of 109937ms total Dropped 1099 nodes (cum <= 549.68ms) flat flat% sum% cum cum% 0 0% 0% 109482ms 99.59% __libc_start_call_main 0 0% 0% 109482ms 99.59% __libc_start_main_impl 0 0% 0% 109482ms 99.59% _start 0 0% 0% 109461ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109461ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109461ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109461ms 99.57% main 0 0% 0% 109422ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109422ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109422ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 109414ms 99.52% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.019% 57126ms 51.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.039% 53966ms 49.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 116ms 0.11% 0.14% 52853ms 48.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 376ms 0.34% 0.49% 40681ms 37.00% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.49% 39158ms 35.62% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.49% 24272ms 22.08% VertexBasedCellPopulation::Update 0 0% 0.49% 24122ms 21.94% MutableVertexMesh::ReMesh 14455ms 13.15% 13.64% 22860ms 20.79% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.068% 13.71% 17684ms 16.09% Cell::ReadyToDivide 95ms 0.086% 13.79% 16585ms 15.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 324ms 0.29% 14.09% 15389ms 14.00% NagaiHondaForce::GetAdhesionParameter 415ms 0.38% 14.47% 14541ms 13.23% boost::numeric::ublas::c_vector::c_vector (partial-inline) 127ms 0.12% 14.58% 14073ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 133ms 0.12% 14.70% 14066ms 12.79% CellPropertyCollection::GetPropertiesType (inline) 405ms 0.37% 15.07% 13029ms 11.85% boost::numeric::ublas::vector_assign (inline) 156ms 0.14% 15.21% 12102ms 11.01% MutableVertexMesh::CheckForIntersections 85ms 0.077% 15.29% 11649ms 10.60% VertexBasedCellPopulation::GetDampingConstant 3208ms 2.92% 18.21% 11585ms 10.54% __dynamic_cast 74ms 0.067% 18.28% 11488ms 10.45% AbstractCellProperty::IsSubType (inline) 86ms 0.078% 18.35% 10623ms 9.66% AbstractTargetAreaModifier::UpdateTargetAreas 81ms 0.074% 18.43% 10512ms 9.56% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1319ms 1.20% 19.63% 10385ms 9.45% std::__new_allocator::allocate (inline) 19ms 0.017% 19.64% 10287ms 9.36% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.64% 9838ms 8.95% std::allocator_traits::allocate (inline) 0 0% 19.64% 9805ms 8.92% std::_Rb_tree::_M_create_node (inline) 2730ms 2.48% 22.13% 9695ms 8.82% boost::numeric::ublas::indexing_vector_assign 1391ms 1.27% 23.39% 9469ms 8.61% std::_Rb_tree::_M_erase 854ms 0.78% 24.17% 9161ms 8.33% operator new 0 0% 24.17% 9129ms 8.30% std::_Rb_tree::_M_get_node (inline) 80ms 0.073% 24.24% 9012ms 8.20% Cell::GetMutationState 805ms 0.73% 24.97% 8974ms 8.16% VertexMesh::ElementIncludesPoint 356ms 0.32% 25.30% 8828ms 8.03% VertexMesh::GetNextEdgeGradientOfElementAtNode 38ms 0.035% 25.33% 8819ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.33% 8665ms 7.88% std::_Rb_tree::_Alloc_node::operator() (inline) 204ms 0.19% 25.52% 8617ms 7.84% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.52% 8405ms 7.65% std::_Rb_tree::_M_drop_node (inline) 470ms 0.43% 25.95% 8354ms 7.60% VertexMesh::GetCentroidOfElement 292ms 0.27% 26.21% 8178ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 26.21% 8147ms 7.41% std::allocator_traits::deallocate (inline) 0 0% 26.21% 8146ms 7.41% std::set::~set (inline) 3134ms 2.85% 29.06% 8114ms 7.38% __GI___libc_malloc 0 0% 29.06% 8083ms 7.35% std::_Rb_tree::_M_put_node (inline) 3183ms 2.90% 31.96% 7884ms 7.17% __GI___libc_free 24ms 0.022% 31.98% 7713ms 7.02% MutableVertexMesh::RemoveDeletedNodesAndElements 467ms 0.42% 32.40% 7304ms 6.64% std::map::operator[] (partial-inline) 1393ms 1.27% 33.67% 7146ms 6.50% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 157ms 0.14% 33.81% 7025ms 6.39% std::_Rb_tree::_Rb_tree (partial-inline) 6738ms 6.13% 39.94% 6738ms 6.13% __strcmp_avx2 658ms 0.6% 40.54% 6646ms 6.05% std::_Rb_tree::_M_copy (inline) 9ms 0.0082% 40.55% 6555ms 5.96% std::set::set (inline) 94ms 0.086% 40.64% 6399ms 5.82% SimpleWntCellCycleModel::GetWntLevel 147ms 0.13% 40.77% 6212ms 5.65% WntConcentration::GetWntLevel 6180ms 5.62% 46.39% 6180ms 5.62% boost::numeric::ublas::c_vector::operator() 2752ms 2.50% 48.89% 5882ms 5.35% __cxxabiv1::__si_class_type_info::__do_dyncast 2426ms 2.21% 51.10% 5842ms 5.31% std::_Rb_tree::_M_lower_bound (inline) 722ms 0.66% 51.76% 5688ms 5.17% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.76% 5589ms 5.08% std::set::insert (inline) 34ms 0.031% 51.79% 5343ms 4.86% MutableVertexMesh::RemoveDeletedNodes 27ms 0.025% 51.81% 5164ms 4.70% EdgeHelper::RemoveDeletedEdges 30ms 0.027% 51.84% 4882ms 4.44% EdgeHelper::UpdateEdgesMapKey 1504ms 1.37% 53.21% 4840ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 54ms 0.049% 53.26% 4785ms 4.35% std::set_intersection (inline) 206ms 0.19% 53.44% 4781ms 4.35% MutableElement::ResetIndex 542ms 0.49% 53.94% 4755ms 4.33% std::_Rb_tree::_M_insert_ (inline) 282ms 0.26% 54.19% 4731ms 4.30% std::__set_intersection 4388ms 3.99% 58.19% 4696ms 4.27% _int_free 0 0% 58.19% 4669ms 4.25% std::_Rb_tree::lower_bound (inline) 0 0% 58.19% 4669ms 4.25% std::map::lower_bound (inline) 0 0% 58.19% 4590ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 101ms 0.092% 58.28% 4127ms 3.75% AbstractCellPopulation::GetCellUsingLocationIndex 4052ms 3.69% 61.96% 4052ms 3.69% boost::numeric::ublas::same_impl_ex 48ms 0.044% 62.01% 3951ms 3.59% Cell::GetCellProliferativeType 64ms 0.058% 62.06% 3712ms 3.38% AbstractCellProperty::IsType (inline) 10ms 0.0091% 62.07% 3503ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.07% 3328ms 3.03% std::insert_iterator::operator= (inline) 2311ms 2.10% 64.18% 3306ms 3.01% _int_malloc 790ms 0.72% 64.89% 3230ms 2.94% AbstractElement::GetNodeLocation 49ms 0.045% 64.94% 3170ms 2.88% Cell::SetCellProliferativeType 426ms 0.39% 65.33% 3053ms 2.78% std::_Rb_tree_const_iterator::operator++ (inline) 33ms 0.03% 65.36% 3022ms 2.75% std::_Rb_tree::erase 2911ms 2.65% 68.00% 2911ms 2.65% std::_Rb_tree::_S_right (inline) 674ms 0.61% 68.62% 2875ms 2.62% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 68.62% 2870ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.62% 2719ms 2.47% std::_Rb_tree::_M_insert_unique (inline) 699ms 0.64% 69.26% 2607ms 2.37% AbstractCellProperty::IsSame 32ms 0.029% 69.28% 2566ms 2.33% CellPropertyCollection::HasProperty 0 0% 69.28% 2494ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.28% 2472ms 2.25% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.28% 2454ms 2.23% Cell::HasCellProperty (inline) 0 0% 69.28% 2440ms 2.22% boost::numeric::ublas::c_vector::operator-= (inline) 226ms 0.21% 69.49% 2435ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 2413ms 2.19% 71.68% 2413ms 2.19% std::_Rb_tree_increment 126ms 0.11% 71.80% 2402ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 28ms 0.025% 71.82% 2349ms 2.14% Cell::GetCellData 2ms 0.0018% 71.83% 2222ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 0.091% 71.92% 2212ms 2.01% VertexMesh::GetVolumeOfElement 201ms 0.18% 72.10% 2206ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 25ms 0.023% 72.12% 2108ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.12% 2041ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1346ms 1.22% 73.35% 2030ms 1.85% std::_Rb_tree::equal_range (inline) 1ms 0.00091% 73.35% 2023ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 442ms 0.4% 73.75% 1908ms 1.74% std::type_info::operator== (inline) 1ms 0.00091% 73.75% 1825ms 1.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.75% 1825ms 1.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 54ms 0.049% 73.80% 1820ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.80% 1806ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 40ms 0.036% 73.84% 1716ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 195ms 0.18% 74.01% 1684ms 1.53% CellPropertyCollection::AddProperty 20ms 0.018% 74.03% 1649ms 1.50% VertexMesh::GetSurfaceAreaOfElement 45ms 0.041% 74.07% 1569ms 1.43% Node::RemoveElement 132ms 0.12% 74.19% 1537ms 1.40% boost::numeric::ublas::vector_reference::operator() (inline) 16ms 0.015% 74.21% 1530ms 1.39% std::set::erase (inline) 23ms 0.021% 74.23% 1512ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 79ms 0.072% 74.30% 1502ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.30% 1478ms 1.34% tcache_get (inline) 1478ms 1.34% 75.65% 1478ms 1.34% tcache_get_n (inline) 0 0% 75.65% 1428ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 75.65% 1255ms 1.14% OffLatticeSimulation::ApplyBoundaries 81ms 0.074% 75.72% 1212ms 1.10% std::less::operator() (inline) 1208ms 1.10% 76.82% 1208ms 1.10% [libchaste_cell_based.so] 1186ms 1.08% 77.90% 1186ms 1.08% Node::rGetLocation 115ms 0.1% 78.00% 1178ms 1.07% std::_Rb_tree::find (inline) 69ms 0.063% 78.07% 1169ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.07% 1157ms 1.05% boost::numeric::ublas::norm_2 (inline) 499ms 0.45% 78.52% 1149ms 1.05% boost::numeric::ublas::vector_norm_2::apply 0 0% 78.52% 1140ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 930ms 0.85% 79.37% 1131ms 1.03% std::operator< (inline) 1118ms 1.02% 80.38% 1118ms 1.02% std::_Rb_tree_insert_and_rebalance 30ms 0.027% 80.41% 1104ms 1.00% CellPropertyRegistry::Get 1ms 0.00091% 80.41% 1063ms 0.97% std::_Rb_tree::clear (inline) 12ms 0.011% 80.42% 1054ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.42% 1040ms 0.95% std::map::clear (inline) 14ms 0.013% 80.43% 1033ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1005ms 0.91% 81.35% 1005ms 0.91% std::vector::size (inline) 160ms 0.15% 81.49% 973ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 81.49% 973ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.49% 964ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 81.50% 964ms 0.88% boost::numeric::ublas::c_vector::swap 0 0% 81.50% 960ms 0.87% std::map::find (inline) 74ms 0.067% 81.57% 958ms 0.87% std::swap_ranges (inline) 924ms 0.84% 82.41% 924ms 0.84% [libchaste_mesh.so] 389ms 0.35% 82.76% 913ms 0.83% Edge::GetMapIndex 17ms 0.015% 82.78% 908ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 886ms 0.81% 83.58% 886ms 0.81% std::swap (inline) 0 0% 83.58% 884ms 0.8% std::iter_swap (inline) 163ms 0.15% 83.73% 882ms 0.8% boost::numeric::ublas::detail::equals 102ms 0.093% 83.82% 865ms 0.79% MutableElement::GetNodeLocalIndex 0 0% 83.82% 862ms 0.78% VertexMeshWriter::MakeVtkMesh 108ms 0.098% 83.92% 815ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.023% 83.94% 810ms 0.74% MutableElement::RegisterWithEdges (inline) 17ms 0.015% 83.96% 795ms 0.72% Edge::AddElement 781ms 0.71% 84.67% 787ms 0.72% boost::detail::sp_counted_base::release 147ms 0.13% 84.80% 746ms 0.68% boost::shared_ptr::shared_ptr (inline) 133ms 0.12% 84.93% 735ms 0.67% std::__new_allocator::construct (inline) 0 0% 84.93% 735ms 0.67% std::allocator_traits::construct (inline) 728ms 0.66% 85.59% 728ms 0.66% Node::GetIndex 434ms 0.39% 85.98% 717ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.98% 706ms 0.64% std::_Vector_base::_M_allocate (inline) 0 0% 85.98% 676ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 0 0% 85.98% 676ms 0.61% std::_Rb_tree::_M_construct_node (inline) 18ms 0.016% 86.00% 676ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.00% 668ms 0.61% boost::numeric::ublas::norm_inf (inline) 341ms 0.31% 86.31% 668ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.31% 661ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 659ms 0.6% 86.91% 659ms 0.6% operator delete 0 0% 86.91% 620ms 0.56% vtkPolygon::New 0 0% 86.91% 620ms 0.56% vtkPolygon::vtkPolygon 572ms 0.52% 87.43% 599ms 0.54% boost::detail::shared_count::shared_count (inline) 596ms 0.54% 87.97% 596ms 0.54% [libstdc++.so.6.0.33] 30ms 0.027% 88.00% 588ms 0.53% MutableElement::RegisterWithNodes (inline) 4ms 0.0036% 88.00% 580ms 0.53% std::vector::_M_default_append (inline) 30ms 0.027% 88.03% 577ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.03% 577ms 0.52% boost::numeric::ublas::vector::vector (inline) 566ms 0.51% 88.54% 566ms 0.51% boost::shared_ptr::operator-> (inline) 22ms 0.02% 88.56% 553ms 0.5% Node::AddElement 415ms 0.38% 88.94% 551ms 0.5% malloc_consolidate