File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97128ms, 88.23% of 110088ms total Dropped 1128 nodes (cum <= 550.44ms) flat flat% sum% cum cum% 0 0% 0% 109700ms 99.65% __libc_start_call_main 0 0% 0% 109700ms 99.65% __libc_start_main_impl 0 0% 0% 109700ms 99.65% _start 0 0% 0% 109678ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109678ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109678ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109678ms 99.63% main 0 0% 0% 109638ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109638ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109638ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 109630ms 99.58% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.022% 57168ms 51.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.035% 53842ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 138ms 0.13% 0.16% 52742ms 47.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 301ms 0.27% 0.43% 40298ms 36.61% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.43% 39378ms 35.77% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.44% 24052ms 21.85% VertexBasedCellPopulation::Update 2ms 0.0018% 0.44% 23910ms 21.72% MutableVertexMesh::ReMesh 14909ms 13.54% 13.98% 23590ms 21.43% Cylindrical2dVertexMesh::GetVectorFromAtoB 88ms 0.08% 14.06% 17867ms 16.23% Cell::ReadyToDivide 46ms 0.042% 14.10% 16583ms 15.06% AbstractPhaseBasedCellCycleModel::ReadyToDivide 312ms 0.28% 14.39% 14475ms 13.15% NagaiHondaForce::GetAdhesionParameter 130ms 0.12% 14.50% 14206ms 12.90% SimpleWntCellCycleModel::UpdateCellCyclePhase 447ms 0.41% 14.91% 13918ms 12.64% boost::numeric::ublas::c_vector::c_vector (partial-inline) 96ms 0.087% 15.00% 13398ms 12.17% CellPropertyCollection::GetPropertiesType (inline) 330ms 0.3% 15.30% 12458ms 11.32% boost::numeric::ublas::vector_assign (inline) 128ms 0.12% 15.41% 11903ms 10.81% MutableVertexMesh::CheckForIntersections 72ms 0.065% 15.48% 11805ms 10.72% VertexBasedCellPopulation::GetDampingConstant 3465ms 3.15% 18.63% 11367ms 10.33% __dynamic_cast 77ms 0.07% 18.70% 11267ms 10.23% AbstractCellProperty::IsSubType (inline) 64ms 0.058% 18.75% 10596ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 29ms 0.026% 18.78% 10553ms 9.59% AbstractCellBasedSimulation::DoCellBirth 34ms 0.031% 18.81% 10518ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1261ms 1.15% 19.96% 9854ms 8.95% std::__new_allocator::allocate (inline) 339ms 0.31% 20.27% 9431ms 8.57% VertexMesh::GetNextEdgeGradientOfElementAtNode 2914ms 2.65% 22.91% 9341ms 8.49% boost::numeric::ublas::indexing_vector_assign 0 0% 22.91% 9317ms 8.46% std::_Rb_tree::_M_create_node (inline) 0 0% 22.91% 9242ms 8.40% std::allocator_traits::allocate (inline) 1378ms 1.25% 24.16% 9139ms 8.30% std::_Rb_tree::_M_erase 32ms 0.029% 24.19% 8973ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 902ms 0.82% 25.01% 8736ms 7.94% VertexMesh::ElementIncludesPoint 758ms 0.69% 25.70% 8651ms 7.86% operator new 157ms 0.14% 25.84% 8616ms 7.83% Cell::GetMutationState 0 0% 25.84% 8544ms 7.76% std::_Rb_tree::_M_get_node (inline) 474ms 0.43% 26.27% 8382ms 7.61% VertexMesh::GetCentroidOfElement 0 0% 26.27% 8290ms 7.53% std::_Rb_tree::_Alloc_node::operator() (inline) 253ms 0.23% 26.50% 8283ms 7.52% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.50% 8141ms 7.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.50% 7840ms 7.12% std::set::~set (inline) 231ms 0.21% 26.71% 7787ms 7.07% std::__new_allocator::deallocate (inline) 507ms 0.46% 27.17% 7786ms 7.07% std::map::operator[] (partial-inline) 0 0% 27.17% 7780ms 7.07% std::allocator_traits::deallocate (inline) 18ms 0.016% 27.19% 7769ms 7.06% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 27.19% 7713ms 7.01% std::_Rb_tree::_M_put_node (inline) 2988ms 2.71% 29.91% 7698ms 6.99% __GI___libc_malloc 1467ms 1.33% 31.24% 7433ms 6.75% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 232ms 0.21% 31.45% 7234ms 6.57% std::_Rb_tree::_Rb_tree (partial-inline) 2348ms 2.13% 33.58% 7181ms 6.52% __GI___libc_free 839ms 0.76% 34.34% 6759ms 6.14% std::_Rb_tree::_M_copy (inline) 23ms 0.021% 34.36% 6741ms 6.12% std::set::set (inline) 136ms 0.12% 34.49% 6532ms 5.93% SimpleWntCellCycleModel::GetWntLevel 2543ms 2.31% 36.80% 6346ms 5.76% std::_Rb_tree::_M_lower_bound (inline) 6309ms 5.73% 42.53% 6309ms 5.73% __strcmp_avx2 171ms 0.16% 42.68% 6276ms 5.70% WntConcentration::GetWntLevel 6145ms 5.58% 48.27% 6145ms 5.58% boost::numeric::ublas::c_vector::operator() 814ms 0.74% 49.01% 5661ms 5.14% std::_Rb_tree::_M_clone_node (inline) 2856ms 2.59% 51.60% 5540ms 5.03% __cxxabiv1::__si_class_type_info::__do_dyncast 1933ms 1.76% 53.36% 5409ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 23ms 0.021% 53.38% 5383ms 4.89% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.38% 5290ms 4.81% std::set::insert (inline) 40ms 0.036% 53.41% 5192ms 4.72% EdgeHelper::RemoveDeletedEdges 0 0% 53.41% 5150ms 4.68% std::_Rb_tree::lower_bound (inline) 0 0% 53.41% 5150ms 4.68% std::map::lower_bound (inline) 42ms 0.038% 53.45% 4884ms 4.44% EdgeHelper::UpdateEdgesMapKey 4356ms 3.96% 57.41% 4817ms 4.38% _int_free 176ms 0.16% 57.57% 4815ms 4.37% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.57% 4754ms 4.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 204ms 0.19% 57.75% 4737ms 4.30% MutableElement::ResetIndex 518ms 0.47% 58.22% 4455ms 4.05% std::_Rb_tree::_M_insert_ (inline) 134ms 0.12% 58.35% 4368ms 3.97% std::set_intersection (inline) 238ms 0.22% 58.56% 4234ms 3.85% std::__set_intersection 45ms 0.041% 58.60% 3936ms 3.58% Cell::GetCellProliferativeType 61ms 0.055% 58.66% 3821ms 3.47% AbstractCellProperty::IsType (inline) 3719ms 3.38% 62.04% 3719ms 3.38% boost::numeric::ublas::same_impl_ex 20ms 0.018% 62.05% 3641ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 60ms 0.055% 62.11% 3249ms 2.95% Cell::SetCellProliferativeType 3163ms 2.87% 64.98% 3163ms 2.87% std::_Rb_tree::_S_right (inline) 0 0% 64.98% 3147ms 2.86% std::insert_iterator::operator= (inline) 2157ms 1.96% 66.94% 3102ms 2.82% _int_malloc 846ms 0.77% 67.71% 3032ms 2.75% AbstractElement::GetNodeLocation 54ms 0.049% 67.76% 2980ms 2.71% std::_Rb_tree::erase 4ms 0.0036% 67.76% 2790ms 2.53% std::_Rb_tree::_M_insert_unique_ (inline) 730ms 0.66% 68.43% 2716ms 2.47% AbstractCellProperty::IsSame 270ms 0.25% 68.67% 2706ms 2.46% VertexMesh::GetAreaGradientOfElementAtNode 36ms 0.033% 68.70% 2693ms 2.45% CellPropertyCollection::HasProperty 0 0% 68.70% 2656ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 68.70% 2588ms 2.35% Cell::HasCellProperty (inline) 672ms 0.61% 69.31% 2580ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.31% 2557ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 291ms 0.26% 69.58% 2530ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0018% 69.58% 2500ms 2.27% std::_Rb_tree::_M_insert_unique (inline) 17ms 0.015% 69.60% 2467ms 2.24% Cell::GetCellData 0 0% 69.60% 2447ms 2.22% AbstractCellPopulation::WriteResultsToFiles 90ms 0.082% 69.68% 2399ms 2.18% VertexMesh::GetVolumeOfElement 5ms 0.0045% 69.68% 2319ms 2.11% AbstractCellPopulation::Iterator::operator++ (inline) 60ms 0.055% 69.74% 2310ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 182ms 0.17% 69.90% 2299ms 2.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 36ms 0.033% 69.93% 2072ms 1.88% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0027% 69.94% 2024ms 1.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.94% 2024ms 1.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 69.94% 2004ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 69.94% 1989ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 468ms 0.43% 70.36% 1986ms 1.80% std::type_info::operator== (inline) 1946ms 1.77% 72.13% 1946ms 1.77% std::_Rb_tree_increment 1310ms 1.19% 73.32% 1944ms 1.77% std::_Rb_tree::equal_range (inline) 31ms 0.028% 73.35% 1831ms 1.66% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 75ms 0.068% 73.42% 1804ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.42% 1786ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 84ms 0.076% 73.49% 1649ms 1.50% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 43ms 0.039% 73.53% 1630ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 30ms 0.027% 73.56% 1566ms 1.42% VertexMesh::GetSurfaceAreaOfElement 50ms 0.045% 73.60% 1517ms 1.38% Node::RemoveElement 158ms 0.14% 73.75% 1488ms 1.35% CellPropertyCollection::AddProperty 10ms 0.0091% 73.76% 1470ms 1.34% std::set::erase (inline) 1451ms 1.32% 75.08% 1451ms 1.32% [libchaste_cell_based.so] 0 0% 75.08% 1397ms 1.27% tcache_get (inline) 1397ms 1.27% 76.34% 1397ms 1.27% tcache_get_n (inline) 4ms 0.0036% 76.35% 1334ms 1.21% OffLatticeSimulation::ApplyBoundaries 71ms 0.064% 76.41% 1329ms 1.21% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.41% 1304ms 1.18% boost::numeric::ublas::vector_binary::operator() (inline) 69ms 0.063% 76.48% 1299ms 1.18% std::less::operator() (inline) 88ms 0.08% 76.56% 1293ms 1.17% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 76.56% 1278ms 1.16% boost::numeric::ublas::norm_2 (inline) 546ms 0.5% 77.05% 1259ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1019ms 0.93% 77.98% 1230ms 1.12% std::operator< (inline) 77ms 0.07% 78.05% 1177ms 1.07% std::_Rb_tree::find (inline) 0 0% 78.05% 1172ms 1.06% boost::numeric::ublas::c_vector::assign_temporary (inline) 14ms 0.013% 78.06% 1172ms 1.06% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.069% 78.13% 1158ms 1.05% std::swap_ranges (inline) 30ms 0.027% 78.16% 1155ms 1.05% CellPropertyRegistry::Get 149ms 0.14% 78.29% 1138ms 1.03% boost::detail::shared_count::~shared_count (inline) 0 0% 78.29% 1138ms 1.03% boost::shared_ptr::~shared_ptr (inline) 14ms 0.013% 78.30% 1134ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.30% 1114ms 1.01% std::_Rb_tree::clear (inline) 0 0% 78.30% 1097ms 1% std::map::clear (inline) 1083ms 0.98% 79.29% 1083ms 0.98% std::swap (inline) 0 0% 79.29% 1082ms 0.98% std::iter_swap (inline) 1081ms 0.98% 80.27% 1081ms 0.98% std::_Rb_tree_insert_and_rebalance 7ms 0.0064% 80.28% 1071ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 15ms 0.014% 80.29% 1056ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 223ms 0.2% 80.49% 1030ms 0.94% boost::numeric::ublas::detail::equals 0 0% 80.49% 1027ms 0.93% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 80.49% 1011ms 0.92% std::map::find (inline) 1003ms 0.91% 81.40% 1003ms 0.91% Node::rGetLocation 935ms 0.85% 82.25% 962ms 0.87% boost::detail::sp_counted_base::release 866ms 0.79% 83.04% 866ms 0.79% std::vector::size (inline) 0 0% 83.04% 865ms 0.79% VertexMeshWriter::MakeVtkMesh 238ms 0.22% 83.26% 842ms 0.76% std::__new_allocator::construct (inline) 0 0% 83.26% 842ms 0.76% std::allocator_traits::construct (inline) 109ms 0.099% 83.35% 831ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 168ms 0.15% 83.51% 812ms 0.74% boost::shared_ptr::shared_ptr (inline) 801ms 0.73% 84.23% 801ms 0.73% [libchaste_mesh.so] 0 0% 84.23% 788ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 396ms 0.36% 84.59% 786ms 0.71% Edge::GetMapIndex 19ms 0.017% 84.61% 777ms 0.71% MutableElement::RegisterWithEdges (inline) 0 0% 84.61% 773ms 0.7% std::_Rb_tree::_M_construct_node (inline) 24ms 0.022% 84.63% 769ms 0.7% Edge::AddElement 457ms 0.42% 85.05% 762ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.05% 747ms 0.68% boost::numeric::ublas::norm_inf (inline) 384ms 0.35% 85.40% 747ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 117ms 0.11% 85.50% 697ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 85.50% 692ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 85.50% 688ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.50% 679ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 85.52% 679ms 0.62% std::_Rb_tree::_M_insert_node (inline) 669ms 0.61% 86.13% 669ms 0.61% [libstdc++.so.6.0.33] 649ms 0.59% 86.72% 649ms 0.59% Node::GetIndex 619ms 0.56% 87.28% 644ms 0.58% boost::detail::shared_count::shared_count (inline) 1ms 0.00091% 87.28% 642ms 0.58% vtkPolygon::New 28ms 0.025% 87.31% 640ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.31% 640ms 0.58% boost::numeric::ublas::vector::vector (inline) 1ms 0.00091% 87.31% 640ms 0.58% vtkPolygon::vtkPolygon 38ms 0.035% 87.34% 607ms 0.55% MutableElement::RegisterWithNodes (inline) 362ms 0.33% 87.67% 574ms 0.52% CellPropertyCollection::GetProperty 6ms 0.0055% 87.68% 574ms 0.52% std::vector::_M_default_append (inline) 41ms 0.037% 87.72% 567ms 0.52% Node::AddElement 564ms 0.51% 88.23% 564ms 0.51% tcache_put (inline)