File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97073ms, 88.40% of 109817ms total Dropped 1144 nodes (cum <= 549.09ms) flat flat% sum% cum cum% 0 0% 0% 109512ms 99.72% __libc_start_call_main 0 0% 0% 109512ms 99.72% __libc_start_main_impl 0 0% 0% 109512ms 99.72% _start 0 0% 0% 109490ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109490ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109490ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109490ms 99.70% main 0 0% 0% 109444ms 99.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109444ms 99.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109444ms 99.66% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 109436ms 99.65% AbstractCellBasedSimulation::Solve 27ms 0.025% 0.03% 57021ms 51.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.017% 0.047% 53605ms 48.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.17% 52469ms 47.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 348ms 0.32% 0.49% 40289ms 36.69% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.49% 39337ms 35.82% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.49% 24323ms 22.15% VertexBasedCellPopulation::Update 1ms 0.00091% 0.49% 24161ms 22.00% MutableVertexMesh::ReMesh 14511ms 13.21% 13.71% 23258ms 21.18% Cylindrical2dVertexMesh::GetVectorFromAtoB 85ms 0.077% 13.79% 17705ms 16.12% Cell::ReadyToDivide 76ms 0.069% 13.85% 16441ms 14.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 299ms 0.27% 14.13% 14645ms 13.34% NagaiHondaForce::GetAdhesionParameter 153ms 0.14% 14.27% 14095ms 12.83% SimpleWntCellCycleModel::UpdateCellCyclePhase 477ms 0.43% 14.70% 13811ms 12.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 101ms 0.092% 14.79% 13562ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 308ms 0.28% 15.07% 12341ms 11.24% boost::numeric::ublas::vector_assign (inline) 152ms 0.14% 15.21% 11774ms 10.72% MutableVertexMesh::CheckForIntersections 93ms 0.085% 15.30% 11606ms 10.57% VertexBasedCellPopulation::GetDampingConstant 3491ms 3.18% 18.48% 11504ms 10.48% __dynamic_cast 83ms 0.076% 18.55% 11398ms 10.38% AbstractCellProperty::IsSubType (inline) 82ms 0.075% 18.63% 10557ms 9.61% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.038% 18.66% 10455ms 9.52% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.69% 10424ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1449ms 1.32% 20.01% 10182ms 9.27% std::__new_allocator::allocate (inline) 0 0% 20.01% 9608ms 8.75% std::allocator_traits::allocate (inline) 0 0% 20.01% 9604ms 8.75% std::_Rb_tree::_M_create_node (inline) 2813ms 2.56% 22.57% 9435ms 8.59% boost::numeric::ublas::indexing_vector_assign 353ms 0.32% 22.89% 9393ms 8.55% VertexMesh::GetNextEdgeGradientOfElementAtNode 1286ms 1.17% 24.06% 9135ms 8.32% std::_Rb_tree::_M_erase 0 0% 24.06% 8932ms 8.13% std::_Rb_tree::_M_get_node (inline) 33ms 0.03% 24.09% 8833ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 775ms 0.71% 24.80% 8766ms 7.98% operator new 814ms 0.74% 25.54% 8561ms 7.80% VertexMesh::ElementIncludesPoint 106ms 0.097% 25.63% 8541ms 7.78% Cell::GetMutationState 0 0% 25.63% 8416ms 7.66% std::_Rb_tree::_Alloc_node::operator() (inline) 446ms 0.41% 26.04% 8254ms 7.52% VertexMesh::GetCentroidOfElement 527ms 0.48% 26.52% 8231ms 7.50% std::map::operator[] (partial-inline) 212ms 0.19% 26.71% 8199ms 7.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.71% 8185ms 7.45% std::_Rb_tree::_M_drop_node (inline) 232ms 0.21% 26.92% 7922ms 7.21% std::__new_allocator::deallocate (inline) 14ms 0.013% 26.94% 7918ms 7.21% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.94% 7913ms 7.21% std::allocator_traits::deallocate (inline) 0 0% 26.94% 7840ms 7.14% std::_Rb_tree::_M_put_node (inline) 0 0% 26.94% 7797ms 7.10% std::set::~set (inline) 2898ms 2.64% 29.58% 7771ms 7.08% __GI___libc_malloc 1625ms 1.48% 31.06% 7546ms 6.87% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2295ms 2.09% 33.15% 7457ms 6.79% __GI___libc_free 163ms 0.15% 33.29% 7276ms 6.63% std::_Rb_tree::_Rb_tree (partial-inline) 815ms 0.74% 34.04% 6879ms 6.26% std::_Rb_tree::_M_copy (inline) 32ms 0.029% 34.06% 6840ms 6.23% std::set::set (inline) 2617ms 2.38% 36.45% 6536ms 5.95% std::_Rb_tree::_M_lower_bound (inline) 132ms 0.12% 36.57% 6387ms 5.82% SimpleWntCellCycleModel::GetWntLevel 6343ms 5.78% 42.34% 6343ms 5.78% __strcmp_avx2 155ms 0.14% 42.49% 6187ms 5.63% WntConcentration::GetWntLevel 6032ms 5.49% 47.98% 6032ms 5.49% boost::numeric::ublas::c_vector::operator() 802ms 0.73% 48.71% 5835ms 5.31% std::_Rb_tree::_M_clone_node (inline) 19ms 0.017% 48.73% 5572ms 5.07% MutableVertexMesh::RemoveDeletedNodes 2841ms 2.59% 51.31% 5486ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.029% 51.34% 5390ms 4.91% EdgeHelper::RemoveDeletedEdges 0 0% 51.34% 5356ms 4.88% std::_Rb_tree::lower_bound (inline) 0 0% 51.34% 5356ms 4.88% std::map::lower_bound (inline) 1962ms 1.79% 53.13% 5306ms 4.83% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.13% 5231ms 4.76% std::set::insert (inline) 4672ms 4.25% 57.38% 5152ms 4.69% _int_free 38ms 0.035% 57.42% 5094ms 4.64% EdgeHelper::UpdateEdgesMapKey 185ms 0.17% 57.59% 4765ms 4.34% MutableElement::ResetIndex 130ms 0.12% 57.70% 4625ms 4.21% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.00091% 57.71% 4579ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 512ms 0.47% 58.17% 4429ms 4.03% std::_Rb_tree::_M_insert_ (inline) 129ms 0.12% 58.29% 4295ms 3.91% std::set_intersection (inline) 245ms 0.22% 58.51% 4166ms 3.79% std::__set_intersection 50ms 0.046% 58.56% 3990ms 3.63% Cell::GetCellProliferativeType 57ms 0.052% 58.61% 3774ms 3.44% AbstractCellProperty::IsType (inline) 3771ms 3.43% 62.04% 3771ms 3.43% boost::numeric::ublas::same_impl_ex 13ms 0.012% 62.06% 3524ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3252ms 2.96% 65.02% 3252ms 2.96% std::_Rb_tree::_S_right (inline) 65ms 0.059% 65.08% 3200ms 2.91% Cell::SetCellProliferativeType 2250ms 2.05% 67.12% 3181ms 2.90% _int_malloc 0 0% 67.12% 3129ms 2.85% std::insert_iterator::operator= (inline) 924ms 0.84% 67.97% 3071ms 2.80% AbstractElement::GetNodeLocation 46ms 0.042% 68.01% 3051ms 2.78% std::_Rb_tree::erase 8ms 0.0073% 68.01% 2732ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 213ms 0.19% 68.21% 2606ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 672ms 0.61% 68.82% 2600ms 2.37% AbstractCellProperty::IsSame 21ms 0.019% 68.84% 2593ms 2.36% CellPropertyCollection::HasProperty 246ms 0.22% 69.06% 2577ms 2.35% std::_Rb_tree_const_iterator::operator++ (inline) 639ms 0.58% 69.65% 2569ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.65% 2561ms 2.33% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.65% 2520ms 2.29% Cell::HasCellProperty (inline) 3ms 0.0027% 69.65% 2499ms 2.28% std::_Rb_tree::_M_insert_unique 0 0% 69.65% 2481ms 2.26% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.65% 2468ms 2.25% boost::numeric::ublas::c_vector::assign (inline) 30ms 0.027% 69.68% 2432ms 2.21% Cell::GetCellData 41ms 0.037% 69.71% 2307ms 2.10% std::_Rb_tree::_M_emplace_hint_unique 94ms 0.086% 69.80% 2298ms 2.09% VertexMesh::GetVolumeOfElement 2ms 0.0018% 69.80% 2273ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 182ms 0.17% 69.97% 2260ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 54ms 0.049% 70.02% 2256ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2065ms 1.88% 71.90% 2065ms 1.88% std::_Rb_tree_increment 1374ms 1.25% 73.15% 2042ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 73.15% 2030ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.15% 2020ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 76ms 0.069% 73.22% 1968ms 1.79% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 73.22% 1955ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.22% 1955ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 487ms 0.44% 73.66% 1928ms 1.76% std::type_info::operator== (inline) 0 0% 73.66% 1809ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 23ms 0.021% 73.68% 1783ms 1.62% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 33ms 0.03% 73.71% 1635ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 66ms 0.06% 73.77% 1578ms 1.44% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 39ms 0.036% 73.81% 1567ms 1.43% VertexMesh::GetSurfaceAreaOfElement 35ms 0.032% 73.84% 1511ms 1.38% Node::RemoveElement 0 0% 73.84% 1486ms 1.35% tcache_get (inline) 1486ms 1.35% 75.19% 1486ms 1.35% tcache_get_n (inline) 8ms 0.0073% 75.20% 1478ms 1.35% std::set::erase (inline) 2ms 0.0018% 75.20% 1411ms 1.28% OffLatticeSimulation::ApplyBoundaries 150ms 0.14% 75.34% 1401ms 1.28% CellPropertyCollection::AddProperty 1354ms 1.23% 76.57% 1354ms 1.23% [libchaste_cell_based.so] 53ms 0.048% 76.62% 1348ms 1.23% std::less::operator() (inline) 70ms 0.064% 76.68% 1346ms 1.23% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.68% 1321ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 1061ms 0.97% 77.65% 1295ms 1.18% std::operator< (inline) 0 0% 77.65% 1257ms 1.14% boost::numeric::ublas::norm_2 (inline) 546ms 0.5% 78.15% 1239ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 25ms 0.023% 78.17% 1195ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.17% 1188ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 95ms 0.087% 78.26% 1177ms 1.07% std::_Rb_tree::find (inline) 72ms 0.066% 78.32% 1156ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 30ms 0.027% 78.35% 1154ms 1.05% CellPropertyRegistry::Get 1151ms 1.05% 79.40% 1151ms 1.05% std::_Rb_tree_insert_and_rebalance 0 0% 79.40% 1149ms 1.05% std::_Rb_tree::clear (inline) 0 0% 79.40% 1130ms 1.03% std::map::clear (inline) 0 0% 79.40% 1125ms 1.02% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0091% 79.41% 1125ms 1.02% boost::numeric::ublas::c_vector::swap (inline) 87ms 0.079% 79.49% 1115ms 1.02% std::swap_ranges (inline) 118ms 0.11% 79.59% 1047ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 79.59% 1047ms 0.95% boost::shared_ptr::~shared_ptr (inline) 1029ms 0.94% 80.53% 1029ms 0.94% std::swap (inline) 0 0% 80.53% 1028ms 0.94% std::iter_swap (inline) 9ms 0.0082% 80.54% 1014ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.54% 1008ms 0.92% std::map::find (inline) 989ms 0.9% 81.44% 989ms 0.9% Node::rGetLocation 9ms 0.0082% 81.45% 947ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 172ms 0.16% 81.60% 927ms 0.84% boost::numeric::ublas::detail::equals 860ms 0.78% 82.39% 889ms 0.81% boost::detail::sp_counted_base::release 0 0% 82.39% 865ms 0.79% VertexMeshWriter::MakeVtkMesh 826ms 0.75% 83.14% 826ms 0.75% std::vector::size (inline) 112ms 0.1% 83.24% 814ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 806ms 0.73% 83.98% 806ms 0.73% [libchaste_mesh.so] 21ms 0.019% 83.99% 800ms 0.73% MutableElement::RegisterWithEdges (inline) 27ms 0.025% 84.02% 789ms 0.72% Edge::AddElement 403ms 0.37% 84.39% 781ms 0.71% Edge::GetMapIndex 400ms 0.36% 84.75% 741ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.75% 731ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 151ms 0.14% 84.89% 730ms 0.66% boost::shared_ptr::shared_ptr (inline) 0 0% 84.89% 725ms 0.66% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 84.91% 725ms 0.66% std::_Rb_tree::_M_insert_node (inline) 210ms 0.19% 85.10% 722ms 0.66% std::__new_allocator::construct (inline) 0 0% 85.10% 722ms 0.66% std::allocator_traits::construct (inline) 136ms 0.12% 85.23% 702ms 0.64% MutableElement::GetNodeLocalIndex 0 0% 85.23% 698ms 0.64% boost::numeric::ublas::norm_inf (inline) 391ms 0.36% 85.58% 698ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 676ms 0.62% 86.20% 676ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.20% 673ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.20% 672ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.20% 663ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 623ms 0.57% 86.77% 623ms 0.57% Node::GetIndex 0 0% 86.77% 618ms 0.56% vtkPolygon::New 1ms 0.00091% 86.77% 618ms 0.56% vtkPolygon::vtkPolygon 27ms 0.025% 86.79% 612ms 0.56% MutableElement::RegisterWithNodes (inline) 37ms 0.034% 86.82% 611ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.82% 611ms 0.56% boost::numeric::ublas::vector::vector (inline) 588ms 0.54% 87.36% 588ms 0.54% boost::shared_ptr::operator-> (inline) 23ms 0.021% 87.38% 585ms 0.53% Node::AddElement 544ms 0.5% 87.88% 579ms 0.53% boost::detail::shared_count::shared_count (inline) 570ms 0.52% 88.40% 570ms 0.52% tcache_put (inline)