File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95326ms, 88.16% of 108127ms total Dropped 1132 nodes (cum <= 540.63ms) flat flat% sum% cum cum% 0 0% 0% 107657ms 99.57% __libc_start_call_main 0 0% 0% 107657ms 99.57% __libc_start_main_impl 0 0% 0% 107657ms 99.57% _start 0 0% 0% 107636ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107636ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107636ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107636ms 99.55% main 0 0% 0% 107598ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107598ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107598ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107591ms 99.50% AbstractCellBasedSimulation::Solve 10ms 0.0092% 0.011% 55916ms 51.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.019% 0.031% 52755ms 48.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 138ms 0.13% 0.16% 51257ms 47.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 370ms 0.34% 0.5% 39592ms 36.62% NagaiHondaForce::AddForceContribution 0 0% 0.5% 38794ms 35.88% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.5% 24007ms 22.20% VertexBasedCellPopulation::Update 1ms 0.00092% 0.5% 23880ms 22.09% MutableVertexMesh::ReMesh 14291ms 13.22% 13.72% 22659ms 20.96% Cylindrical2dVertexMesh::GetVectorFromAtoB 104ms 0.096% 13.82% 17445ms 16.13% Cell::ReadyToDivide 88ms 0.081% 13.90% 16185ms 14.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 380ms 0.35% 14.25% 14839ms 13.72% NagaiHondaForce::GetAdhesionParameter 412ms 0.38% 14.63% 14024ms 12.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 158ms 0.15% 14.78% 13801ms 12.76% CellPropertyCollection::GetPropertiesType (inline) 101ms 0.093% 14.87% 13693ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 372ms 0.34% 15.21% 12425ms 11.49% boost::numeric::ublas::vector_assign (inline) 134ms 0.12% 15.34% 12103ms 11.19% MutableVertexMesh::CheckForIntersections 3248ms 3.00% 18.34% 11371ms 10.52% __dynamic_cast 80ms 0.074% 18.42% 11274ms 10.43% AbstractCellProperty::IsSubType (inline) 83ms 0.077% 18.49% 11158ms 10.32% VertexBasedCellPopulation::GetDampingConstant 65ms 0.06% 18.55% 10457ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 54ms 0.05% 18.60% 10364ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1262ms 1.17% 19.77% 10262ms 9.49% std::__new_allocator::allocate (inline) 17ms 0.016% 19.79% 10189ms 9.42% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.79% 9727ms 9.00% std::allocator_traits::allocate (inline) 0 0% 19.79% 9673ms 8.95% std::_Rb_tree::_M_create_node (inline) 2582ms 2.39% 22.17% 9280ms 8.58% boost::numeric::ublas::indexing_vector_assign 885ms 0.82% 22.99% 9113ms 8.43% operator new 0 0% 22.99% 9050ms 8.37% std::_Rb_tree::_M_get_node (inline) 1279ms 1.18% 24.17% 9046ms 8.37% std::_Rb_tree::_M_erase 794ms 0.73% 24.91% 9016ms 8.34% VertexMesh::ElementIncludesPoint 334ms 0.31% 25.22% 8669ms 8.02% VertexMesh::GetNextEdgeGradientOfElementAtNode 63ms 0.058% 25.28% 8589ms 7.94% Cell::GetMutationState 0 0% 25.28% 8492ms 7.85% std::_Rb_tree::_Alloc_node::operator() (inline) 23ms 0.021% 25.30% 8447ms 7.81% VertexBasedCellPopulation::GetLocationOfCellCentre 238ms 0.22% 25.52% 8287ms 7.66% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.52% 8193ms 7.58% std::_Rb_tree::_M_drop_node (inline) 3624ms 3.35% 28.87% 8073ms 7.47% __GI___libc_malloc 480ms 0.44% 29.31% 8069ms 7.46% VertexMesh::GetCentroidOfElement 256ms 0.24% 29.55% 7985ms 7.38% std::__new_allocator::deallocate (inline) 0 0% 29.55% 7957ms 7.36% std::allocator_traits::deallocate (inline) 0 0% 29.55% 7871ms 7.28% std::_Rb_tree::_M_put_node (inline) 0 0% 29.55% 7801ms 7.21% std::set::~set (inline) 2705ms 2.50% 32.05% 7774ms 7.19% __GI___libc_free 15ms 0.014% 32.07% 7418ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 462ms 0.43% 32.49% 7197ms 6.66% std::map::operator[] (partial-inline) 1408ms 1.30% 33.79% 7120ms 6.58% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 164ms 0.15% 33.95% 6861ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 6559ms 6.07% 40.01% 6559ms 6.07% __strcmp_avx2 615ms 0.57% 40.58% 6491ms 6.00% std::_Rb_tree::_M_copy (inline) 7ms 0.0065% 40.59% 6463ms 5.98% std::set::set (inline) 6220ms 5.75% 46.34% 6220ms 5.75% boost::numeric::ublas::c_vector::operator() 95ms 0.088% 46.43% 6069ms 5.61% SimpleWntCellCycleModel::GetWntLevel 159ms 0.15% 46.57% 5907ms 5.46% WntConcentration::GetWntLevel 2711ms 2.51% 49.08% 5654ms 5.23% __cxxabiv1::__si_class_type_info::__do_dyncast 699ms 0.65% 49.73% 5595ms 5.17% std::_Rb_tree::_M_clone_node (inline) 2476ms 2.29% 52.02% 5571ms 5.15% std::_Rb_tree::_M_lower_bound (inline) 0 0% 52.02% 5531ms 5.12% std::set::insert (inline) 23ms 0.021% 52.04% 5289ms 4.89% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 52.07% 5087ms 4.70% EdgeHelper::RemoveDeletedEdges 4748ms 4.39% 56.46% 5062ms 4.68% _int_free 1565ms 1.45% 57.91% 4964ms 4.59% boost::numeric::ublas::c_vector::operator[] (inline) 35ms 0.032% 57.94% 4820ms 4.46% EdgeHelper::UpdateEdgesMapKey 535ms 0.49% 58.44% 4669ms 4.32% std::_Rb_tree::_M_insert_ (inline) 211ms 0.2% 58.63% 4601ms 4.26% MutableElement::ResetIndex 56ms 0.052% 58.68% 4591ms 4.25% std::set_intersection (inline) 1ms 0.00092% 58.69% 4589ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.69% 4547ms 4.21% std::_Rb_tree::lower_bound (inline) 0 0% 58.69% 4547ms 4.21% std::map::lower_bound (inline) 284ms 0.26% 58.95% 4535ms 4.19% std::__set_intersection 39ms 0.036% 58.98% 4121ms 3.81% Cell::GetCellProliferativeType 3967ms 3.67% 62.65% 3967ms 3.67% boost::numeric::ublas::same_impl_ex 122ms 0.11% 62.77% 3953ms 3.66% AbstractCellPopulation::GetCellUsingLocationIndex 74ms 0.068% 62.83% 3829ms 3.54% AbstractCellProperty::IsType (inline) 10ms 0.0092% 62.84% 3507ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.84% 3263ms 3.02% std::insert_iterator::operator= (inline) 29ms 0.027% 62.87% 3200ms 2.96% Cell::SetCellProliferativeType 838ms 0.78% 63.65% 3164ms 2.93% AbstractElement::GetNodeLocation 2122ms 1.96% 65.61% 3035ms 2.81% _int_malloc 4ms 0.0037% 65.61% 2902ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 33ms 0.031% 65.64% 2896ms 2.68% std::_Rb_tree::erase 613ms 0.57% 66.21% 2841ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 432ms 0.4% 66.61% 2804ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 713ms 0.66% 67.27% 2770ms 2.56% AbstractCellProperty::IsSame 40ms 0.037% 67.31% 2680ms 2.48% CellPropertyCollection::HasProperty 0 0% 67.31% 2629ms 2.43% std::_Rb_tree::_M_insert_unique 2599ms 2.40% 69.71% 2599ms 2.40% std::_Rb_tree::_S_right (inline) 0 0% 69.71% 2573ms 2.38% Cell::HasCellProperty (inline) 224ms 0.21% 69.92% 2480ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 15ms 0.014% 69.93% 2422ms 2.24% Cell::GetCellData 0 0% 69.93% 2398ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.93% 2386ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 112ms 0.1% 70.03% 2385ms 2.21% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.03% 2378ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.00092% 70.03% 2224ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 233ms 0.22% 70.25% 2217ms 2.05% AbstractCellPopulation::Iterator::IsRealCell 88ms 0.081% 70.33% 2199ms 2.03% VertexMesh::GetVolumeOfElement 2187ms 2.02% 72.35% 2187ms 2.02% std::_Rb_tree_increment 36ms 0.033% 72.39% 2150ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 490ms 0.45% 72.84% 2057ms 1.90% std::type_info::operator== (inline) 0 0% 72.84% 1947ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.84% 1941ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0028% 72.84% 1941ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.84% 1941ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1307ms 1.21% 74.05% 1929ms 1.78% std::_Rb_tree::equal_range (inline) 46ms 0.043% 74.10% 1833ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 74.10% 1759ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 34ms 0.031% 74.13% 1704ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 19ms 0.018% 74.15% 1641ms 1.52% VertexMesh::GetSurfaceAreaOfElement 151ms 0.14% 74.28% 1594ms 1.47% CellPropertyCollection::AddProperty 122ms 0.11% 74.40% 1531ms 1.42% boost::numeric::ublas::vector_reference::operator() (inline) 27ms 0.025% 74.42% 1511ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 81ms 0.075% 74.50% 1504ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 41ms 0.038% 74.54% 1486ms 1.37% Node::RemoveElement 17ms 0.016% 74.55% 1456ms 1.35% std::set::erase (inline) 0 0% 74.55% 1414ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 74.55% 1295ms 1.20% OffLatticeSimulation::ApplyBoundaries 0 0% 74.55% 1253ms 1.16% boost::numeric::ublas::norm_2 (inline) 0 0% 74.55% 1251ms 1.16% tcache_get (inline) 1251ms 1.16% 75.71% 1251ms 1.16% tcache_get_n (inline) 562ms 0.52% 76.23% 1248ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.23% 1181ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1149ms 1.06% 77.29% 1149ms 1.06% Node::rGetLocation 23ms 0.021% 77.31% 1146ms 1.06% CellPropertyRegistry::Get 1146ms 1.06% 78.37% 1146ms 1.06% [libchaste_cell_based.so] 89ms 0.082% 78.46% 1129ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 65ms 0.06% 78.52% 1127ms 1.04% std::less::operator() (inline) 1110ms 1.03% 79.54% 1110ms 1.03% std::_Rb_tree_insert_and_rebalance 13ms 0.012% 79.55% 1083ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 866ms 0.8% 80.36% 1062ms 0.98% std::operator< (inline) 121ms 0.11% 80.47% 1051ms 0.97% std::_Rb_tree::find (inline) 6ms 0.0055% 80.47% 1023ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00092% 80.47% 1003ms 0.93% std::_Rb_tree::clear (inline) 0 0% 80.47% 984ms 0.91% std::map::clear (inline) 26ms 0.024% 80.50% 945ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.50% 941ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 80.50% 941ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 140ms 0.13% 80.63% 940ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 80.63% 940ms 0.87% boost::shared_ptr::~shared_ptr (inline) 85ms 0.079% 80.71% 937ms 0.87% std::swap_ranges (inline) 934ms 0.86% 81.57% 934ms 0.86% std::vector::size (inline) 388ms 0.36% 81.93% 919ms 0.85% Edge::GetMapIndex 186ms 0.17% 82.10% 908ms 0.84% boost::numeric::ublas::detail::equals 893ms 0.83% 82.93% 893ms 0.83% [libchaste_mesh.so] 0 0% 82.93% 852ms 0.79% std::iter_swap (inline) 852ms 0.79% 83.72% 852ms 0.79% std::swap (inline) 0 0% 83.72% 843ms 0.78% std::map::find (inline) 0 0% 83.72% 837ms 0.77% VertexMeshWriter::MakeVtkMesh 114ms 0.11% 83.82% 829ms 0.77% MutableElement::GetNodeLocalIndex 93ms 0.086% 83.91% 797ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 24ms 0.022% 83.93% 766ms 0.71% Edge::AddElement 761ms 0.7% 84.64% 764ms 0.71% boost::detail::sp_counted_base::release 151ms 0.14% 84.78% 763ms 0.71% boost::shared_ptr::shared_ptr (inline) 16ms 0.015% 84.79% 759ms 0.7% MutableElement::RegisterWithEdges (inline) 458ms 0.42% 85.21% 750ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 741ms 0.69% 85.90% 741ms 0.69% Node::GetIndex 0 0% 85.90% 722ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 12ms 0.011% 85.91% 697ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.91% 688ms 0.64% boost::numeric::ublas::norm_inf (inline) 359ms 0.33% 86.24% 688ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 102ms 0.094% 86.34% 685ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 3ms 0.0028% 86.34% 679ms 0.63% std::_Vector_base::_M_allocate (inline) 109ms 0.1% 86.44% 674ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.44% 674ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.44% 647ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.46% 647ms 0.6% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.46% 623ms 0.58% std::_Rb_tree::_M_construct_node (inline) 580ms 0.54% 86.99% 612ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 86.99% 610ms 0.56% vtkPolygon::New 1ms 0.00092% 86.99% 609ms 0.56% vtkPolygon::vtkPolygon 28ms 0.026% 87.02% 597ms 0.55% MutableElement::RegisterWithNodes (inline) 594ms 0.55% 87.57% 594ms 0.55% operator delete 0 0% 87.57% 590ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 581ms 0.54% 88.11% 581ms 0.54% [libstdc++.so.6.0.33] 8ms 0.0074% 88.11% 576ms 0.53% std::vector::_M_default_append (inline) 31ms 0.029% 88.14% 557ms 0.52% Node::AddElement 19ms 0.018% 88.16% 554ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.16% 554ms 0.51% boost::numeric::ublas::vector::vector (inline)