File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94065ms, 87.34% of 107702ms total Dropped 1071 nodes (cum <= 538.51ms) flat flat% sum% cum cum% 0 0% 0% 107327ms 99.65% __libc_start_call_main 0 0% 0% 107327ms 99.65% __libc_start_main_impl 0 0% 0% 107327ms 99.65% _start 0 0% 0% 107306ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107306ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107306ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107306ms 99.63% main 0 0% 0% 107267ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107267ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107267ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107259ms 99.59% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.022% 55929ms 51.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.019% 0.042% 52588ms 48.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 120ms 0.11% 0.15% 51439ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 361ms 0.34% 0.49% 39833ms 36.98% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.49% 38486ms 35.73% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0019% 0.49% 23651ms 21.96% VertexBasedCellPopulation::Update 1ms 0.00093% 0.49% 23509ms 21.83% MutableVertexMesh::ReMesh 14652ms 13.60% 14.10% 23356ms 21.69% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.089% 14.19% 17523ms 16.27% Cell::ReadyToDivide 74ms 0.069% 14.25% 16318ms 15.15% AbstractPhaseBasedCellCycleModel::ReadyToDivide 314ms 0.29% 14.55% 14509ms 13.47% NagaiHondaForce::GetAdhesionParameter 176ms 0.16% 14.71% 13989ms 12.99% SimpleWntCellCycleModel::UpdateCellCyclePhase 476ms 0.44% 15.15% 13835ms 12.85% boost::numeric::ublas::c_vector::c_vector (partial-inline) 116ms 0.11% 15.26% 13328ms 12.37% CellPropertyCollection::GetPropertiesType (inline) 267ms 0.25% 15.51% 12330ms 11.45% boost::numeric::ublas::vector_assign (inline) 132ms 0.12% 15.63% 11839ms 10.99% MutableVertexMesh::CheckForIntersections 3394ms 3.15% 18.78% 11316ms 10.51% __dynamic_cast 79ms 0.073% 18.85% 11223ms 10.42% AbstractCellProperty::IsSubType (inline) 87ms 0.081% 18.93% 11056ms 10.27% VertexBasedCellPopulation::GetDampingConstant 63ms 0.058% 18.99% 10392ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 39ms 0.036% 19.03% 10318ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 26ms 0.024% 19.05% 10257ms 9.52% AbstractCellBasedSimulation::DoCellBirth 1319ms 1.22% 20.28% 9774ms 9.08% std::__new_allocator::allocate (inline) 2801ms 2.60% 22.88% 9426ms 8.75% boost::numeric::ublas::indexing_vector_assign 362ms 0.34% 23.21% 9357ms 8.69% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.21% 9280ms 8.62% std::_Rb_tree::_M_create_node (inline) 0 0% 23.21% 9232ms 8.57% std::allocator_traits::allocate (inline) 1205ms 1.12% 24.33% 9023ms 8.38% std::_Rb_tree::_M_erase 38ms 0.035% 24.37% 8740ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 835ms 0.78% 25.14% 8644ms 8.03% VertexMesh::ElementIncludesPoint 0 0% 25.14% 8573ms 7.96% std::_Rb_tree::_M_get_node (inline) 761ms 0.71% 25.85% 8474ms 7.87% operator new 101ms 0.094% 25.94% 8449ms 7.84% Cell::GetMutationState 456ms 0.42% 26.37% 8266ms 7.67% VertexMesh::GetCentroidOfElement 182ms 0.17% 26.54% 8196ms 7.61% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.54% 8188ms 7.60% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.54% 8163ms 7.58% std::_Rb_tree::_Alloc_node::operator() (inline) 229ms 0.21% 26.75% 7926ms 7.36% std::__new_allocator::deallocate (inline) 0 0% 26.75% 7921ms 7.35% std::allocator_traits::deallocate (inline) 0 0% 26.75% 7865ms 7.30% std::_Rb_tree::_M_put_node (inline) 0 0% 26.75% 7821ms 7.26% std::set::~set (inline) 1392ms 1.29% 28.04% 7522ms 6.98% AbstractMesh::GetDistanceBetweenNodes 2900ms 2.69% 30.73% 7492ms 6.96% __GI___libc_malloc 16ms 0.015% 30.75% 7482ms 6.95% MutableVertexMesh::RemoveDeletedNodesAndElements 2629ms 2.44% 33.19% 7450ms 6.92% __GI___libc_free 483ms 0.45% 33.64% 7410ms 6.88% std::map::operator[] (partial-inline) 185ms 0.17% 33.81% 7152ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 755ms 0.7% 34.51% 6724ms 6.24% std::_Rb_tree::_M_copy (inline) 31ms 0.029% 34.54% 6646ms 6.17% std::set::set (inline) 137ms 0.13% 34.67% 6301ms 5.85% SimpleWntCellCycleModel::GetWntLevel 6241ms 5.79% 40.46% 6241ms 5.79% boost::numeric::ublas::c_vector::operator() 6189ms 5.75% 46.21% 6189ms 5.75% __strcmp_avx2 157ms 0.15% 46.35% 6069ms 5.63% WntConcentration::GetWntLevel 812ms 0.75% 47.11% 5711ms 5.30% std::_Rb_tree::_M_clone_node (inline) 2416ms 2.24% 49.35% 5625ms 5.22% std::_Rb_tree::_M_lower_bound (inline) 1978ms 1.84% 51.19% 5418ms 5.03% boost::numeric::ublas::c_vector::operator[] (inline) 2865ms 2.66% 53.85% 5384ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.017% 53.87% 5245ms 4.87% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.87% 5197ms 4.83% std::set::insert (inline) 33ms 0.031% 53.90% 5057ms 4.70% EdgeHelper::RemoveDeletedEdges 4320ms 4.01% 57.91% 4811ms 4.47% _int_free 40ms 0.037% 57.94% 4757ms 4.42% EdgeHelper::UpdateEdgesMapKey 0 0% 57.94% 4658ms 4.32% std::_Rb_tree::lower_bound (inline) 0 0% 57.94% 4658ms 4.32% std::map::lower_bound (inline) 2ms 0.0019% 57.95% 4563ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 190ms 0.18% 58.12% 4535ms 4.21% MutableElement::ResetIndex 569ms 0.53% 58.65% 4365ms 4.05% std::_Rb_tree::_M_insert_ (inline) 138ms 0.13% 58.78% 4244ms 3.94% std::set_intersection (inline) 100ms 0.093% 58.87% 4118ms 3.82% AbstractCellPopulation::GetCellUsingLocationIndex 242ms 0.22% 59.10% 4106ms 3.81% std::__set_intersection 56ms 0.052% 59.15% 3972ms 3.69% Cell::GetCellProliferativeType 3898ms 3.62% 62.77% 3898ms 3.62% boost::numeric::ublas::same_impl_ex 63ms 0.058% 62.83% 3679ms 3.42% AbstractCellProperty::IsType (inline) 18ms 0.017% 62.84% 3562ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 58ms 0.054% 62.90% 3166ms 2.94% Cell::SetCellProliferativeType 2212ms 2.05% 64.95% 3108ms 2.89% _int_malloc 0 0% 64.95% 3101ms 2.88% std::insert_iterator::operator= (inline) 878ms 0.82% 65.77% 3070ms 2.85% AbstractElement::GetNodeLocation 54ms 0.05% 65.82% 2803ms 2.60% std::_Rb_tree::erase 9ms 0.0084% 65.82% 2707ms 2.51% std::_Rb_tree::_M_insert_unique_ (inline) 218ms 0.2% 66.03% 2674ms 2.48% VertexMesh::GetAreaGradientOfElementAtNode 2668ms 2.48% 68.50% 2668ms 2.48% std::_Rb_tree::_S_right (inline) 596ms 0.55% 69.06% 2607ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.06% 2563ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 657ms 0.61% 69.67% 2541ms 2.36% AbstractCellProperty::IsSame 19ms 0.018% 69.68% 2532ms 2.35% CellPropertyCollection::HasProperty 0 0% 69.68% 2529ms 2.35% boost::numeric::ublas::c_vector::assign (inline) 284ms 0.26% 69.95% 2493ms 2.31% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.95% 2490ms 2.31% std::_Rb_tree::_M_insert_unique 0 0% 69.95% 2453ms 2.28% Cell::HasCellProperty (inline) 1ms 0.00093% 69.95% 2415ms 2.24% AbstractCellPopulation::WriteResultsToFiles 80ms 0.074% 70.02% 2316ms 2.15% VertexMesh::GetVolumeOfElement 20ms 0.019% 70.04% 2304ms 2.14% Cell::GetCellData 47ms 0.044% 70.09% 2242ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 50ms 0.046% 70.13% 2227ms 2.07% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0037% 70.14% 2139ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 159ms 0.15% 70.28% 2115ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.00093% 70.28% 2109ms 1.96% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.28% 2109ms 1.96% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.28% 1963ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1952ms 1.81% 72.10% 1952ms 1.81% std::_Rb_tree_increment 0 0% 72.10% 1947ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 458ms 0.43% 72.52% 1884ms 1.75% std::type_info::operator== (inline) 1184ms 1.10% 73.62% 1828ms 1.70% std::_Rb_tree::equal_range (inline) 67ms 0.062% 73.68% 1826ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.68% 1758ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 36ms 0.033% 73.72% 1622ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 36ms 0.033% 73.75% 1566ms 1.45% VertexMesh::GetSurfaceAreaOfElement 38ms 0.035% 73.79% 1429ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.053% 73.84% 1425ms 1.32% Node::RemoveElement 69ms 0.064% 73.90% 1419ms 1.32% boost::numeric::ublas::vector_reference::operator() (inline) 71ms 0.066% 73.97% 1413ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 158ms 0.15% 74.12% 1394ms 1.29% CellPropertyCollection::AddProperty 0 0% 74.12% 1386ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 9ms 0.0084% 74.12% 1369ms 1.27% std::set::erase (inline) 1365ms 1.27% 75.39% 1365ms 1.27% [libchaste_cell_based.so] 0 0% 75.39% 1361ms 1.26% boost::numeric::ublas::norm_2 (inline) 600ms 0.56% 75.95% 1352ms 1.26% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0019% 75.95% 1307ms 1.21% OffLatticeSimulation::ApplyBoundaries 0 0% 75.95% 1304ms 1.21% tcache_get (inline) 1304ms 1.21% 77.16% 1304ms 1.21% tcache_get_n (inline) 46ms 0.043% 77.20% 1216ms 1.13% std::less::operator() (inline) 963ms 0.89% 78.10% 1170ms 1.09% std::operator< (inline) 1157ms 1.07% 79.17% 1157ms 1.07% std::_Rb_tree_insert_and_rebalance 36ms 0.033% 79.21% 1151ms 1.07% CellPropertyRegistry::Get 94ms 0.087% 79.29% 1130ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.29% 1117ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.29% 1110ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 16ms 0.015% 79.31% 1110ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 12ms 0.011% 79.32% 1098ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 81ms 0.075% 79.39% 1094ms 1.02% std::swap_ranges (inline) 105ms 0.097% 79.49% 1032ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.49% 1032ms 0.96% boost::shared_ptr::~shared_ptr (inline) 4ms 0.0037% 79.50% 1020ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 1014ms 0.94% 80.44% 1014ms 0.94% std::swap (inline) 1ms 0.00093% 80.44% 1013ms 0.94% std::_Rb_tree::clear (inline) 0 0% 80.44% 1013ms 0.94% std::iter_swap (inline) 192ms 0.18% 80.62% 1002ms 0.93% boost::numeric::ublas::detail::equals 98ms 0.091% 80.71% 995ms 0.92% std::_Rb_tree::find (inline) 0 0% 80.71% 993ms 0.92% std::map::clear (inline) 967ms 0.9% 81.60% 967ms 0.9% Node::rGetLocation 5ms 0.0046% 81.61% 963ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 844ms 0.78% 82.39% 881ms 0.82% boost::detail::sp_counted_base::release 95ms 0.088% 82.48% 879ms 0.82% boost::numeric::ublas::c_vector::operator= (inline) 853ms 0.79% 83.27% 853ms 0.79% std::vector::size (inline) 0 0% 83.27% 848ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 83.27% 839ms 0.78% std::map::find (inline) 19ms 0.018% 83.29% 793ms 0.74% Edge::AddElement 12ms 0.011% 83.30% 776ms 0.72% MutableElement::RegisterWithEdges (inline) 235ms 0.22% 83.52% 766ms 0.71% std::__new_allocator::construct (inline) 0 0% 83.52% 766ms 0.71% std::allocator_traits::construct (inline) 407ms 0.38% 83.90% 752ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 83.90% 748ms 0.69% boost::numeric::ublas::norm_inf (inline) 364ms 0.34% 84.24% 748ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 745ms 0.69% 84.93% 745ms 0.69% [libchaste_mesh.so] 170ms 0.16% 85.09% 745ms 0.69% boost::shared_ptr::shared_ptr (inline) 0 0% 85.09% 743ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 383ms 0.36% 85.44% 718ms 0.67% Edge::GetMapIndex 0 0% 85.44% 717ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.023% 85.46% 717ms 0.67% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.46% 707ms 0.66% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.46% 695ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 136ms 0.13% 85.59% 681ms 0.63% MutableElement::GetNodeLocalIndex 668ms 0.62% 86.21% 668ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.21% 650ms 0.6% std::_Vector_base::_M_allocate (inline) 32ms 0.03% 86.24% 621ms 0.58% MutableElement::RegisterWithNodes (inline) 1ms 0.00093% 86.24% 615ms 0.57% vtkPolygon::New 3ms 0.0028% 86.24% 614ms 0.57% vtkPolygon::vtkPolygon 19ms 0.018% 86.26% 584ms 0.54% Node::AddElement 580ms 0.54% 86.80% 580ms 0.54% Node::GetIndex 549ms 0.51% 87.31% 575ms 0.53% boost::detail::shared_count::shared_count (inline) 6ms 0.0056% 87.32% 569ms 0.53% std::vector::_M_default_append (inline) 24ms 0.022% 87.34% 566ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.34% 566ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 87.34% 545ms 0.51% std::map::map (inline)