File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95654ms, 88.35% of 108264ms total Dropped 1053 nodes (cum <= 541.32ms) flat flat% sum% cum cum% 0 0% 0% 107793ms 99.56% __libc_start_call_main 0 0% 0% 107793ms 99.56% __libc_start_main_impl 0 0% 0% 107793ms 99.56% _start 0 0% 0% 107773ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107773ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107773ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107773ms 99.55% main 0 0% 0% 107737ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107737ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107737ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107730ms 99.51% AbstractCellBasedSimulation::Solve 15ms 0.014% 0.016% 55709ms 51.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.028% 52577ms 48.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 113ms 0.1% 0.13% 51463ms 47.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 344ms 0.32% 0.45% 39752ms 36.72% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.45% 38863ms 35.90% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.45% 23940ms 22.11% VertexBasedCellPopulation::Update 0 0% 0.45% 23823ms 22.00% MutableVertexMesh::ReMesh 14475ms 13.37% 13.82% 22943ms 21.19% Cylindrical2dVertexMesh::GetVectorFromAtoB 62ms 0.057% 13.88% 17757ms 16.40% Cell::ReadyToDivide 64ms 0.059% 13.94% 16507ms 15.25% AbstractPhaseBasedCellCycleModel::ReadyToDivide 301ms 0.28% 14.22% 14811ms 13.68% NagaiHondaForce::GetAdhesionParameter 422ms 0.39% 14.61% 14276ms 13.19% boost::numeric::ublas::c_vector::c_vector (partial-inline) 121ms 0.11% 14.72% 14057ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 135ms 0.12% 14.84% 13892ms 12.83% CellPropertyCollection::GetPropertiesType (inline) 378ms 0.35% 15.19% 12724ms 11.75% boost::numeric::ublas::vector_assign (inline) 129ms 0.12% 15.31% 12046ms 11.13% MutableVertexMesh::CheckForIntersections 3102ms 2.87% 18.18% 11550ms 10.67% __dynamic_cast 75ms 0.069% 18.25% 11434ms 10.56% AbstractCellProperty::IsSubType (inline) 104ms 0.096% 18.34% 11262ms 10.40% VertexBasedCellPopulation::GetDampingConstant 84ms 0.078% 18.42% 10780ms 9.96% AbstractTargetAreaModifier::UpdateTargetAreas 72ms 0.067% 18.49% 10673ms 9.86% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.029% 18.51% 10308ms 9.52% AbstractCellBasedSimulation::DoCellBirth 1195ms 1.10% 19.62% 10065ms 9.30% std::__new_allocator::allocate (inline) 0 0% 19.62% 9536ms 8.81% std::allocator_traits::allocate (inline) 0 0% 19.62% 9534ms 8.81% std::_Rb_tree::_M_create_node (inline) 2672ms 2.47% 22.09% 9516ms 8.79% boost::numeric::ublas::indexing_vector_assign 1396ms 1.29% 23.38% 9400ms 8.68% std::_Rb_tree::_M_erase 815ms 0.75% 24.13% 9005ms 8.32% VertexMesh::ElementIncludesPoint 792ms 0.73% 24.86% 8940ms 8.26% operator new 345ms 0.32% 25.18% 8888ms 8.21% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.18% 8880ms 8.20% std::_Rb_tree::_M_get_node (inline) 101ms 0.093% 25.27% 8829ms 8.16% Cell::GetMutationState 28ms 0.026% 25.30% 8755ms 8.09% VertexBasedCellPopulation::GetLocationOfCellCentre 219ms 0.2% 25.50% 8645ms 7.99% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.50% 8376ms 7.74% std::_Rb_tree::_Alloc_node::operator() (inline) 498ms 0.46% 25.96% 8323ms 7.69% VertexMesh::GetCentroidOfElement 0 0% 25.96% 8293ms 7.66% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.96% 8197ms 7.57% std::set::~set (inline) 235ms 0.22% 26.18% 8029ms 7.42% std::__new_allocator::deallocate (inline) 0 0% 26.18% 7995ms 7.38% std::allocator_traits::deallocate (inline) 3239ms 2.99% 29.17% 7964ms 7.36% __GI___libc_malloc 0 0% 29.17% 7948ms 7.34% std::_Rb_tree::_M_put_node (inline) 3185ms 2.94% 32.11% 7838ms 7.24% __GI___libc_free 16ms 0.015% 32.13% 7437ms 6.87% MutableVertexMesh::RemoveDeletedNodesAndElements 396ms 0.37% 32.49% 7401ms 6.84% std::map::operator[] (partial-inline) 1411ms 1.30% 33.80% 7095ms 6.55% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 6909ms 6.38% 40.18% 6909ms 6.38% __strcmp_avx2 142ms 0.13% 40.31% 6815ms 6.29% std::_Rb_tree::_Rb_tree (partial-inline) 702ms 0.65% 40.96% 6439ms 5.95% std::_Rb_tree::_M_copy (inline) 8ms 0.0074% 40.96% 6396ms 5.91% std::set::set (inline) 79ms 0.073% 41.04% 6225ms 5.75% SimpleWntCellCycleModel::GetWntLevel 6039ms 5.58% 46.61% 6039ms 5.58% boost::numeric::ublas::c_vector::operator() 150ms 0.14% 46.75% 6030ms 5.57% WntConcentration::GetWntLevel 2772ms 2.56% 49.31% 5911ms 5.46% __cxxabiv1::__si_class_type_info::__do_dyncast 2571ms 2.37% 51.69% 5871ms 5.42% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.69% 5465ms 5.05% std::set::insert (inline) 719ms 0.66% 52.35% 5428ms 5.01% std::_Rb_tree::_M_clone_node (inline) 20ms 0.018% 52.37% 5262ms 4.86% MutableVertexMesh::RemoveDeletedNodes 33ms 0.03% 52.40% 5105ms 4.72% EdgeHelper::RemoveDeletedEdges 26ms 0.024% 52.43% 4850ms 4.48% EdgeHelper::UpdateEdgesMapKey 1557ms 1.44% 53.86% 4805ms 4.44% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.86% 4791ms 4.43% std::_Rb_tree::lower_bound (inline) 0 0% 53.86% 4791ms 4.43% std::map::lower_bound (inline) 488ms 0.45% 54.31% 4670ms 4.31% std::_Rb_tree::_M_insert_ (inline) 4311ms 3.98% 58.30% 4641ms 4.29% _int_free 207ms 0.19% 58.49% 4635ms 4.28% MutableElement::ResetIndex 1ms 0.00092% 58.49% 4610ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 51ms 0.047% 58.54% 4342ms 4.01% std::set_intersection (inline) 254ms 0.23% 58.77% 4291ms 3.96% std::__set_intersection 4059ms 3.75% 62.52% 4059ms 3.75% boost::numeric::ublas::same_impl_ex 31ms 0.029% 62.55% 4034ms 3.73% Cell::GetCellProliferativeType 124ms 0.11% 62.66% 4009ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 84ms 0.078% 62.74% 3986ms 3.68% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.75% 3562ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.75% 3223ms 2.98% std::insert_iterator::operator= (inline) 28ms 0.026% 62.78% 3160ms 2.92% Cell::SetCellProliferativeType 819ms 0.76% 63.53% 3102ms 2.87% AbstractElement::GetNodeLocation 2184ms 2.02% 65.55% 3082ms 2.85% _int_malloc 46ms 0.042% 65.59% 2892ms 2.67% std::_Rb_tree::erase 48ms 0.044% 65.64% 2842ms 2.63% CellPropertyCollection::HasProperty 733ms 0.68% 66.31% 2831ms 2.61% AbstractCellProperty::IsSame 3ms 0.0028% 66.32% 2795ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 653ms 0.6% 66.92% 2789ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 391ms 0.36% 67.28% 2725ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 67.28% 2709ms 2.50% Cell::HasCellProperty (inline) 2707ms 2.50% 69.78% 2707ms 2.50% std::_Rb_tree::_S_right (inline) 3ms 0.0028% 69.78% 2670ms 2.47% std::_Rb_tree::_M_insert_unique 260ms 0.24% 70.02% 2470ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.02% 2448ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 35ms 0.032% 70.06% 2418ms 2.23% Cell::GetCellData 0 0% 70.06% 2380ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 109ms 0.1% 70.16% 2364ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.16% 2353ms 2.17% AbstractCellPopulation::WriteResultsToFiles 3ms 0.0028% 70.16% 2159ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.028% 70.19% 2157ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2155ms 1.99% 72.18% 2155ms 1.99% std::_Rb_tree_increment 192ms 0.18% 72.36% 2137ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 97ms 0.09% 72.45% 2133ms 1.97% VertexMesh::GetVolumeOfElement 511ms 0.47% 72.92% 2098ms 1.94% std::type_info::operator== (inline) 0 0% 72.92% 1928ms 1.78% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.92% 1915ms 1.77% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1287ms 1.19% 74.11% 1893ms 1.75% std::_Rb_tree::equal_range (inline) 4ms 0.0037% 74.11% 1890ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.11% 1890ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 79ms 0.073% 74.18% 1808ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.18% 1712ms 1.58% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.028% 74.21% 1705ms 1.57% VertexMesh::GetSurfaceAreaOfElement 23ms 0.021% 74.23% 1677ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 146ms 0.13% 74.37% 1636ms 1.51% CellPropertyCollection::AddProperty 50ms 0.046% 74.41% 1561ms 1.44% Node::RemoveElement 26ms 0.024% 74.44% 1528ms 1.41% std::set::erase (inline) 24ms 0.022% 74.46% 1487ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 91ms 0.084% 74.54% 1481ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 143ms 0.13% 74.68% 1479ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.68% 1437ms 1.33% tcache_get (inline) 1437ms 1.33% 76.00% 1437ms 1.33% tcache_get_n (inline) 0 0% 76.00% 1368ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 76.00% 1220ms 1.13% OffLatticeSimulation::ApplyBoundaries 87ms 0.08% 76.09% 1220ms 1.13% std::less::operator() (inline) 0 0% 76.09% 1197ms 1.11% boost::numeric::ublas::norm_2 (inline) 489ms 0.45% 76.54% 1187ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.54% 1158ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 927ms 0.86% 77.39% 1133ms 1.05% std::operator< (inline) 64ms 0.059% 77.45% 1122ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 1115ms 1.03% 78.48% 1115ms 1.03% std::_Rb_tree_insert_and_rebalance 20ms 0.018% 78.50% 1114ms 1.03% CellPropertyRegistry::Get 1108ms 1.02% 79.52% 1108ms 1.02% Node::rGetLocation 1096ms 1.01% 80.54% 1096ms 1.01% [libchaste_cell_based.so] 107ms 0.099% 80.64% 1086ms 1.00% std::_Rb_tree::find (inline) 19ms 0.018% 80.65% 1042ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 128ms 0.12% 80.77% 1010ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.77% 1010ms 0.93% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0074% 80.78% 996ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 988ms 0.91% 81.69% 988ms 0.91% [libchaste_mesh.so] 0 0% 81.69% 978ms 0.9% std::_Rb_tree::clear (inline) 0 0% 81.69% 965ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 81.70% 965ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 0 0% 81.70% 959ms 0.89% std::map::clear (inline) 89ms 0.082% 81.78% 959ms 0.89% std::swap_ranges (inline) 953ms 0.88% 82.66% 953ms 0.88% std::vector::size (inline) 18ms 0.017% 82.68% 910ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 154ms 0.14% 82.82% 883ms 0.82% boost::numeric::ublas::detail::equals 871ms 0.8% 83.62% 871ms 0.8% std::swap (inline) 0 0% 83.62% 870ms 0.8% std::iter_swap (inline) 350ms 0.32% 83.95% 867ms 0.8% Edge::GetMapIndex 129ms 0.12% 84.06% 863ms 0.8% MutableElement::GetNodeLocalIndex 0 0% 84.06% 859ms 0.79% std::map::find (inline) 855ms 0.79% 84.85% 858ms 0.79% boost::detail::sp_counted_base::release 2ms 0.0018% 84.86% 839ms 0.77% VertexMeshWriter::MakeVtkMesh 28ms 0.026% 84.88% 811ms 0.75% MutableElement::RegisterWithEdges (inline) 122ms 0.11% 85.00% 810ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.023% 85.02% 798ms 0.74% Edge::AddElement 127ms 0.12% 85.14% 793ms 0.73% boost::shared_ptr::shared_ptr (inline) 752ms 0.69% 85.83% 752ms 0.69% Node::GetIndex 0 0% 85.83% 734ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 93ms 0.086% 85.92% 698ms 0.64% std::__new_allocator::construct (inline) 0 0% 85.92% 698ms 0.64% std::allocator_traits::construct (inline) 0 0% 85.92% 693ms 0.64% boost::numeric::ublas::norm_inf (inline) 322ms 0.3% 86.21% 693ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.21% 686ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.24% 686ms 0.63% std::_Rb_tree::_M_insert_node (inline) 393ms 0.36% 86.60% 674ms 0.62% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 637ms 0.59% 87.19% 666ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 87.19% 654ms 0.6% std::_Rb_tree::_M_construct_node (inline) 1ms 0.00092% 87.19% 653ms 0.6% std::_Vector_base::_M_allocate (inline) 616ms 0.57% 87.76% 616ms 0.57% operator delete 0 0% 87.76% 591ms 0.55% vtkPolygon::New 0 0% 87.76% 590ms 0.54% vtkPolygon::vtkPolygon 0 0% 87.76% 575ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 30ms 0.028% 87.79% 566ms 0.52% MutableElement::RegisterWithNodes (inline) 566ms 0.52% 88.31% 566ms 0.52% [libstdc++.so.6.0.33] 32ms 0.03% 88.34% 561ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.34% 561ms 0.52% boost::numeric::ublas::vector::vector (inline) 14ms 0.013% 88.35% 545ms 0.5% std::vector::_M_default_append (inline)