File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95687ms, 88.94% of 107581ms total Dropped 1090 nodes (cum <= 537.90ms) flat flat% sum% cum cum% 0 0% 0% 107059ms 99.51% __libc_start_call_main 0 0% 0% 107059ms 99.51% __libc_start_main_impl 0 0% 0% 107059ms 99.51% _start 0 0% 0% 107040ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107040ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107040ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107040ms 99.50% main 0 0% 0% 107003ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107003ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107003ms 99.46% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00093% 0.00093% 106994ms 99.45% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.014% 55696ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.027% 52533ms 48.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 123ms 0.11% 0.14% 51493ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 395ms 0.37% 0.51% 39997ms 37.18% NagaiHondaForce::AddForceContribution 0 0% 0.51% 38587ms 35.87% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.51% 23892ms 22.21% VertexBasedCellPopulation::Update 1ms 0.00093% 0.51% 23769ms 22.09% MutableVertexMesh::ReMesh 14480ms 13.46% 13.97% 22967ms 21.35% Cylindrical2dVertexMesh::GetVectorFromAtoB 61ms 0.057% 14.03% 17271ms 16.05% Cell::ReadyToDivide 118ms 0.11% 14.14% 16129ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 349ms 0.32% 14.46% 14851ms 13.80% NagaiHondaForce::GetAdhesionParameter 412ms 0.38% 14.85% 14516ms 13.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 126ms 0.12% 14.96% 13662ms 12.70% SimpleWntCellCycleModel::UpdateCellCyclePhase 139ms 0.13% 15.09% 13398ms 12.45% CellPropertyCollection::GetPropertiesType (inline) 451ms 0.42% 15.51% 12950ms 12.04% boost::numeric::ublas::vector_assign (inline) 124ms 0.12% 15.63% 12103ms 11.25% MutableVertexMesh::CheckForIntersections 3137ms 2.92% 18.54% 11137ms 10.35% __dynamic_cast 75ms 0.07% 18.61% 11044ms 10.27% AbstractCellProperty::IsSubType (inline) 66ms 0.061% 18.67% 11011ms 10.24% VertexBasedCellPopulation::GetDampingConstant 84ms 0.078% 18.75% 10301ms 9.58% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.056% 18.81% 10198ms 9.48% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.83% 10087ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1217ms 1.13% 19.96% 9787ms 9.10% std::__new_allocator::allocate (inline) 2776ms 2.58% 22.54% 9623ms 8.94% boost::numeric::ublas::indexing_vector_assign 0 0% 22.54% 9219ms 8.57% std::allocator_traits::allocate (inline) 1381ms 1.28% 23.82% 9193ms 8.55% std::_Rb_tree::_M_erase 0 0% 23.82% 9191ms 8.54% std::_Rb_tree::_M_create_node (inline) 827ms 0.77% 24.59% 9079ms 8.44% VertexMesh::ElementIncludesPoint 377ms 0.35% 24.94% 9029ms 8.39% VertexMesh::GetNextEdgeGradientOfElementAtNode 25ms 0.023% 24.97% 8751ms 8.13% VertexBasedCellPopulation::GetLocationOfCellCentre 843ms 0.78% 25.75% 8672ms 8.06% operator new 0 0% 25.75% 8590ms 7.98% std::_Rb_tree::_M_get_node (inline) 257ms 0.24% 25.99% 8435ms 7.84% std::_Rb_tree::~_Rb_tree (inline) 87ms 0.081% 26.07% 8363ms 7.77% Cell::GetMutationState 498ms 0.46% 26.53% 8279ms 7.70% VertexMesh::GetCentroidOfElement 0 0% 26.53% 8142ms 7.57% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.53% 8054ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.53% 8001ms 7.44% std::set::~set (inline) 302ms 0.28% 26.81% 7925ms 7.37% std::__new_allocator::deallocate (inline) 0 0% 26.81% 7892ms 7.34% std::allocator_traits::deallocate (inline) 0 0% 26.81% 7837ms 7.28% std::_Rb_tree::_M_put_node (inline) 3153ms 2.93% 29.74% 7656ms 7.12% __GI___libc_malloc 3085ms 2.87% 32.61% 7640ms 7.10% __GI___libc_free 493ms 0.46% 33.07% 7383ms 6.86% std::map::operator[] (partial-inline) 18ms 0.017% 33.09% 7375ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 1407ms 1.31% 34.39% 7193ms 6.69% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 157ms 0.15% 34.54% 6578ms 6.11% std::_Rb_tree::_Rb_tree (partial-inline) 6367ms 5.92% 40.46% 6367ms 5.92% __strcmp_avx2 110ms 0.1% 40.56% 6313ms 5.87% SimpleWntCellCycleModel::GetWntLevel 6205ms 5.77% 46.33% 6205ms 5.77% boost::numeric::ublas::c_vector::operator() 672ms 0.62% 46.95% 6197ms 5.76% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 46.97% 6152ms 5.72% std::set::set (inline) 150ms 0.14% 47.10% 6103ms 5.67% WntConcentration::GetWntLevel 2386ms 2.22% 49.32% 5770ms 5.36% std::_Rb_tree::_M_lower_bound (inline) 2612ms 2.43% 51.75% 5659ms 5.26% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.75% 5441ms 5.06% std::set::insert (inline) 725ms 0.67% 52.42% 5262ms 4.89% std::_Rb_tree::_M_clone_node (inline) 29ms 0.027% 52.45% 5112ms 4.75% MutableVertexMesh::RemoveDeletedNodes 41ms 0.038% 52.49% 4941ms 4.59% EdgeHelper::RemoveDeletedEdges 1475ms 1.37% 53.86% 4771ms 4.43% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.86% 4688ms 4.36% std::_Rb_tree::lower_bound (inline) 0 0% 53.86% 4688ms 4.36% std::map::lower_bound (inline) 26ms 0.024% 53.88% 4680ms 4.35% EdgeHelper::UpdateEdgesMapKey 204ms 0.19% 54.07% 4632ms 4.31% MutableElement::ResetIndex 3ms 0.0028% 54.08% 4597ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 54ms 0.05% 54.13% 4573ms 4.25% std::set_intersection (inline) 504ms 0.47% 54.60% 4554ms 4.23% std::_Rb_tree::_M_insert_ (inline) 4225ms 3.93% 58.52% 4547ms 4.23% _int_free 269ms 0.25% 58.77% 4519ms 4.20% std::__set_intersection 100ms 0.093% 58.87% 4066ms 3.78% AbstractCellPopulation::GetCellUsingLocationIndex 45ms 0.042% 58.91% 4033ms 3.75% Cell::GetCellProliferativeType 4031ms 3.75% 62.66% 4031ms 3.75% boost::numeric::ublas::same_impl_ex 8ms 0.0074% 62.66% 3573ms 3.32% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 76ms 0.071% 62.73% 3565ms 3.31% AbstractCellProperty::IsType (inline) 822ms 0.76% 63.50% 3303ms 3.07% AbstractElement::GetNodeLocation 0 0% 63.50% 3283ms 3.05% std::insert_iterator::operator= (inline) 42ms 0.039% 63.54% 3171ms 2.95% Cell::SetCellProliferativeType 2125ms 1.98% 65.51% 2992ms 2.78% _int_malloc 8ms 0.0074% 65.52% 2933ms 2.73% std::_Rb_tree::_M_insert_unique_ (inline) 46ms 0.043% 65.56% 2911ms 2.71% std::_Rb_tree::erase 609ms 0.57% 66.13% 2896ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 2826ms 2.63% 68.75% 2826ms 2.63% std::_Rb_tree::_S_right (inline) 470ms 0.44% 69.19% 2746ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 729ms 0.68% 69.87% 2526ms 2.35% AbstractCellProperty::IsSame 2ms 0.0019% 69.87% 2508ms 2.33% std::_Rb_tree::_M_insert_unique 50ms 0.046% 69.92% 2503ms 2.33% CellPropertyCollection::HasProperty 235ms 0.22% 70.14% 2487ms 2.31% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.14% 2415ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.14% 2398ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.14% 2389ms 2.22% Cell::HasCellProperty (inline) 0 0% 70.14% 2376ms 2.21% AbstractCellPopulation::WriteResultsToFiles 25ms 0.023% 70.16% 2350ms 2.18% Cell::GetCellData 107ms 0.099% 70.26% 2324ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 88ms 0.082% 70.34% 2295ms 2.13% VertexMesh::GetVolumeOfElement 1ms 0.00093% 70.34% 2224ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 223ms 0.21% 70.55% 2218ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 35ms 0.033% 70.58% 2151ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 2073ms 1.93% 72.51% 2073ms 1.93% std::_Rb_tree_increment 0 0% 72.51% 1964ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00093% 72.51% 1952ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1347ms 1.25% 73.76% 1933ms 1.80% std::_Rb_tree::equal_range (inline) 1ms 0.00093% 73.76% 1931ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.76% 1931ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 64ms 0.059% 73.82% 1868ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 426ms 0.4% 74.22% 1797ms 1.67% std::type_info::operator== (inline) 0 0% 74.22% 1745ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 35ms 0.033% 74.25% 1687ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 148ms 0.14% 74.39% 1580ms 1.47% boost::numeric::ublas::vector_reference::operator() (inline) 23ms 0.021% 74.41% 1579ms 1.47% VertexMesh::GetSurfaceAreaOfElement 39ms 0.036% 74.45% 1548ms 1.44% Node::RemoveElement 12ms 0.011% 74.46% 1514ms 1.41% std::set::erase (inline) 25ms 0.023% 74.48% 1504ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 158ms 0.15% 74.63% 1500ms 1.39% CellPropertyCollection::AddProperty 81ms 0.075% 74.70% 1459ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.70% 1445ms 1.34% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.70% 1335ms 1.24% tcache_get (inline) 1335ms 1.24% 75.94% 1335ms 1.24% tcache_get_n (inline) 2ms 0.0019% 75.94% 1240ms 1.15% OffLatticeSimulation::ApplyBoundaries 1209ms 1.12% 77.07% 1209ms 1.12% Node::rGetLocation 0 0% 77.07% 1188ms 1.10% boost::numeric::ublas::norm_2 (inline) 546ms 0.51% 77.58% 1183ms 1.10% boost::numeric::ublas::vector_norm_2::apply 84ms 0.078% 77.65% 1169ms 1.09% std::less::operator() (inline) 0 0% 77.65% 1137ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1121ms 1.04% 78.70% 1121ms 1.04% std::_Rb_tree_insert_and_rebalance 75ms 0.07% 78.77% 1112ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1108ms 1.03% 79.80% 1108ms 1.03% [libchaste_cell_based.so] 901ms 0.84% 80.63% 1085ms 1.01% std::operator< (inline) 15ms 0.014% 80.65% 1054ms 0.98% CellPropertyRegistry::Get 87ms 0.081% 80.73% 1054ms 0.98% std::_Rb_tree::find (inline) 18ms 0.017% 80.74% 1051ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1023ms 0.95% 81.70% 1023ms 0.95% std::vector::size (inline) 0 0% 81.70% 1017ms 0.95% std::_Rb_tree::clear (inline) 0 0% 81.70% 1003ms 0.93% std::map::clear (inline) 6ms 0.0056% 81.70% 979ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 969ms 0.9% 82.60% 969ms 0.9% [libchaste_mesh.so] 133ms 0.12% 82.73% 961ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 82.73% 961ms 0.89% boost::shared_ptr::~shared_ptr (inline) 15ms 0.014% 82.74% 945ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 153ms 0.14% 82.88% 920ms 0.86% boost::numeric::ublas::detail::equals 0 0% 82.88% 850ms 0.79% std::map::find (inline) 1ms 0.00093% 82.88% 849ms 0.79% VertexMeshWriter::MakeVtkMesh 334ms 0.31% 83.19% 847ms 0.79% Edge::GetMapIndex 99ms 0.092% 83.29% 845ms 0.79% MutableElement::GetNodeLocalIndex 0 0% 83.29% 841ms 0.78% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 83.29% 841ms 0.78% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.07% 83.36% 836ms 0.78% std::swap_ranges (inline) 794ms 0.74% 84.10% 799ms 0.74% boost::detail::sp_counted_base::release 136ms 0.13% 84.22% 785ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 165ms 0.15% 84.38% 781ms 0.73% boost::shared_ptr::shared_ptr (inline) 470ms 0.44% 84.81% 775ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 762ms 0.71% 85.52% 762ms 0.71% std::swap (inline) 0 0% 85.52% 761ms 0.71% std::iter_swap (inline) 23ms 0.021% 85.54% 754ms 0.7% MutableElement::RegisterWithEdges (inline) 28ms 0.026% 85.57% 747ms 0.69% Edge::AddElement 0 0% 85.57% 743ms 0.69% boost::numeric::ublas::norm_inf (inline) 366ms 0.34% 85.91% 743ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 718ms 0.67% 86.58% 718ms 0.67% Node::GetIndex 0 0% 86.58% 691ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.58% 684ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 86.60% 684ms 0.64% std::_Rb_tree::_M_insert_node (inline) 93ms 0.086% 86.69% 653ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.69% 653ms 0.61% std::allocator_traits::construct (inline) 1ms 0.00093% 86.69% 628ms 0.58% vtkPolygon::New 2ms 0.0019% 86.69% 627ms 0.58% vtkPolygon::vtkPolygon 1ms 0.00093% 86.69% 624ms 0.58% std::_Vector_base::_M_allocate (inline) 33ms 0.031% 86.72% 616ms 0.57% MutableElement::RegisterWithNodes (inline) 588ms 0.55% 87.27% 616ms 0.57% boost::detail::shared_count::shared_count (inline) 601ms 0.56% 87.83% 601ms 0.56% [libstdc++.so.6.0.33] 33ms 0.031% 87.86% 601ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.86% 601ms 0.56% boost::numeric::ublas::vector::vector (inline) 0 0% 87.86% 601ms 0.56% std::_Rb_tree::_M_construct_node (inline) 34ms 0.032% 87.89% 580ms 0.54% Node::AddElement 580ms 0.54% 88.43% 580ms 0.54% operator delete 554ms 0.51% 88.94% 554ms 0.51% boost::shared_ptr::operator-> (inline)