File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 93735ms, 87.47% of 107164ms total Dropped 1082 nodes (cum <= 535.82ms) flat flat% sum% cum cum% 0 0% 0% 106699ms 99.57% __libc_start_call_main 0 0% 0% 106699ms 99.57% __libc_start_main_impl 0 0% 0% 106699ms 99.57% _start 0 0% 0% 106680ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106680ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106680ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106680ms 99.55% main 0 0% 0% 106643ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106643ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106643ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 106634ms 99.51% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.017% 55572ms 51.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.031% 52481ms 48.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 101ms 0.094% 0.13% 51411ms 47.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 409ms 0.38% 0.51% 40185ms 37.50% NagaiHondaForce::AddForceContribution 3ms 0.0028% 0.51% 38392ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.51% 23735ms 22.15% VertexBasedCellPopulation::Update 0 0% 0.51% 23619ms 22.04% MutableVertexMesh::ReMesh 14597ms 13.62% 14.13% 23063ms 21.52% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.076% 14.21% 17366ms 16.21% Cell::ReadyToDivide 78ms 0.073% 14.28% 16187ms 15.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 355ms 0.33% 14.61% 15060ms 14.05% NagaiHondaForce::GetAdhesionParameter 397ms 0.37% 14.98% 14474ms 13.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 122ms 0.11% 15.09% 13715ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 129ms 0.12% 15.21% 13210ms 12.33% CellPropertyCollection::GetPropertiesType (inline) 372ms 0.35% 15.56% 12893ms 12.03% boost::numeric::ublas::vector_assign (inline) 134ms 0.13% 15.69% 12113ms 11.30% MutableVertexMesh::CheckForIntersections 3087ms 2.88% 18.57% 10922ms 10.19% __dynamic_cast 117ms 0.11% 18.68% 10880ms 10.15% AbstractCellProperty::IsSubType (inline) 75ms 0.07% 18.75% 10755ms 10.04% VertexBasedCellPopulation::GetDampingConstant 83ms 0.077% 18.82% 10266ms 9.58% AbstractTargetAreaModifier::UpdateTargetAreas 55ms 0.051% 18.88% 10160ms 9.48% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 24ms 0.022% 18.90% 10114ms 9.44% AbstractCellBasedSimulation::DoCellBirth 1202ms 1.12% 20.02% 9808ms 9.15% std::__new_allocator::allocate (inline) 2681ms 2.50% 22.52% 9542ms 8.90% boost::numeric::ublas::indexing_vector_assign 0 0% 22.52% 9200ms 8.58% std::allocator_traits::allocate (inline) 0 0% 22.52% 9182ms 8.57% std::_Rb_tree::_M_create_node (inline) 1367ms 1.28% 23.80% 9161ms 8.55% std::_Rb_tree::_M_erase 707ms 0.66% 24.46% 8994ms 8.39% VertexMesh::ElementIncludesPoint 389ms 0.36% 24.82% 8962ms 8.36% VertexMesh::GetNextEdgeGradientOfElementAtNode 825ms 0.77% 25.59% 8709ms 8.13% operator new 27ms 0.025% 25.61% 8689ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.61% 8519ms 7.95% std::_Rb_tree::_M_get_node (inline) 232ms 0.22% 25.83% 8459ms 7.89% std::_Rb_tree::~_Rb_tree (inline) 483ms 0.45% 26.28% 8314ms 7.76% VertexMesh::GetCentroidOfElement 78ms 0.073% 26.35% 8271ms 7.72% Cell::GetMutationState 0 0% 26.35% 8134ms 7.59% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.35% 8097ms 7.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.35% 7998ms 7.46% std::set::~set (inline) 258ms 0.24% 26.60% 7909ms 7.38% std::__new_allocator::deallocate (inline) 0 0% 26.60% 7875ms 7.35% std::allocator_traits::deallocate (inline) 0 0% 26.60% 7826ms 7.30% std::_Rb_tree::_M_put_node (inline) 3025ms 2.82% 29.42% 7760ms 7.24% __GI___libc_free 3106ms 2.90% 32.32% 7714ms 7.20% __GI___libc_malloc 1288ms 1.20% 33.52% 7250ms 6.77% AbstractMesh::GetDistanceBetweenNodes 26ms 0.024% 33.54% 7227ms 6.74% MutableVertexMesh::RemoveDeletedNodesAndElements 450ms 0.42% 33.96% 6938ms 6.47% std::map::operator[] (partial-inline) 139ms 0.13% 34.09% 6603ms 6.16% std::_Rb_tree::_Rb_tree (partial-inline) 100ms 0.093% 34.19% 6323ms 5.90% SimpleWntCellCycleModel::GetWntLevel 6263ms 5.84% 40.03% 6263ms 5.84% boost::numeric::ublas::c_vector::operator() 6252ms 5.83% 45.86% 6252ms 5.83% __strcmp_avx2 646ms 0.6% 46.47% 6216ms 5.80% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 46.48% 6180ms 5.77% std::set::set (inline) 119ms 0.11% 46.59% 6082ms 5.68% WntConcentration::GetWntLevel 0 0% 46.59% 5685ms 5.30% std::set::insert (inline) 2672ms 2.49% 49.08% 5544ms 5.17% __cxxabiv1::__si_class_type_info::__do_dyncast 2373ms 2.21% 51.30% 5450ms 5.09% std::_Rb_tree::_M_lower_bound (inline) 701ms 0.65% 51.95% 5241ms 4.89% std::_Rb_tree::_M_clone_node (inline) 32ms 0.03% 51.98% 5133ms 4.79% MutableVertexMesh::RemoveDeletedNodes 42ms 0.039% 52.02% 4963ms 4.63% EdgeHelper::RemoveDeletedEdges 1492ms 1.39% 53.41% 4876ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 58ms 0.054% 53.47% 4846ms 4.52% std::set_intersection (inline) 555ms 0.52% 53.98% 4840ms 4.52% std::_Rb_tree::_M_insert_ (inline) 311ms 0.29% 54.27% 4788ms 4.47% std::__set_intersection 4377ms 4.08% 58.36% 4729ms 4.41% _int_free 30ms 0.028% 58.39% 4694ms 4.38% EdgeHelper::UpdateEdgesMapKey 0 0% 58.39% 4531ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 178ms 0.17% 58.55% 4478ms 4.18% MutableElement::ResetIndex 0 0% 58.55% 4393ms 4.10% std::_Rb_tree::lower_bound (inline) 0 0% 58.55% 4393ms 4.10% std::map::lower_bound (inline) 4093ms 3.82% 62.37% 4093ms 3.82% boost::numeric::ublas::same_impl_ex 33ms 0.031% 62.40% 4078ms 3.81% Cell::GetCellProliferativeType 102ms 0.095% 62.50% 3814ms 3.56% AbstractCellPopulation::GetCellUsingLocationIndex 65ms 0.061% 62.56% 3633ms 3.39% AbstractCellProperty::IsType (inline) 0 0% 62.56% 3507ms 3.27% std::insert_iterator::operator= (inline) 3ms 0.0028% 62.56% 3494ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 50ms 0.047% 62.61% 3157ms 2.95% Cell::SetCellProliferativeType 4ms 0.0037% 62.61% 3132ms 2.92% std::_Rb_tree::_M_insert_unique_ (inline) 751ms 0.7% 63.31% 3071ms 2.87% AbstractElement::GetNodeLocation 2182ms 2.04% 65.35% 3036ms 2.83% _int_malloc 607ms 0.57% 65.92% 2926ms 2.73% boost::numeric::ublas::vector_binary::size (inline) 44ms 0.041% 65.96% 2825ms 2.64% std::_Rb_tree::erase 475ms 0.44% 66.40% 2663ms 2.48% std::_Rb_tree_const_iterator::operator++ (inline) 724ms 0.68% 67.08% 2583ms 2.41% AbstractCellProperty::IsSame 2564ms 2.39% 69.47% 2564ms 2.39% std::_Rb_tree::_S_right (inline) 0 0% 69.47% 2553ms 2.38% std::_Rb_tree::_M_insert_unique (inline) 49ms 0.046% 69.51% 2496ms 2.33% CellPropertyCollection::HasProperty 234ms 0.22% 69.73% 2478ms 2.31% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.73% 2465ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.73% 2383ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.73% 2383ms 2.22% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.73% 2381ms 2.22% Cell::HasCellProperty (inline) 126ms 0.12% 69.85% 2377ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 27ms 0.025% 69.88% 2253ms 2.10% Cell::GetCellData 1ms 0.00093% 69.88% 2212ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 206ms 0.19% 70.07% 2185ms 2.04% AbstractCellPopulation::Iterator::IsRealCell (inline) 104ms 0.097% 70.17% 2162ms 2.02% VertexMesh::GetVolumeOfElement 32ms 0.03% 70.20% 2039ms 1.90% std::_Rb_tree::_M_emplace_hint_unique 2032ms 1.90% 72.09% 2032ms 1.90% std::_Rb_tree_increment 3ms 0.0028% 72.09% 1963ms 1.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.09% 1963ms 1.83% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.09% 1957ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 72.10% 1940ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 440ms 0.41% 72.51% 1859ms 1.73% std::type_info::operator== (inline) 59ms 0.055% 72.56% 1829ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 1166ms 1.09% 73.65% 1817ms 1.70% std::_Rb_tree::equal_range (inline) 0 0% 73.65% 1743ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 28ms 0.026% 73.68% 1659ms 1.55% VertexMesh::GetSurfaceAreaOfElement 37ms 0.035% 73.71% 1651ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 175ms 0.16% 73.87% 1627ms 1.52% CellPropertyCollection::AddProperty 149ms 0.14% 74.01% 1595ms 1.49% boost::numeric::ublas::vector_reference::operator() (inline) 59ms 0.055% 74.07% 1489ms 1.39% Node::RemoveElement 0 0% 74.07% 1489ms 1.39% boost::numeric::ublas::vector_binary::operator() (inline) 32ms 0.03% 74.10% 1477ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.015% 74.11% 1442ms 1.35% std::set::erase (inline) 70ms 0.065% 74.18% 1424ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.18% 1405ms 1.31% tcache_get (inline) 1405ms 1.31% 75.49% 1405ms 1.31% tcache_get_n (inline) 1279ms 1.19% 76.68% 1279ms 1.19% std::_Rb_tree_insert_and_rebalance 0 0% 76.68% 1239ms 1.16% OffLatticeSimulation::ApplyBoundaries 0 0% 76.68% 1224ms 1.14% boost::numeric::ublas::norm_2 (inline) 537ms 0.5% 77.18% 1214ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 78ms 0.073% 77.26% 1150ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 83ms 0.077% 77.33% 1127ms 1.05% std::less::operator() (inline) 1121ms 1.05% 78.38% 1121ms 1.05% Node::rGetLocation 0 0% 78.38% 1085ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 24ms 0.022% 78.40% 1057ms 0.99% CellPropertyRegistry::Get 16ms 0.015% 78.42% 1050ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 112ms 0.1% 78.52% 1049ms 0.98% std::_Rb_tree::find (inline) 862ms 0.8% 79.33% 1044ms 0.97% std::operator< (inline) 1005ms 0.94% 80.26% 1005ms 0.94% [libchaste_mesh.so] 25ms 0.023% 80.29% 996ms 0.93% boost::numeric::ublas::detail::expression_type_check (inline) 5ms 0.0047% 80.29% 990ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 983ms 0.92% 81.21% 983ms 0.92% [libchaste_cell_based.so] 171ms 0.16% 81.37% 955ms 0.89% boost::numeric::ublas::detail::equals 950ms 0.89% 82.26% 950ms 0.89% std::vector::size (inline) 1ms 0.00093% 82.26% 937ms 0.87% std::_Rb_tree::clear (inline) 149ms 0.14% 82.40% 930ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 82.40% 930ms 0.87% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.40% 929ms 0.87% std::map::clear (inline) 391ms 0.36% 82.76% 917ms 0.86% Edge::GetMapIndex 0 0% 82.76% 876ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.76% 876ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 88ms 0.082% 82.85% 872ms 0.81% std::swap_ranges (inline) 1ms 0.00093% 82.85% 858ms 0.8% std::map::find (inline) 176ms 0.16% 83.01% 849ms 0.79% boost::shared_ptr::shared_ptr (inline) 0 0% 83.01% 846ms 0.79% VertexMeshWriter::MakeVtkMesh 106ms 0.099% 83.11% 832ms 0.78% MutableElement::GetNodeLocalIndex 472ms 0.44% 83.55% 787ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 785ms 0.73% 84.28% 785ms 0.73% std::swap (inline) 0 0% 84.28% 784ms 0.73% std::iter_swap (inline) 0 0% 84.28% 757ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 752ms 0.7% 84.98% 756ms 0.71% boost::detail::sp_counted_base::release 747ms 0.7% 85.68% 747ms 0.7% Node::GetIndex 116ms 0.11% 85.79% 747ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.026% 85.82% 740ms 0.69% MutableElement::RegisterWithEdges (inline) 0 0% 85.82% 739ms 0.69% boost::numeric::ublas::norm_inf (inline) 341ms 0.32% 86.13% 739ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 32ms 0.03% 86.16% 724ms 0.68% Edge::AddElement 110ms 0.1% 86.27% 713ms 0.67% std::__new_allocator::construct (inline) 0 0% 86.27% 713ms 0.67% std::allocator_traits::construct (inline) 0 0% 86.27% 678ms 0.63% std::_Vector_base::_M_allocate (inline) 644ms 0.6% 86.87% 672ms 0.63% boost::detail::shared_count::shared_count (inline) 0 0% 86.87% 663ms 0.62% std::_Rb_tree::_M_construct_node (inline) 24ms 0.022% 86.89% 632ms 0.59% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.89% 632ms 0.59% boost::numeric::ublas::vector::vector (inline) 0 0% 86.89% 618ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.02% 86.91% 618ms 0.58% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.91% 600ms 0.56% vtkPolygon::New 0 0% 86.91% 598ms 0.56% vtkPolygon::vtkPolygon 0 0% 86.91% 573ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 571ms 0.53% 87.44% 571ms 0.53% operator delete 25ms 0.023% 87.47% 554ms 0.52% MutableElement::RegisterWithNodes (inline) 3ms 0.0028% 87.47% 546ms 0.51% std::vector::_M_default_append (inline)