File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96831ms, 88.38% of 109568ms total Dropped 1111 nodes (cum <= 547.84ms) flat flat% sum% cum cum% 0 0% 0% 109078ms 99.55% __libc_start_call_main 0 0% 0% 109078ms 99.55% __libc_start_main_impl 0 0% 0% 109078ms 99.55% _start 0 0% 0% 109057ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109057ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109057ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109057ms 99.53% main 0 0% 0% 109022ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109022ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109022ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 109014ms 99.49% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.018% 56525ms 51.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.019% 0.037% 53286ms 48.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 131ms 0.12% 0.16% 51721ms 47.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 332ms 0.3% 0.46% 39738ms 36.27% NagaiHondaForce::AddForceContribution 0 0% 0.46% 39334ms 35.90% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.46% 24325ms 22.20% VertexBasedCellPopulation::Update 2ms 0.0018% 0.47% 24197ms 22.08% MutableVertexMesh::ReMesh 14515ms 13.25% 13.71% 22835ms 20.84% Cylindrical2dVertexMesh::GetVectorFromAtoB 88ms 0.08% 13.79% 17793ms 16.24% Cell::ReadyToDivide 75ms 0.068% 13.86% 16530ms 15.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 325ms 0.3% 14.16% 14693ms 13.41% NagaiHondaForce::GetAdhesionParameter 459ms 0.42% 14.58% 14271ms 13.02% boost::numeric::ublas::c_vector::c_vector (partial-inline) 114ms 0.1% 14.68% 14086ms 12.86% SimpleWntCellCycleModel::UpdateCellCyclePhase 138ms 0.13% 14.81% 14071ms 12.84% CellPropertyCollection::GetPropertiesType (inline) 381ms 0.35% 15.15% 12709ms 11.60% boost::numeric::ublas::vector_assign (inline) 125ms 0.11% 15.27% 12086ms 11.03% MutableVertexMesh::CheckForIntersections 3279ms 2.99% 18.26% 11736ms 10.71% __dynamic_cast 74ms 0.068% 18.33% 11630ms 10.61% AbstractCellProperty::IsSubType (inline) 71ms 0.065% 18.39% 11484ms 10.48% VertexBasedCellPopulation::GetDampingConstant 84ms 0.077% 18.47% 10656ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 33ms 0.03% 18.50% 10528ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.52% 10397ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1343ms 1.23% 19.75% 10214ms 9.32% std::__new_allocator::allocate (inline) 0 0% 19.75% 9700ms 8.85% std::allocator_traits::allocate (inline) 0 0% 19.75% 9648ms 8.81% std::_Rb_tree::_M_create_node (inline) 2773ms 2.53% 22.28% 9529ms 8.70% boost::numeric::ublas::indexing_vector_assign 1418ms 1.29% 23.57% 9176ms 8.37% std::_Rb_tree::_M_erase 0 0% 23.57% 9037ms 8.25% std::_Rb_tree::_M_get_node (inline) 736ms 0.67% 24.24% 9025ms 8.24% operator new 806ms 0.74% 24.98% 8999ms 8.21% VertexMesh::ElementIncludesPoint 79ms 0.072% 25.05% 8898ms 8.12% Cell::GetMutationState 17ms 0.016% 25.07% 8809ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 377ms 0.34% 25.41% 8777ms 8.01% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.41% 8408ms 7.67% std::_Rb_tree::_Alloc_node::operator() (inline) 239ms 0.22% 25.63% 8371ms 7.64% std::_Rb_tree::~_Rb_tree (inline) 511ms 0.47% 26.10% 8314ms 7.59% VertexMesh::GetCentroidOfElement 0 0% 26.10% 8149ms 7.44% std::_Rb_tree::_M_drop_node (inline) 3148ms 2.87% 28.97% 8091ms 7.38% __GI___libc_malloc 261ms 0.24% 29.21% 7979ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 29.21% 7951ms 7.26% std::allocator_traits::deallocate (inline) 0 0% 29.21% 7882ms 7.19% std::set::~set (inline) 0 0% 29.21% 7865ms 7.18% std::_Rb_tree::_M_put_node (inline) 3081ms 2.81% 32.02% 7784ms 7.10% __GI___libc_free 14ms 0.013% 32.03% 7772ms 7.09% MutableVertexMesh::RemoveDeletedNodesAndElements 468ms 0.43% 32.46% 7402ms 6.76% std::map::operator[] (partial-inline) 152ms 0.14% 32.60% 6987ms 6.38% std::_Rb_tree::_Rb_tree (partial-inline) 1272ms 1.16% 33.76% 6986ms 6.38% AbstractMesh::GetDistanceBetweenNodes 6940ms 6.33% 40.09% 6940ms 6.33% __strcmp_avx2 671ms 0.61% 40.70% 6624ms 6.05% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 40.72% 6542ms 5.97% std::set::set (inline) 104ms 0.095% 40.81% 6370ms 5.81% SimpleWntCellCycleModel::GetWntLevel 151ms 0.14% 40.95% 6180ms 5.64% WntConcentration::GetWntLevel 6024ms 5.50% 46.45% 6024ms 5.50% boost::numeric::ublas::c_vector::operator() 2704ms 2.47% 48.92% 6005ms 5.48% __cxxabiv1::__si_class_type_info::__do_dyncast 2468ms 2.25% 51.17% 5760ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 780ms 0.71% 51.88% 5653ms 5.16% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.88% 5463ms 4.99% std::set::insert (inline) 32ms 0.029% 51.91% 5389ms 4.92% MutableVertexMesh::RemoveDeletedNodes 47ms 0.043% 51.95% 5203ms 4.75% EdgeHelper::RemoveDeletedEdges 31ms 0.028% 51.98% 4904ms 4.48% EdgeHelper::UpdateEdgesMapKey 229ms 0.21% 52.19% 4832ms 4.41% MutableElement::ResetIndex 1473ms 1.34% 53.53% 4828ms 4.41% boost::numeric::ublas::c_vector::operator[] (inline) 4352ms 3.97% 57.51% 4690ms 4.28% _int_free 0 0% 57.51% 4656ms 4.25% std::_Rb_tree::lower_bound (inline) 0 0% 57.51% 4656ms 4.25% std::map::lower_bound (inline) 1ms 0.00091% 57.51% 4603ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 532ms 0.49% 57.99% 4584ms 4.18% std::_Rb_tree::_M_insert_ (inline) 60ms 0.055% 58.05% 4460ms 4.07% std::set_intersection (inline) 279ms 0.25% 58.30% 4400ms 4.02% std::__set_intersection 108ms 0.099% 58.40% 4054ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 4034ms 3.68% 62.08% 4034ms 3.68% boost::numeric::ublas::same_impl_ex 26ms 0.024% 62.11% 4033ms 3.68% Cell::GetCellProliferativeType 74ms 0.068% 62.17% 3892ms 3.55% AbstractCellProperty::IsType (inline) 9ms 0.0082% 62.18% 3520ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 873ms 0.8% 62.98% 3263ms 2.98% AbstractElement::GetNodeLocation 0 0% 62.98% 3227ms 2.95% std::insert_iterator::operator= (inline) 2258ms 2.06% 65.04% 3222ms 2.94% _int_malloc 41ms 0.037% 65.08% 3205ms 2.93% Cell::SetCellProliferativeType 44ms 0.04% 65.12% 3098ms 2.83% std::_Rb_tree::erase 641ms 0.59% 65.70% 2880ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.0027% 65.70% 2845ms 2.60% std::_Rb_tree::_M_insert_unique_ (inline) 2782ms 2.54% 68.24% 2782ms 2.54% std::_Rb_tree::_S_right (inline) 740ms 0.68% 68.92% 2755ms 2.51% AbstractCellProperty::IsSame 36ms 0.033% 68.95% 2719ms 2.48% CellPropertyCollection::HasProperty 443ms 0.4% 69.36% 2707ms 2.47% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0018% 69.36% 2618ms 2.39% std::_Rb_tree::_M_insert_unique 0 0% 69.36% 2600ms 2.37% Cell::HasCellProperty (inline) 0 0% 69.36% 2552ms 2.33% boost::numeric::ublas::c_vector::operator-= (inline) 220ms 0.2% 69.56% 2501ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.56% 2468ms 2.25% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.56% 2403ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 24ms 0.022% 69.58% 2400ms 2.19% Cell::GetCellData 108ms 0.099% 69.68% 2349ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 115ms 0.1% 69.78% 2306ms 2.10% VertexMesh::GetVolumeOfElement 31ms 0.028% 69.81% 2230ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 69.81% 2148ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 201ms 0.18% 70.00% 2138ms 1.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 1437ms 1.31% 71.31% 2120ms 1.93% std::_Rb_tree::equal_range (inline) 2088ms 1.91% 73.21% 2088ms 1.91% std::_Rb_tree_increment 1ms 0.00091% 73.22% 2024ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 465ms 0.42% 73.64% 2015ms 1.84% std::type_info::operator== (inline) 0 0% 73.64% 2011ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 73.64% 1902ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.64% 1902ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 78ms 0.071% 73.71% 1823ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.71% 1799ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 37ms 0.034% 73.75% 1659ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.022% 73.77% 1589ms 1.45% VertexMesh::GetSurfaceAreaOfElement 40ms 0.037% 73.80% 1585ms 1.45% Node::RemoveElement 24ms 0.022% 73.83% 1558ms 1.42% std::set::erase (inline) 0 0% 73.83% 1556ms 1.42% tcache_get (inline) 1556ms 1.42% 75.25% 1556ms 1.42% tcache_get_n (inline) 149ms 0.14% 75.38% 1554ms 1.42% CellPropertyCollection::AddProperty 15ms 0.014% 75.40% 1452ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 81ms 0.074% 75.47% 1447ms 1.32% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 138ms 0.13% 75.60% 1439ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.60% 1347ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.60% 1240ms 1.13% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0018% 75.60% 1233ms 1.13% OffLatticeSimulation::ApplyBoundaries 0 0% 75.60% 1205ms 1.10% boost::numeric::ublas::norm_2 (inline) 71ms 0.065% 75.66% 1203ms 1.10% std::less::operator() (inline) 529ms 0.48% 76.14% 1199ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 26ms 0.024% 76.17% 1154ms 1.05% CellPropertyRegistry::Get 1141ms 1.04% 77.21% 1141ms 1.04% Node::rGetLocation 1141ms 1.04% 78.25% 1141ms 1.04% std::_Rb_tree_insert_and_rebalance 899ms 0.82% 79.07% 1132ms 1.03% std::operator< (inline) 109ms 0.099% 79.17% 1115ms 1.02% std::_Rb_tree::find (inline) 83ms 0.076% 79.25% 1112ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 1109ms 1.01% 80.26% 1109ms 1.01% [libchaste_cell_based.so] 0 0% 80.26% 1046ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.26% 1028ms 0.94% std::map::clear (inline) 11ms 0.01% 80.27% 1026ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 16ms 0.015% 80.28% 1020ms 0.93% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 121ms 0.11% 80.39% 956ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 80.39% 956ms 0.87% boost::shared_ptr::~shared_ptr (inline) 955ms 0.87% 81.27% 955ms 0.87% std::vector::size (inline) 940ms 0.86% 82.12% 940ms 0.86% [libchaste_mesh.so] 0 0% 82.12% 934ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0018% 82.13% 934ms 0.85% boost::numeric::ublas::c_vector::swap (inline) 31ms 0.028% 82.15% 934ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 425ms 0.39% 82.54% 933ms 0.85% Edge::GetMapIndex 96ms 0.088% 82.63% 932ms 0.85% std::swap_ranges (inline) 154ms 0.14% 82.77% 896ms 0.82% boost::numeric::ublas::detail::equals 1ms 0.00091% 82.77% 883ms 0.81% std::map::find (inline) 0 0% 82.77% 855ms 0.78% VertexMeshWriter::MakeVtkMesh 837ms 0.76% 83.53% 837ms 0.76% std::swap (inline) 0 0% 83.53% 836ms 0.76% std::iter_swap (inline) 802ms 0.73% 84.27% 810ms 0.74% boost::detail::sp_counted_base::release 100ms 0.091% 84.36% 782ms 0.71% MutableElement::GetNodeLocalIndex 111ms 0.1% 84.46% 768ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 29ms 0.026% 84.49% 763ms 0.7% Edge::AddElement 15ms 0.014% 84.50% 762ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.50% 720ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 430ms 0.39% 84.89% 716ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 18ms 0.016% 84.91% 714ms 0.65% AbstractNumericalMethod::DetectStepSizeExceptions 118ms 0.11% 85.02% 711ms 0.65% boost::shared_ptr::shared_ptr (inline) 0 0% 85.02% 697ms 0.64% boost::numeric::ublas::norm_inf (inline) 366ms 0.33% 85.35% 697ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 139ms 0.13% 85.48% 696ms 0.64% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.48% 693ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 85.49% 693ms 0.63% std::_Rb_tree::_M_insert_node (inline) 682ms 0.62% 86.12% 682ms 0.62% Node::GetIndex 1ms 0.00091% 86.12% 660ms 0.6% std::_Vector_base::_M_allocate (inline) 116ms 0.11% 86.22% 660ms 0.6% std::__new_allocator::construct (inline) 0 0% 86.22% 660ms 0.6% std::allocator_traits::construct (inline) 616ms 0.56% 86.79% 616ms 0.56% operator delete 29ms 0.026% 86.81% 611ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 86.81% 611ms 0.56% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.81% 599ms 0.55% vtkPolygon::New 1ms 0.00091% 86.81% 599ms 0.55% vtkPolygon::vtkPolygon 558ms 0.51% 87.32% 593ms 0.54% boost::detail::shared_count::shared_count (inline) 16ms 0.015% 87.34% 583ms 0.53% Node::AddElement 580ms 0.53% 87.87% 580ms 0.53% [libstdc++.so.6.0.33] 0 0% 87.87% 576ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 9ms 0.0082% 87.88% 571ms 0.52% std::vector::_M_default_append (inline) 548ms 0.5% 88.38% 548ms 0.5% boost::shared_ptr::operator-> (inline)