File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94444ms, 88.31% of 106945ms total Dropped 1107 nodes (cum <= 534.73ms) flat flat% sum% cum cum% 0 0% 0% 106670ms 99.74% __libc_start_call_main 0 0% 0% 106670ms 99.74% __libc_start_main_impl 0 0% 0% 106670ms 99.74% _start 0 0% 0% 106647ms 99.72% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106647ms 99.72% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106647ms 99.72% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106647ms 99.72% main 0 0% 0% 106613ms 99.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106613ms 99.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106613ms 99.69% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0047% 0.0047% 106606ms 99.68% AbstractCellBasedSimulation::Solve 15ms 0.014% 0.019% 55588ms 51.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.032% 51918ms 48.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 80ms 0.075% 0.11% 50494ms 47.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 307ms 0.29% 0.39% 38991ms 36.46% NagaiHondaForce::AddForceContribution 0 0% 0.39% 37258ms 34.84% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0019% 0.4% 21977ms 20.55% VertexBasedCellPopulation::Update 1ms 0.00094% 0.4% 21849ms 20.43% MutableVertexMesh::ReMesh 115ms 0.11% 0.5% 18511ms 17.31% Cell::ReadyToDivide 9187ms 8.59% 9.09% 17887ms 16.73% Cylindrical2dVertexMesh::GetVectorFromAtoB 26ms 0.024% 9.12% 17272ms 16.15% AbstractPhaseBasedCellCycleModel::ReadyToDivide 98ms 0.092% 9.21% 15986ms 14.95% NagaiHondaForce::GetAdhesionParameter 70ms 0.065% 9.28% 14877ms 13.91% SimpleWntCellCycleModel::UpdateCellCyclePhase 853ms 0.8% 10.07% 13524ms 12.65% std::__new_allocator::allocate (inline) 66ms 0.062% 10.14% 13503ms 12.63% CellPropertyCollection::GetPropertiesType (inline) 385ms 0.36% 10.50% 13442ms 12.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.50% 13081ms 12.23% std::allocator_traits::allocate (inline) 0 0% 10.50% 12801ms 11.97% std::_Rb_tree::_M_create_node (inline) 829ms 0.78% 11.27% 12602ms 11.78% operator new 0 0% 11.27% 12433ms 11.63% std::_Rb_tree::_M_get_node (inline) 296ms 0.28% 11.55% 12032ms 11.25% boost::numeric::ublas::vector_assign (inline) 3872ms 3.62% 15.17% 11411ms 10.67% __GI___libc_malloc 50ms 0.047% 15.21% 11328ms 10.59% AbstractTargetAreaModifier::UpdateTargetAreas 50ms 0.047% 15.26% 11234ms 10.50% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 102ms 0.095% 15.36% 11129ms 10.41% VertexBasedCellPopulation::GetDampingConstant 0 0% 15.36% 11071ms 10.35% std::_Rb_tree::_Alloc_node::operator() (inline) 92ms 0.086% 15.44% 11067ms 10.35% AbstractCellProperty::IsSubType (inline) 2805ms 2.62% 18.07% 10987ms 10.27% __dynamic_cast 13ms 0.012% 18.08% 10883ms 10.18% AbstractCellBasedSimulation::DoCellBirth 132ms 0.12% 18.20% 9754ms 9.12% MutableVertexMesh::CheckForIntersections 0 0% 18.20% 9288ms 8.68% std::_Rb_tree::_M_drop_node (inline) 1018ms 0.95% 19.15% 9233ms 8.63% std::_Rb_tree::_M_erase 524ms 0.49% 19.64% 8927ms 8.35% std::map::operator[] (partial-inline) 2584ms 2.42% 22.06% 8698ms 8.13% boost::numeric::ublas::indexing_vector_assign 300ms 0.28% 22.34% 8637ms 8.08% std::_Rb_tree::~_Rb_tree (inline) 102ms 0.095% 22.43% 8469ms 7.92% std::__new_allocator::deallocate (inline) 0 0% 22.43% 8455ms 7.91% std::allocator_traits::deallocate (inline) 52ms 0.049% 22.48% 8404ms 7.86% Cell::GetMutationState 61ms 0.057% 22.54% 8369ms 7.83% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 22.54% 8369ms 7.83% std::_Rb_tree::_M_put_node (inline) 2151ms 2.01% 24.55% 8237ms 7.70% __GI___libc_free 0 0% 24.55% 8190ms 7.66% std::set::~set (inline) 0 0% 24.55% 7901ms 7.39% std::set::insert (inline) 5ms 0.0047% 24.56% 7863ms 7.35% MutableVertexMesh::RemoveDeletedNodesAndElements 700ms 0.65% 25.21% 7805ms 7.30% VertexMesh::GetCentroidOfElement 445ms 0.42% 25.63% 7627ms 7.13% VertexMesh::GetNextEdgeGradientOfElementAtNode 495ms 0.46% 26.09% 7293ms 6.82% VertexMesh::ElementIncludesPoint 869ms 0.81% 26.90% 7279ms 6.81% std::_Rb_tree::_M_insert_ (inline) 126ms 0.12% 27.02% 7123ms 6.66% std::_Rb_tree::_Rb_tree (partial-inline) 660ms 0.62% 27.64% 6800ms 6.36% std::_Rb_tree::_M_copy (inline) 6680ms 6.25% 33.88% 6680ms 6.25% __strcmp_evex 8ms 0.0075% 33.89% 6648ms 6.22% std::set::set (inline) 6570ms 6.14% 40.03% 6570ms 6.14% boost::numeric::ublas::c_vector::operator() 139ms 0.13% 40.16% 6518ms 6.09% SimpleWntCellCycleModel::GetWntLevel 2513ms 2.35% 42.51% 6417ms 6.00% std::_Rb_tree::_M_lower_bound (inline) 124ms 0.12% 42.63% 6255ms 5.85% WntConcentration::GetWntLevel 52ms 0.049% 42.68% 6150ms 5.75% std::set_intersection (inline) 241ms 0.23% 42.90% 6098ms 5.70% std::__set_intersection 5250ms 4.91% 47.81% 6022ms 5.63% _int_free 952ms 0.89% 48.70% 5963ms 5.58% AbstractMesh::GetDistanceBetweenNodes 810ms 0.76% 49.46% 5943ms 5.56% std::_Rb_tree::_M_clone_node (inline) 4651ms 4.35% 53.81% 5613ms 5.25% _int_malloc 28ms 0.026% 53.84% 5607ms 5.24% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.84% 5526ms 5.17% std::_Rb_tree::lower_bound (inline) 0 0% 53.84% 5526ms 5.17% std::map::lower_bound (inline) 59ms 0.055% 53.89% 5468ms 5.11% EdgeHelper::RemoveDeletedEdges 616ms 0.58% 54.47% 5460ms 5.11% boost::numeric::ublas::c_vector::operator[] (inline) 2352ms 2.20% 56.67% 5320ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.012% 56.68% 5176ms 4.84% EdgeHelper::UpdateEdgesMapKey 0 0% 56.68% 4809ms 4.50% std::insert_iterator::operator= (inline) 136ms 0.13% 56.81% 4805ms 4.49% MutableElement::ResetIndex 74ms 0.069% 56.88% 4766ms 4.46% AbstractCellPopulation::GetCellUsingLocationIndex 28ms 0.026% 56.90% 4550ms 4.25% Cell::GetCellProliferativeType 0 0% 56.90% 4531ms 4.24% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.00094% 56.90% 4393ms 4.11% AbstractCellBasedSimulation::DoCellRemoval (inline) 4325ms 4.04% 60.95% 4325ms 4.04% boost::numeric::ublas::same_impl_ex 121ms 0.11% 61.06% 3568ms 3.34% AbstractCellProperty::IsType (inline) 103ms 0.096% 61.16% 3412ms 3.19% Cell::SetCellProliferativeType 3377ms 3.16% 64.31% 3377ms 3.16% std::_Rb_tree::_S_right (inline) 4ms 0.0037% 64.32% 3370ms 3.15% std::_Rb_tree::_M_insert_unique 3352ms 3.13% 67.45% 3352ms 3.13% [libchaste_cell_based.so] 53ms 0.05% 67.50% 3332ms 3.12% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 789ms 0.74% 68.24% 3166ms 2.96% AbstractElement::GetNodeLocation 128ms 0.12% 68.36% 2995ms 2.80% boost::detail::shared_count::~shared_count (inline) 0 0% 68.36% 2995ms 2.80% boost::shared_ptr::~shared_ptr (inline) 11ms 0.01% 68.37% 2846ms 2.66% AbstractCellPopulation::Iterator::operator++ (inline) 241ms 0.23% 68.59% 2844ms 2.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 45ms 0.042% 68.64% 2836ms 2.65% std::_Rb_tree::_M_emplace_hint_unique 2788ms 2.61% 71.24% 2819ms 2.64% boost::detail::sp_counted_base::release 80ms 0.075% 71.32% 2763ms 2.58% std::_Rb_tree::erase 14ms 0.013% 71.33% 2686ms 2.51% Cell::GetCellData 135ms 0.13% 71.46% 2537ms 2.37% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.46% 2530ms 2.37% boost::numeric::ublas::c_vector::assign (inline) 0 0% 71.46% 2491ms 2.33% boost::numeric::ublas::c_vector::operator-= (inline) 47ms 0.044% 71.50% 2477ms 2.32% CellPropertyCollection::HasProperty 0 0% 71.50% 2408ms 2.25% Cell::HasCellProperty (inline) 0 0% 71.50% 2393ms 2.24% AbstractCellPopulation::WriteResultsToFiles 295ms 0.28% 71.78% 2349ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 499ms 0.47% 72.24% 2345ms 2.19% AbstractCellProperty::IsSame 58ms 0.054% 72.30% 2342ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 289ms 0.27% 72.57% 2231ms 2.09% VertexMesh::GetAreaGradientOfElementAtNode 34ms 0.032% 72.60% 2171ms 2.03% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2124ms 1.99% 74.59% 2124ms 1.99% [libchaste_mesh.so] 332ms 0.31% 74.90% 1976ms 1.85% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.90% 1976ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0037% 74.90% 1964ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 147ms 0.14% 75.04% 1908ms 1.78% CellPropertyCollection::AddProperty 208ms 0.19% 75.23% 1846ms 1.73% std::type_info::operator== (inline) 95ms 0.089% 75.32% 1784ms 1.67% VertexMesh::GetVolumeOfElement 0 0% 75.32% 1762ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 81ms 0.076% 75.40% 1757ms 1.64% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.40% 1730ms 1.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 6ms 0.0056% 75.40% 1714ms 1.60% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.40% 1714ms 1.60% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.064% 75.47% 1637ms 1.53% MutableVertexMesh::CheckForSwapsFromShortEdges 60ms 0.056% 75.52% 1556ms 1.45% std::_Rb_tree::_M_erase_aux (partial-inline) 2ms 0.0019% 75.52% 1547ms 1.45% OffLatticeSimulation::ApplyBoundaries 1ms 0.00094% 75.52% 1496ms 1.40% tcache_get (inline) 1495ms 1.40% 76.92% 1495ms 1.40% tcache_get_n (inline) 0 0% 76.92% 1484ms 1.39% boost::numeric::ublas::vector_binary::operator() (inline) 75ms 0.07% 76.99% 1444ms 1.35% VertexMesh::GetSurfaceAreaOfElement 1401ms 1.31% 78.30% 1401ms 1.31% std::_Rb_tree_increment 46ms 0.043% 78.35% 1358ms 1.27% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 41ms 0.038% 78.38% 1309ms 1.22% Node::RemoveElement 789ms 0.74% 79.12% 1296ms 1.21% std::_Rb_tree::equal_range (inline) 3ms 0.0028% 79.12% 1271ms 1.19% std::set::erase (inline) 62ms 0.058% 79.18% 1250ms 1.17% CellPropertyRegistry::Get 109ms 0.1% 79.28% 1224ms 1.14% boost::numeric::ublas::vector_reference::operator() (inline) 18ms 0.017% 79.30% 1197ms 1.12% MutableElement::RegisterWithEdges (inline) 39ms 0.036% 79.34% 1190ms 1.11% Edge::AddElement 1159ms 1.08% 80.42% 1159ms 1.08% [libstdc++.so.6.0.33] 1118ms 1.05% 81.47% 1118ms 1.05% Node::rGetLocation 0 0% 81.47% 1111ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 81.47% 1111ms 1.04% boost::numeric::ublas::c_vector::swap (inline) 141ms 0.13% 81.60% 1107ms 1.04% std::swap_ranges (inline) 0 0% 81.60% 1103ms 1.03% CellPropertyCollection::~CellPropertyCollection (inline) 10ms 0.0094% 81.61% 1026ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1023ms 0.96% 82.57% 1023ms 0.96% std::_Rb_tree_insert_and_rebalance 4ms 0.0037% 82.57% 1017ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.57% 1002ms 0.94% boost::numeric::ublas::norm_2 (inline) 157ms 0.15% 82.72% 985ms 0.92% boost::numeric::ublas::detail::equals 504ms 0.47% 83.19% 967ms 0.9% boost::numeric::ublas::vector_norm_2::apply 0 0% 83.19% 966ms 0.9% std::iter_swap (inline) 966ms 0.9% 84.09% 966ms 0.9% std::swap (inline) 106ms 0.099% 84.19% 953ms 0.89% std::_Rb_tree::find (inline) 0 0% 84.19% 922ms 0.86% std::__new_allocator::destroy (inline) 0 0% 84.19% 922ms 0.86% std::allocator_traits::destroy (inline) 0 0% 84.19% 920ms 0.86% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.0019% 84.19% 908ms 0.85% VertexMeshWriter::MakeVtkMesh 1ms 0.00094% 84.20% 903ms 0.84% std::_Rb_tree::clear (inline) 0 0% 84.20% 881ms 0.82% std::map::clear (inline) 855ms 0.8% 85.00% 855ms 0.8% tcache_put (inline) 659ms 0.62% 85.61% 833ms 0.78% CellPropertyCollection::GetProperty 47ms 0.044% 85.66% 816ms 0.76% std::less::operator() (inline) 0 0% 85.66% 809ms 0.76% std::map::find (inline) 46ms 0.043% 85.70% 796ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 601ms 0.56% 86.26% 769ms 0.72% std::operator< (inline) 0 0% 86.26% 721ms 0.67% boost::numeric::ublas::norm_inf (inline) 249ms 0.23% 86.49% 721ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.49% 716ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.019% 86.51% 716ms 0.67% std::_Rb_tree::_M_insert_node (inline) 701ms 0.66% 87.17% 701ms 0.66% std::vector::size (inline) 343ms 0.32% 87.49% 698ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 73ms 0.068% 87.56% 695ms 0.65% MutableElement::GetNodeLocalIndex 25ms 0.023% 87.58% 682ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 1ms 0.00094% 87.58% 666ms 0.62% vtkPolygon::New 0 0% 87.58% 663ms 0.62% vtkPolygon::vtkPolygon 110ms 0.1% 87.68% 657ms 0.61% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 87.68% 641ms 0.6% std::_Vector_base::_M_allocate (inline) 26ms 0.024% 87.71% 626ms 0.59% MutableElement::RegisterWithNodes (inline) 605ms 0.57% 88.27% 605ms 0.57% Node::GetIndex 40ms 0.037% 88.31% 590ms 0.55% Node::AddElement 0 0% 88.31% 564ms 0.53% std::map::map (inline)