File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 66151ms, 88.48% of 74762ms total Dropped 985 nodes (cum <= 373.81ms) flat flat% sum% cum cum% 0 0% 0% 74610ms 99.80% __libc_start_call_main 0 0% 0% 74610ms 99.80% __libc_start_main_impl 0 0% 0% 74610ms 99.80% _start 0 0% 0% 74594ms 99.78% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74594ms 99.78% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74594ms 99.78% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74594ms 99.78% main 0 0% 0% 74556ms 99.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74556ms 99.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74556ms 99.72% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.004% 0.004% 74550ms 99.72% AbstractCellBasedSimulation::Solve 12ms 0.016% 0.02% 39491ms 52.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.008% 0.028% 36725ms 49.12% ForwardEulerNumericalMethod::UpdateAllNodePositions 42ms 0.056% 0.084% 36016ms 48.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 261ms 0.35% 0.43% 28234ms 37.77% NagaiHondaForce::AddForceContribution 1ms 0.0013% 0.43% 26083ms 34.89% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.004% 0.44% 15713ms 21.02% VertexBasedCellPopulation::Update 1ms 0.0013% 0.44% 15601ms 20.87% MutableVertexMesh::ReMesh 6936ms 9.28% 9.72% 13240ms 17.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 68ms 0.091% 9.81% 12139ms 16.24% Cell::ReadyToDivide 68ms 0.091% 9.90% 11749ms 15.72% NagaiHondaForce::GetAdhesionParameter 17ms 0.023% 9.92% 11463ms 15.33% AbstractPhaseBasedCellCycleModel::ReadyToDivide 38ms 0.051% 9.97% 9804ms 13.11% SimpleWntCellCycleModel::UpdateCellCyclePhase 585ms 0.78% 10.76% 9584ms 12.82% std::__new_allocator::allocate (inline) 301ms 0.4% 11.16% 9533ms 12.75% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 11.16% 9197ms 12.30% std::allocator_traits::allocate (inline) 0 0% 11.16% 8972ms 12.00% std::_Rb_tree::_M_create_node (inline) 697ms 0.93% 12.09% 8870ms 11.86% operator new 120ms 0.16% 12.25% 8854ms 11.84% CellPropertyCollection::GetPropertiesType (inline) 0 0% 12.25% 8713ms 11.65% std::_Rb_tree::_M_get_node (inline) 189ms 0.25% 12.50% 8527ms 11.41% boost::numeric::ublas::vector_assign (inline) 2697ms 3.61% 16.11% 7911ms 10.58% __GI___libc_malloc 0 0% 16.11% 7783ms 10.41% std::_Rb_tree::_Alloc_node::operator() (inline) 85ms 0.11% 16.22% 7501ms 10.03% VertexBasedCellPopulation::GetDampingConstant 35ms 0.047% 16.27% 7323ms 9.80% AbstractTargetAreaModifier::UpdateTargetAreas 112ms 0.15% 16.42% 7273ms 9.73% MutableVertexMesh::CheckForIntersections 33ms 0.044% 16.47% 7258ms 9.71% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 62ms 0.083% 16.55% 7215ms 9.65% AbstractCellProperty::IsSubType (inline) 1815ms 2.43% 18.98% 7157ms 9.57% __dynamic_cast 4ms 0.0054% 18.98% 7137ms 9.55% AbstractCellBasedSimulation::DoCellBirth 684ms 0.91% 19.90% 6573ms 8.79% std::_Rb_tree::_M_erase 0 0% 19.90% 6545ms 8.75% std::_Rb_tree::_M_drop_node (inline) 281ms 0.38% 20.27% 6254ms 8.37% std::_Rb_tree::~_Rb_tree (inline) 1817ms 2.43% 22.70% 6176ms 8.26% boost::numeric::ublas::indexing_vector_assign 396ms 0.53% 23.23% 6082ms 8.14% std::map::operator[] (partial-inline) 0 0% 23.23% 5969ms 7.98% std::set::~set (inline) 75ms 0.1% 23.33% 5865ms 7.84% std::__new_allocator::deallocate (inline) 0 0% 23.33% 5843ms 7.82% std::allocator_traits::deallocate (inline) 0 0% 23.33% 5799ms 7.76% std::_Rb_tree::_M_put_node (inline) 26ms 0.035% 23.37% 5765ms 7.71% VertexBasedCellPopulation::GetLocationOfCellCentre 1561ms 2.09% 25.46% 5693ms 7.61% __GI___libc_free 262ms 0.35% 25.81% 5626ms 7.53% VertexMesh::GetNextEdgeGradientOfElementAtNode 38ms 0.051% 25.86% 5585ms 7.47% Cell::GetMutationState 4ms 0.0054% 25.86% 5500ms 7.36% MutableVertexMesh::RemoveDeletedNodesAndElements 451ms 0.6% 26.47% 5493ms 7.35% VertexMesh::GetCentroidOfElement 0 0% 26.47% 5489ms 7.34% std::set::insert (inline) 346ms 0.46% 26.93% 5368ms 7.18% VertexMesh::ElementIncludesPoint 81ms 0.11% 27.04% 5123ms 6.85% std::_Rb_tree::_Rb_tree (partial-inline) 661ms 0.88% 27.92% 5044ms 6.75% std::_Rb_tree::_M_insert_ (inline) 512ms 0.68% 28.61% 4904ms 6.56% std::_Rb_tree::_M_copy (inline) 4824ms 6.45% 35.06% 4824ms 6.45% boost::numeric::ublas::c_vector::operator() 5ms 0.0067% 35.06% 4759ms 6.37% std::set::set (inline) 34ms 0.045% 35.11% 4572ms 6.12% std::set_intersection (inline) 179ms 0.24% 35.35% 4538ms 6.07% std::__set_intersection 623ms 0.83% 36.18% 4306ms 5.76% AbstractMesh::GetDistanceBetweenNodes 553ms 0.74% 36.92% 4272ms 5.71% std::_Rb_tree::_M_clone_node (inline) 106ms 0.14% 37.06% 4270ms 5.71% SimpleWntCellCycleModel::GetWntLevel 3747ms 5.01% 42.08% 4106ms 5.49% _int_free 96ms 0.13% 42.20% 4071ms 5.45% WntConcentration::GetWntLevel 1577ms 2.11% 44.31% 3997ms 5.35% std::_Rb_tree::_M_lower_bound (inline) 392ms 0.52% 44.84% 3921ms 5.24% boost::numeric::ublas::c_vector::operator[] (inline) 3902ms 5.22% 50.06% 3902ms 5.22% __strcmp_evex 3253ms 4.35% 54.41% 3857ms 5.16% _int_malloc 17ms 0.023% 54.43% 3752ms 5.02% MutableVertexMesh::RemoveDeletedNodes 33ms 0.044% 54.48% 3667ms 4.90% EdgeHelper::RemoveDeletedEdges 1885ms 2.52% 57.00% 3655ms 4.89% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.025% 57.02% 3527ms 4.72% EdgeHelper::UpdateEdgesMapKey 0 0% 57.02% 3512ms 4.70% std::_Rb_tree::lower_bound (inline) 0 0% 57.02% 3512ms 4.70% std::map::lower_bound (inline) 0 0% 57.02% 3500ms 4.68% std::insert_iterator::operator= (inline) 87ms 0.12% 57.14% 3423ms 4.58% MutableElement::ResetIndex 0 0% 57.14% 3285ms 4.39% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 57.14% 3225ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 51ms 0.068% 57.21% 3146ms 4.21% AbstractCellPopulation::GetCellUsingLocationIndex 3137ms 4.20% 61.40% 3137ms 4.20% boost::numeric::ublas::same_impl_ex 21ms 0.028% 61.43% 3060ms 4.09% Cell::GetCellProliferativeType 17ms 0.023% 61.45% 2519ms 3.37% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2517ms 3.37% 64.82% 2517ms 3.37% [libchaste_cell_based.so] 106ms 0.14% 64.96% 2337ms 3.13% AbstractCellProperty::IsType (inline) 81ms 0.11% 65.07% 2236ms 2.99% boost::detail::shared_count::~shared_count (inline) 0 0% 65.07% 2236ms 2.99% boost::shared_ptr::~shared_ptr (inline) 53ms 0.071% 65.14% 2204ms 2.95% Cell::SetCellProliferativeType 2ms 0.0027% 65.14% 2204ms 2.95% std::_Rb_tree::_M_insert_unique 34ms 0.045% 65.19% 2124ms 2.84% std::_Rb_tree::_M_emplace_hint_unique 607ms 0.81% 66.00% 2116ms 2.83% AbstractElement::GetNodeLocation 2103ms 2.81% 68.81% 2108ms 2.82% boost::detail::sp_counted_base::release 162ms 0.22% 69.03% 2074ms 2.77% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.0054% 69.04% 2068ms 2.77% AbstractCellPopulation::Iterator::operator++ (inline) 2062ms 2.76% 71.79% 2062ms 2.76% std::_Rb_tree::_S_right (inline) 74ms 0.099% 71.89% 1979ms 2.65% std::_Rb_tree::erase 0 0% 71.89% 1810ms 2.42% boost::numeric::ublas::c_vector::assign (inline) 53ms 0.071% 71.96% 1780ms 2.38% boost::numeric::ublas::vector_binary::size (inline) 11ms 0.015% 71.98% 1749ms 2.34% Cell::GetCellData 246ms 0.33% 72.31% 1717ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 1670ms 2.23% 74.54% 1670ms 2.23% [libchaste_mesh.so] 28ms 0.037% 74.58% 1627ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 74.58% 1625ms 2.17% AbstractCellPopulation::WriteResultsToFiles 203ms 0.27% 74.85% 1594ms 2.13% VertexMesh::GetAreaGradientOfElementAtNode 32ms 0.043% 74.89% 1549ms 2.07% CellPropertyCollection::HasProperty 9ms 0.012% 74.91% 1539ms 2.06% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.91% 1517ms 2.03% Cell::HasCellProperty (inline) 0 0% 74.91% 1494ms 2.00% boost::numeric::ublas::c_vector::operator-= (inline) 279ms 0.37% 75.28% 1411ms 1.89% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 263ms 0.35% 75.63% 1410ms 1.89% AbstractCellProperty::IsSame 80ms 0.11% 75.74% 1387ms 1.86% VertexMesh::GetVolumeOfElement 0 0% 75.74% 1336ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0027% 75.74% 1330ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0027% 75.74% 1258ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.74% 1258ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.74% 1199ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.74% 1189ms 1.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 101ms 0.14% 75.88% 1173ms 1.57% CellPropertyCollection::AddProperty 35ms 0.047% 75.92% 1162ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 120ms 0.16% 76.09% 1147ms 1.53% std::type_info::operator== (inline) 3ms 0.004% 76.09% 1132ms 1.51% OffLatticeSimulation::ApplyBoundaries 46ms 0.062% 76.15% 1117ms 1.49% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 76.15% 1070ms 1.43% tcache_get (inline) 1070ms 1.43% 77.58% 1070ms 1.43% tcache_get_n (inline) 28ms 0.037% 77.62% 1029ms 1.38% Node::RemoveElement 49ms 0.066% 77.69% 1020ms 1.36% VertexMesh::GetSurfaceAreaOfElement 43ms 0.058% 77.74% 1010ms 1.35% std::_Rb_tree::_M_erase_aux (partial-inline) 639ms 0.85% 78.60% 1010ms 1.35% std::_Rb_tree::equal_range (inline) 2ms 0.0027% 78.60% 1002ms 1.34% std::set::erase (inline) 29ms 0.039% 78.64% 1001ms 1.34% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 978ms 1.31% 79.95% 978ms 1.31% std::_Rb_tree_increment 0 0% 79.95% 974ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 50ms 0.067% 80.01% 873ms 1.17% boost::numeric::ublas::vector_reference::operator() (inline) 29ms 0.039% 80.05% 856ms 1.14% Edge::AddElement 10ms 0.013% 80.07% 854ms 1.14% MutableElement::RegisterWithEdges (inline) 796ms 1.06% 81.13% 796ms 1.06% std::_Rb_tree_insert_and_rebalance 30ms 0.04% 81.17% 792ms 1.06% boost::numeric::ublas::detail::expression_type_check (inline) 38ms 0.051% 81.22% 787ms 1.05% CellPropertyRegistry::Get 0 0% 81.22% 786ms 1.05% CellPropertyCollection::~CellPropertyCollection (inline) 770ms 1.03% 82.25% 770ms 1.03% [libstdc++.so.6.0.33] 0 0% 82.25% 747ms 1% std::__new_allocator::destroy (inline) 0 0% 82.25% 747ms 1% std::allocator_traits::destroy (inline) 0 0% 82.25% 746ms 1% std::_Rb_tree::_M_destroy_node (inline) 126ms 0.17% 82.42% 737ms 0.99% boost::numeric::ublas::detail::equals 0 0% 82.42% 732ms 0.98% boost::numeric::ublas::norm_2 (inline) 334ms 0.45% 82.87% 707ms 0.95% boost::numeric::ublas::vector_norm_2::apply 5ms 0.0067% 82.87% 688ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.87% 667ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0054% 82.88% 667ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 108ms 0.14% 83.02% 663ms 0.89% std::swap_ranges (inline) 1ms 0.0013% 83.02% 645ms 0.86% VertexMeshWriter::MakeVtkMesh 468ms 0.63% 83.65% 626ms 0.84% CellPropertyCollection::GetProperty 622ms 0.83% 84.48% 622ms 0.83% Node::rGetLocation 48ms 0.064% 84.55% 619ms 0.83% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.55% 619ms 0.83% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.033% 84.58% 619ms 0.83% std::_Rb_tree::_M_insert_node (inline) 0 0% 84.58% 602ms 0.81% std::_Rb_tree::clear (inline) 0 0% 84.58% 589ms 0.79% std::map::clear (inline) 41ms 0.055% 84.64% 578ms 0.77% std::less::operator() (inline) 285ms 0.38% 85.02% 564ms 0.75% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.02% 555ms 0.74% std::iter_swap (inline) 555ms 0.74% 85.76% 555ms 0.74% std::swap (inline) 65ms 0.087% 85.85% 546ms 0.73% std::_Rb_tree::find (inline) 74ms 0.099% 85.94% 537ms 0.72% MutableElement::GetNodeLocalIndex 391ms 0.52% 86.47% 537ms 0.72% std::operator< (inline) 0 0% 86.47% 535ms 0.72% boost::numeric::ublas::norm_inf (inline) 182ms 0.24% 86.71% 535ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.71% 481ms 0.64% std::_Vector_base::_M_allocate (inline) 2ms 0.0027% 86.71% 462ms 0.62% std::map::find (inline) 0 0% 86.71% 447ms 0.6% vtkPolygon::New 0 0% 86.71% 447ms 0.6% vtkPolygon::vtkPolygon 439ms 0.59% 87.30% 439ms 0.59% std::vector::size (inline) 15ms 0.02% 87.32% 430ms 0.58% MutableElement::RegisterWithNodes (inline) 421ms 0.56% 87.88% 421ms 0.56% Node::GetIndex 0 0% 87.88% 405ms 0.54% std::map::map (inline) 44ms 0.059% 87.94% 398ms 0.53% Node::AddElement 7ms 0.0094% 87.95% 394ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.95% 394ms 0.53% boost::numeric::ublas::vector::vector (inline) 392ms 0.52% 88.48% 392ms 0.52% tcache_put (inline) 4ms 0.0054% 88.48% 388ms 0.52% std::vector::_M_default_append (inline)