File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 73432ms, 88.80% of 82690ms total Dropped 1018 nodes (cum <= 413.45ms) flat flat% sum% cum cum% 0 0% 0% 82408ms 99.66% __libc_start_call_main 0 0% 0% 82408ms 99.66% __libc_start_main_impl 0 0% 0% 82408ms 99.66% _start 0 0% 0% 82391ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 82391ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 82391ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 82391ms 99.64% main 0 0% 0% 82353ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 82353ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 82353ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0024% 0.0024% 82346ms 99.58% AbstractCellBasedSimulation::Solve 20ms 0.024% 0.027% 43833ms 53.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.017% 0.044% 41361ms 50.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 104ms 0.13% 0.17% 40519ms 49.00% AbstractNumericalMethod::ComputeForcesIncludingDamping 226ms 0.27% 0.44% 30799ms 37.25% NagaiHondaForce::AddForceContribution 4ms 0.0048% 0.45% 28984ms 35.05% AbstractCellBasedSimulation::UpdateCellPopulation 11447ms 13.84% 14.29% 18158ms 21.96% Cylindrical2dVertexMesh::GetVectorFromAtoB 2ms 0.0024% 14.29% 17945ms 21.70% VertexBasedCellPopulation::Update 1ms 0.0012% 14.29% 17849ms 21.59% MutableVertexMesh::ReMesh 85ms 0.1% 14.40% 12938ms 15.65% CellPropertyCollection::GetPropertiesType (inline) 47ms 0.057% 14.45% 12623ms 15.27% Cell::ReadyToDivide 38ms 0.046% 14.50% 12057ms 14.58% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2723ms 3.29% 17.79% 11427ms 13.82% __dynamic_cast 47ms 0.057% 17.85% 11335ms 13.71% AbstractCellProperty::IsSubType (inline) 281ms 0.34% 18.19% 11218ms 13.57% NagaiHondaForce::GetAdhesionParameter 353ms 0.43% 18.62% 10772ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 119ms 0.14% 18.76% 10038ms 12.14% SimpleWntCellCycleModel::UpdateCellCyclePhase 198ms 0.24% 19.00% 9666ms 11.69% boost::numeric::ublas::vector_assign (inline) 76ms 0.092% 19.09% 9332ms 11.29% VertexBasedCellPopulation::GetDampingConstant 125ms 0.15% 19.24% 9242ms 11.18% MutableVertexMesh::CheckForIntersections 62ms 0.075% 19.32% 8050ms 9.74% Cell::GetMutationState 46ms 0.056% 19.37% 7590ms 9.18% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.051% 19.42% 7528ms 9.10% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.03% 19.45% 7501ms 9.07% AbstractCellBasedSimulation::DoCellBirth 2263ms 2.74% 22.19% 7393ms 8.94% boost::numeric::ublas::indexing_vector_assign 860ms 1.04% 23.23% 7232ms 8.75% std::__new_allocator::allocate (inline) 269ms 0.33% 23.56% 7189ms 8.69% VertexMesh::GetNextEdgeGradientOfElementAtNode 874ms 1.06% 24.61% 7039ms 8.51% std::_Rb_tree::_M_erase 0 0% 24.61% 6873ms 8.31% std::_Rb_tree::_M_create_node (inline) 0 0% 24.61% 6835ms 8.27% std::allocator_traits::allocate (inline) 643ms 0.78% 25.39% 6733ms 8.14% VertexMesh::ElementIncludesPoint 21ms 0.025% 25.42% 6579ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 155ms 0.19% 25.60% 6461ms 7.81% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.60% 6447ms 7.80% std::_Rb_tree::_M_drop_node (inline) 608ms 0.74% 26.34% 6385ms 7.72% operator new 378ms 0.46% 26.80% 6339ms 7.67% VertexMesh::GetCentroidOfElement 0 0% 26.80% 6310ms 7.63% std::_Rb_tree::_M_get_node (inline) 182ms 0.22% 27.02% 6216ms 7.52% std::__new_allocator::deallocate (inline) 0 0% 27.02% 6205ms 7.50% std::allocator_traits::deallocate (inline) 3182ms 3.85% 30.86% 6202ms 7.50% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 30.86% 6162ms 7.45% std::_Rb_tree::_M_put_node (inline) 0 0% 30.86% 6138ms 7.42% std::set::~set (inline) 0 0% 30.86% 6104ms 7.38% std::_Rb_tree::_Alloc_node::operator() (inline) 1970ms 2.38% 33.25% 5812ms 7.03% __GI___libc_free 1190ms 1.44% 34.69% 5787ms 7.00% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2212ms 2.68% 37.36% 5626ms 6.80% __GI___libc_malloc 15ms 0.018% 37.38% 5374ms 6.50% MutableVertexMesh::RemoveDeletedNodesAndElements 184ms 0.22% 37.60% 5276ms 6.38% std::_Rb_tree::_Rb_tree (partial-inline) 339ms 0.41% 38.01% 5271ms 6.37% std::map::operator[] (partial-inline) 5258ms 6.36% 44.37% 5258ms 6.36% __strcmp_evex 15ms 0.018% 44.39% 4912ms 5.94% std::set::set (inline) 590ms 0.71% 45.10% 4891ms 5.91% std::_Rb_tree::_M_copy (inline) 113ms 0.14% 45.24% 4755ms 5.75% SimpleWntCellCycleModel::GetWntLevel 4691ms 5.67% 50.91% 4691ms 5.67% boost::numeric::ublas::c_vector::operator() 124ms 0.15% 51.06% 4542ms 5.49% WntConcentration::GetWntLevel 1939ms 2.34% 53.41% 4131ms 5.00% std::_Rb_tree::_M_lower_bound (inline) 552ms 0.67% 54.07% 4084ms 4.94% std::_Rb_tree::_M_clone_node (inline) 1532ms 1.85% 55.93% 4061ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 55.93% 4018ms 4.86% std::set::insert (inline) 3546ms 4.29% 60.22% 3827ms 4.63% _int_free 27ms 0.033% 60.25% 3814ms 4.61% Cell::GetCellProliferativeType 12ms 0.015% 60.26% 3733ms 4.51% MutableVertexMesh::RemoveDeletedNodes 25ms 0.03% 60.29% 3593ms 4.35% EdgeHelper::RemoveDeletedEdges 0 0% 60.29% 3524ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 388ms 0.47% 60.76% 3373ms 4.08% std::_Rb_tree::_M_insert_ (inline) 0 0% 60.76% 3368ms 4.07% std::_Rb_tree::lower_bound (inline) 0 0% 60.76% 3368ms 4.07% std::map::lower_bound (inline) 28ms 0.034% 60.80% 3362ms 4.07% EdgeHelper::UpdateEdgesMapKey 124ms 0.15% 60.95% 3357ms 4.06% MutableElement::ResetIndex 104ms 0.13% 61.07% 3262ms 3.94% std::set_intersection (inline) 158ms 0.19% 61.26% 3158ms 3.82% std::__set_intersection 83ms 0.1% 61.36% 3008ms 3.64% AbstractCellPopulation::GetCellUsingLocationIndex 2990ms 3.62% 64.98% 2990ms 3.62% boost::numeric::ublas::same_impl_ex 36ms 0.044% 65.02% 2744ms 3.32% Cell::SetCellProliferativeType 7ms 0.0085% 65.03% 2691ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 65.03% 2441ms 2.95% std::insert_iterator::operator= (inline) 1555ms 1.88% 66.91% 2272ms 2.75% _int_malloc 29ms 0.035% 66.95% 2218ms 2.68% Cell::GetCellData 621ms 0.75% 67.70% 2196ms 2.66% AbstractElement::GetNodeLocation 11ms 0.013% 67.71% 2121ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 44ms 0.053% 67.76% 2103ms 2.54% std::_Rb_tree::erase 151ms 0.18% 67.95% 2069ms 2.50% VertexMesh::GetAreaGradientOfElementAtNode 464ms 0.56% 68.51% 1997ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 68.51% 1986ms 2.40% boost::numeric::ublas::c_vector::operator-= (inline) 58ms 0.07% 68.58% 1965ms 2.38% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 166ms 0.2% 68.78% 1955ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.78% 1915ms 2.32% AbstractCellPopulation::WriteResultsToFiles 3ms 0.0036% 68.78% 1897ms 2.29% std::_Rb_tree::_M_insert_unique 0 0% 68.78% 1896ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 1811ms 2.19% 70.97% 1811ms 2.19% std::_Rb_tree::_S_right (inline) 2ms 0.0024% 70.97% 1707ms 2.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.97% 1707ms 2.06% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 64ms 0.077% 71.05% 1703ms 2.06% VertexMesh::GetVolumeOfElement 142ms 0.17% 71.22% 1599ms 1.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0036% 71.23% 1595ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 1595ms 1.93% 73.16% 1595ms 1.93% std::_Rb_tree_increment 0 0% 73.16% 1556ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0024% 73.16% 1552ms 1.88% VertexBasedCellPopulation::WriteCellVtkResultsToFile 27ms 0.033% 73.19% 1542ms 1.86% std::_Rb_tree::_M_emplace_hint_unique 56ms 0.068% 73.26% 1473ms 1.78% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.26% 1397ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 895ms 1.08% 74.34% 1369ms 1.66% std::_Rb_tree::equal_range (inline) 29ms 0.035% 74.38% 1226ms 1.48% VertexMesh::GetSurfaceAreaOfElement 21ms 0.025% 74.40% 1222ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.029% 74.43% 1143ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 120ms 0.15% 74.58% 1099ms 1.33% CellPropertyCollection::AddProperty 61ms 0.074% 74.65% 1068ms 1.29% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 43ms 0.052% 74.70% 1056ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 26ms 0.031% 74.73% 1052ms 1.27% CellPropertyCollection::HasProperty 0 0% 74.73% 1040ms 1.26% boost::numeric::ublas::norm_2 (inline) 32ms 0.039% 74.77% 1029ms 1.24% Node::RemoveElement 455ms 0.55% 75.32% 1028ms 1.24% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 75.32% 1027ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.32% 1021ms 1.23% tcache_get (inline) 1021ms 1.23% 76.56% 1021ms 1.23% tcache_get_n (inline) 7ms 0.0085% 76.57% 999ms 1.21% std::set::erase (inline) 0 0% 76.57% 993ms 1.20% Cell::HasCellProperty (inline) 3ms 0.0036% 76.57% 993ms 1.20% OffLatticeSimulation::ApplyBoundaries 38ms 0.046% 76.62% 891ms 1.08% std::less::operator() (inline) 0 0% 76.62% 876ms 1.06% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.006% 76.62% 876ms 1.06% boost::numeric::ublas::c_vector::swap (inline) 74ms 0.089% 76.71% 871ms 1.05% std::swap_ranges (inline) 10ms 0.012% 76.72% 857ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 686ms 0.83% 77.55% 853ms 1.03% std::operator< (inline) 9ms 0.011% 77.56% 850ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 52ms 0.063% 77.63% 844ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 840ms 1.02% 78.64% 840ms 1.02% [libchaste_cell_based.so] 144ms 0.17% 78.82% 832ms 1.01% boost::numeric::ublas::detail::equals 826ms 1% 79.81% 826ms 1% std::_Rb_tree_insert_and_rebalance 9ms 0.011% 79.83% 806ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 118ms 0.14% 79.97% 806ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 79.97% 806ms 0.97% boost::shared_ptr::~shared_ptr (inline) 801ms 0.97% 80.94% 801ms 0.97% std::swap (inline) 0 0% 80.94% 797ms 0.96% std::iter_swap (inline) 70ms 0.085% 81.02% 782ms 0.95% std::_Rb_tree::find (inline) 0 0% 81.02% 769ms 0.93% std::_Rb_tree::_Auto_node::_Auto_node (inline) 317ms 0.38% 81.41% 746ms 0.9% AbstractCellProperty::IsType (inline) 0 0% 81.41% 735ms 0.89% std::_Rb_tree::clear (inline) 0 0% 81.41% 726ms 0.88% std::map::clear (inline) 694ms 0.84% 82.24% 694ms 0.84% Node::rGetLocation 1ms 0.0012% 82.25% 673ms 0.81% VertexMeshWriter::MakeVtkMesh 0 0% 82.25% 667ms 0.81% boost::numeric::ublas::norm_inf (inline) 302ms 0.37% 82.61% 667ms 0.81% boost::numeric::ublas::vector_norm_inf::apply (inline) 64ms 0.077% 82.69% 665ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0012% 82.69% 657ms 0.79% std::map::find (inline) 626ms 0.76% 83.45% 653ms 0.79% boost::detail::sp_counted_base::release 637ms 0.77% 84.22% 637ms 0.77% [libstdc++.so.6.0.33] 109ms 0.13% 84.35% 616ms 0.74% boost::shared_ptr::shared_ptr (inline) 596ms 0.72% 85.07% 596ms 0.72% std::vector::size (inline) 183ms 0.22% 85.29% 594ms 0.72% std::__new_allocator::construct (inline) 0 0% 85.29% 594ms 0.72% std::allocator_traits::construct (inline) 0 0% 85.29% 591ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 17ms 0.021% 85.31% 586ms 0.71% MutableElement::RegisterWithEdges (inline) 328ms 0.4% 85.71% 585ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 16ms 0.019% 85.73% 582ms 0.7% Edge::AddElement 0 0% 85.73% 563ms 0.68% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.73% 563ms 0.68% std::_Rb_tree::_M_construct_node (inline) 559ms 0.68% 86.40% 559ms 0.68% [libchaste_mesh.so] 1ms 0.0012% 86.40% 524ms 0.63% std::_Vector_base::_M_allocate (inline) 491ms 0.59% 87.00% 507ms 0.61% boost::detail::shared_count::shared_count (inline) 222ms 0.27% 87.27% 483ms 0.58% Edge::GetMapIndex 2ms 0.0024% 87.27% 483ms 0.58% vtkPolygon::New 1ms 0.0012% 87.27% 481ms 0.58% vtkPolygon::vtkPolygon 0 0% 87.27% 479ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.021% 87.29% 479ms 0.58% std::_Rb_tree::_M_insert_node (inline) 94ms 0.11% 87.40% 458ms 0.55% MutableElement::GetNodeLocalIndex 23ms 0.028% 87.43% 453ms 0.55% MutableElement::RegisterWithNodes (inline) 5ms 0.006% 87.44% 444ms 0.54% std::vector::_M_default_append (inline) 22ms 0.027% 87.47% 432ms 0.52% Node::AddElement 429ms 0.52% 87.98% 429ms 0.52% CellProperty::GetTypeId 25ms 0.03% 88.01% 422ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.01% 422ms 0.51% boost::numeric::ublas::vector::vector (inline) 238ms 0.29% 88.30% 417ms 0.5% CellPropertyCollection::GetProperty 415ms 0.5% 88.80% 415ms 0.5% operator delete