File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 102571ms, 88.54% of 115841ms total Dropped 1078 nodes (cum <= 579.21ms) flat flat% sum% cum cum% 0 0% 0% 115594ms 99.79% __libc_start_call_main 0 0% 0% 115594ms 99.79% __libc_start_main_impl 0 0% 0% 115594ms 99.79% _start 0 0% 0% 115576ms 99.77% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 115576ms 99.77% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 115576ms 99.77% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 115576ms 99.77% main 0 0% 0% 115545ms 99.74% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 115545ms 99.74% CxxTest::TestRunner::runTest (inline) 0 0% 0% 115545ms 99.74% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0043% 0.0043% 115538ms 99.74% AbstractCellBasedSimulation::Solve 15ms 0.013% 0.017% 61237ms 52.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 28ms 0.024% 0.041% 57417ms 49.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 131ms 0.11% 0.15% 56429ms 48.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 601ms 0.52% 0.67% 44757ms 38.64% NagaiHondaForce::AddForceContribution 1ms 0.00086% 0.67% 39712ms 34.28% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0017% 0.68% 23371ms 20.18% VertexBasedCellPopulation::Update 1ms 0.00086% 0.68% 23224ms 20.05% MutableVertexMesh::ReMesh 10162ms 8.77% 9.45% 20334ms 17.55% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.07% 9.52% 20140ms 17.39% Cell::ReadyToDivide 37ms 0.032% 9.55% 18967ms 16.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 389ms 0.34% 9.89% 17966ms 15.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 118ms 0.1% 9.99% 17212ms 14.86% NagaiHondaForce::GetAdhesionParameter 120ms 0.1% 10.09% 16274ms 14.05% SimpleWntCellCycleModel::UpdateCellCyclePhase 537ms 0.46% 10.56% 15991ms 13.80% boost::numeric::ublas::vector_assign (inline) 1265ms 1.09% 11.65% 14675ms 12.67% std::__new_allocator::allocate (inline) 52ms 0.045% 11.69% 14226ms 12.28% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.69% 13941ms 12.03% std::allocator_traits::allocate (inline) 0 0% 11.69% 13607ms 11.75% std::_Rb_tree::_M_create_node (inline) 902ms 0.78% 12.47% 13293ms 11.48% operator new 0 0% 12.47% 13159ms 11.36% std::_Rb_tree::_M_get_node (inline) 51ms 0.044% 12.52% 12010ms 10.37% AbstractTargetAreaModifier::UpdateTargetAreas 43ms 0.037% 12.55% 11916ms 10.29% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 12.55% 11777ms 10.17% std::_Rb_tree::_Alloc_node::operator() (inline) 178ms 0.15% 12.71% 11761ms 10.15% AbstractCellProperty::IsSubType (inline) 4131ms 3.57% 16.27% 11756ms 10.15% __GI___libc_malloc 6ms 0.0052% 16.28% 11661ms 10.07% AbstractCellBasedSimulation::DoCellBirth 2918ms 2.52% 18.80% 11636ms 10.04% boost::numeric::ublas::indexing_vector_assign 3415ms 2.95% 21.74% 11565ms 9.98% __dynamic_cast 119ms 0.1% 21.85% 11203ms 9.67% VertexBasedCellPopulation::GetDampingConstant 150ms 0.13% 21.98% 10731ms 9.26% MutableVertexMesh::CheckForIntersections 1197ms 1.03% 23.01% 9607ms 8.29% std::_Rb_tree::_M_erase 0 0% 23.01% 9547ms 8.24% std::_Rb_tree::_M_drop_node (inline) 537ms 0.46% 23.47% 9545ms 8.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 64ms 0.055% 23.53% 9306ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 378ms 0.33% 23.86% 8958ms 7.73% std::_Rb_tree::~_Rb_tree (inline) 829ms 0.72% 24.57% 8956ms 7.73% VertexMesh::GetCentroidOfElement 72ms 0.062% 24.63% 8856ms 7.64% Cell::GetMutationState 244ms 0.21% 24.84% 8772ms 7.57% std::__new_allocator::deallocate (inline) 0 0% 24.84% 8764ms 7.57% std::allocator_traits::deallocate (inline) 2124ms 1.83% 26.68% 8685ms 7.50% __GI___libc_free 0 0% 26.68% 8672ms 7.49% std::_Rb_tree::_M_put_node (inline) 0 0% 26.68% 8535ms 7.37% std::set::~set (inline) 115ms 0.099% 26.78% 8504ms 7.34% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.018% 26.79% 8411ms 7.26% MutableVertexMesh::RemoveDeletedNodesAndElements 697ms 0.6% 27.40% 8194ms 7.07% std::_Rb_tree::_M_copy (inline) 698ms 0.6% 28.00% 8071ms 6.97% std::map::operator[] (partial-inline) 586ms 0.51% 28.50% 7983ms 6.89% VertexMesh::ElementIncludesPoint 0 0% 28.50% 7884ms 6.81% std::set::insert (inline) 21ms 0.018% 28.52% 7777ms 6.71% std::set::set (inline) 7330ms 6.33% 34.85% 7330ms 6.33% boost::numeric::ublas::c_vector::operator() 159ms 0.14% 34.99% 7283ms 6.29% SimpleWntCellCycleModel::GetWntLevel 956ms 0.83% 35.81% 7183ms 6.20% std::_Rb_tree::_M_clone_node (inline) 893ms 0.77% 36.58% 6989ms 6.03% std::_Rb_tree::_M_insert_ (inline) 137ms 0.12% 36.70% 6864ms 5.93% WntConcentration::GetWntLevel 5616ms 4.85% 41.55% 6300ms 5.44% _int_free 41ms 0.035% 41.59% 6087ms 5.25% std::set_intersection (inline) 6075ms 5.24% 46.83% 6075ms 5.24% __strcmp_evex 186ms 0.16% 46.99% 6046ms 5.22% std::__set_intersection 945ms 0.82% 47.81% 5954ms 5.14% AbstractMesh::GetDistanceBetweenNodes 21ms 0.018% 47.82% 5594ms 4.83% MutableVertexMesh::RemoveDeletedNodes 4248ms 3.67% 51.49% 5476ms 4.73% _int_malloc 81ms 0.07% 51.56% 5439ms 4.70% EdgeHelper::RemoveDeletedEdges 963ms 0.83% 52.39% 5330ms 4.60% boost::numeric::ublas::c_vector::operator[] (inline) 173ms 0.15% 52.54% 5264ms 4.54% MutableElement::ResetIndex 2020ms 1.74% 54.29% 5263ms 4.54% std::_Rb_tree::_M_lower_bound (inline) 2551ms 2.20% 56.49% 5238ms 4.52% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.022% 56.51% 5138ms 4.44% EdgeHelper::UpdateEdgesMapKey 5114ms 4.41% 60.92% 5114ms 4.41% boost::numeric::ublas::same_impl_ex 0 0% 60.92% 4908ms 4.24% std::insert_iterator::operator= (inline) 43ms 0.037% 60.96% 4791ms 4.14% Cell::GetCellProliferativeType 0 0% 60.96% 4687ms 4.05% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0017% 60.96% 4670ms 4.03% AbstractCellBasedSimulation::DoCellRemoval (inline) 90ms 0.078% 61.04% 4472ms 3.86% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 61.04% 4448ms 3.84% std::_Rb_tree::lower_bound (inline) 0 0% 61.04% 4448ms 3.84% std::map::lower_bound (inline) 867ms 0.75% 61.79% 3775ms 3.26% AbstractElement::GetNodeLocation 162ms 0.14% 61.93% 3774ms 3.26% AbstractCellProperty::IsType (inline) 92ms 0.079% 62.01% 3731ms 3.22% Cell::SetCellProliferativeType 42ms 0.036% 62.05% 3539ms 3.06% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 838ms 0.72% 62.77% 3512ms 3.03% boost::numeric::ublas::vector_binary::size (inline) 0 0% 62.77% 3333ms 2.88% boost::numeric::ublas::c_vector::assign (inline) 3316ms 2.86% 65.63% 3316ms 2.86% [libchaste_cell_based.so] 60ms 0.052% 65.68% 3223ms 2.78% std::_Rb_tree::erase 0 0% 65.68% 3197ms 2.76% std::_Rb_tree::_M_insert_unique 37ms 0.032% 65.72% 2871ms 2.48% std::_Rb_tree::_M_emplace_hint_unique 373ms 0.32% 66.04% 2842ms 2.45% VertexMesh::GetAreaGradientOfElementAtNode 376ms 0.32% 66.36% 2788ms 2.41% std::_Rb_tree_const_iterator::operator++ (inline) 169ms 0.15% 66.51% 2770ms 2.39% boost::detail::shared_count::~shared_count (inline) 0 0% 66.51% 2770ms 2.39% boost::shared_ptr::~shared_ptr (inline) 2681ms 2.31% 68.82% 2681ms 2.31% std::_Rb_tree::_S_right (inline) 6ms 0.0052% 68.83% 2658ms 2.29% AbstractCellPopulation::Iterator::operator++ (inline) 195ms 0.17% 69.00% 2650ms 2.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 52ms 0.045% 69.04% 2632ms 2.27% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.0078% 69.05% 2614ms 2.26% Cell::GetCellData 2443ms 2.11% 71.16% 2542ms 2.19% boost::detail::sp_counted_base::release 0 0% 71.16% 2537ms 2.19% AbstractCellPopulation::WriteResultsToFiles 44ms 0.038% 71.20% 2518ms 2.17% CellPropertyCollection::HasProperty 0 0% 71.20% 2448ms 2.11% Cell::HasCellProperty (inline) 0 0% 71.20% 2443ms 2.11% boost::numeric::ublas::c_vector::operator-= (inline) 651ms 0.56% 71.76% 2436ms 2.10% AbstractCellProperty::IsSame 2369ms 2.05% 73.80% 2369ms 2.05% [libchaste_mesh.so] 118ms 0.1% 73.90% 2140ms 1.85% VertexMesh::GetVolumeOfElement 0 0% 73.90% 2109ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0017% 73.91% 2097ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 33ms 0.028% 73.93% 2028ms 1.75% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.00086% 73.93% 1890ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 0 0% 73.93% 1830ms 1.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.00086% 73.94% 1828ms 1.58% tcache_get (inline) 1827ms 1.58% 75.51% 1827ms 1.58% tcache_get_n (inline) 254ms 0.22% 75.73% 1815ms 1.57% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1791ms 1.55% 77.28% 1791ms 1.55% std::_Rb_tree_increment 16ms 0.014% 77.29% 1788ms 1.54% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.29% 1788ms 1.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 451ms 0.39% 77.68% 1785ms 1.54% std::type_info::operator== (inline) 1069ms 0.92% 78.60% 1758ms 1.52% std::_Rb_tree::equal_range (inline) 138ms 0.12% 78.72% 1730ms 1.49% CellPropertyCollection::AddProperty 0 0% 78.72% 1672ms 1.44% boost::numeric::ublas::vector_binary::operator() (inline) 84ms 0.073% 78.80% 1666ms 1.44% std::_Rb_tree::_M_erase_aux (partial-inline) 123ms 0.11% 78.90% 1664ms 1.44% boost::numeric::ublas::vector_reference::operator() (inline) 84ms 0.073% 78.97% 1570ms 1.36% MutableVertexMesh::CheckForSwapsFromShortEdges 85ms 0.073% 79.05% 1505ms 1.30% AbstractCellPopulation::GetLocationIndexUsingCell 1467ms 1.27% 80.31% 1467ms 1.27% [libstdc++.so.6.0.33] 99ms 0.085% 80.40% 1461ms 1.26% VertexMesh::GetSurfaceAreaOfElement 34ms 0.029% 80.43% 1452ms 1.25% Node::RemoveElement 9ms 0.0078% 80.44% 1418ms 1.22% std::set::erase (inline) 3ms 0.0026% 80.44% 1401ms 1.21% OffLatticeSimulation::ApplyBoundaries 87ms 0.075% 80.51% 1265ms 1.09% CellPropertyRegistry::Get 38ms 0.033% 80.55% 1221ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 48ms 0.041% 80.59% 1145ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 1130ms 0.98% 81.56% 1130ms 0.98% Node::rGetLocation 13ms 0.011% 81.58% 1124ms 0.97% MutableElement::RegisterWithEdges (inline) 30ms 0.026% 81.60% 1120ms 0.97% Edge::AddElement 13ms 0.011% 81.61% 1099ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 217ms 0.19% 81.80% 1072ms 0.93% boost::numeric::ublas::detail::equals 0 0% 81.80% 1031ms 0.89% std::_Rb_tree::clear (inline) 0 0% 81.80% 1015ms 0.88% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.80% 1011ms 0.87% std::map::clear (inline) 615ms 0.53% 82.33% 1010ms 0.87% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 996ms 0.86% 83.19% 996ms 0.86% std::_Rb_tree_insert_and_rebalance 4ms 0.0035% 83.19% 993ms 0.86% VertexMeshWriter::MakeVtkMesh 0 0% 83.19% 970ms 0.84% boost::numeric::ublas::norm_2 (inline) 224ms 0.19% 83.39% 938ms 0.81% boost::numeric::ublas::vector_norm_2::apply 0 0% 83.39% 878ms 0.76% std::__new_allocator::destroy (inline) 0 0% 83.39% 878ms 0.76% std::allocator_traits::destroy (inline) 0 0% 83.39% 875ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 44ms 0.038% 83.43% 870ms 0.75% std::less::operator() (inline) 86ms 0.074% 83.50% 838ms 0.72% std::_Rb_tree::find (inline) 629ms 0.54% 84.04% 826ms 0.71% std::operator< (inline) 0 0% 84.04% 821ms 0.71% boost::numeric::ublas::norm_inf (inline) 423ms 0.37% 84.41% 821ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 628ms 0.54% 84.95% 806ms 0.7% CellPropertyCollection::GetProperty 0 0% 84.95% 805ms 0.69% boost::numeric::ublas::c_vector::assign_temporary (inline) 15ms 0.013% 84.96% 805ms 0.69% boost::numeric::ublas::c_vector::swap (inline) 792ms 0.68% 85.65% 792ms 0.68% tcache_put (inline) 85ms 0.073% 85.72% 790ms 0.68% std::swap_ranges (inline) 0 0% 85.72% 788ms 0.68% std::map::map (inline) 87ms 0.075% 85.80% 786ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 783ms 0.68% 86.47% 783ms 0.68% std::vector::size (inline) 47ms 0.041% 86.51% 781ms 0.67% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.51% 781ms 0.67% boost::numeric::ublas::vector::vector (inline) 0 0% 86.51% 776ms 0.67% std::_Vector_base::_M_allocate (inline) 124ms 0.11% 86.62% 762ms 0.66% MutableElement::GetNodeLocalIndex 0 0% 86.62% 705ms 0.61% std::iter_swap (inline) 705ms 0.61% 87.23% 705ms 0.61% std::swap (inline) 0 0% 87.23% 694ms 0.6% vtkPolygon::New 2ms 0.0017% 87.23% 693ms 0.6% vtkPolygon::vtkPolygon 0 0% 87.23% 685ms 0.59% std::map::find (inline) 22ms 0.019% 87.25% 660ms 0.57% MutableElement::RegisterWithNodes (inline) 28ms 0.024% 87.27% 628ms 0.54% Node::AddElement 7ms 0.006% 87.28% 624ms 0.54% std::vector::_M_default_append (inline) 610ms 0.53% 87.80% 610ms 0.53% Node::GetIndex 0 0% 87.80% 607ms 0.52% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.016% 87.82% 607ms 0.52% std::_Rb_tree::_M_insert_node (inline) 501ms 0.43% 88.25% 600ms 0.52% malloc_consolidate 337ms 0.29% 88.54% 595ms 0.51% Edge::GetMapIndex