File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95787ms, 88.49% of 108249ms total Dropped 1122 nodes (cum <= 541.25ms) flat flat% sum% cum cum% 0 0% 0% 107777ms 99.56% __libc_start_call_main 0 0% 0% 107777ms 99.56% __libc_start_main_impl 0 0% 0% 107777ms 99.56% _start 0 0% 0% 107757ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107757ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107757ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107757ms 99.55% main 0 0% 0% 107717ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107717ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107717ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107710ms 99.50% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.013% 55924ms 51.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.016% 0.029% 52793ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 115ms 0.11% 0.13% 51282ms 47.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 338ms 0.31% 0.45% 39523ms 36.51% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.45% 38744ms 35.79% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.45% 23873ms 22.05% VertexBasedCellPopulation::Update 2ms 0.0018% 0.45% 23747ms 21.94% MutableVertexMesh::ReMesh 14501ms 13.40% 13.85% 22880ms 21.14% Cylindrical2dVertexMesh::GetVectorFromAtoB 90ms 0.083% 13.93% 17662ms 16.32% Cell::ReadyToDivide 77ms 0.071% 14.00% 16308ms 15.07% AbstractPhaseBasedCellCycleModel::ReadyToDivide 378ms 0.35% 14.35% 14654ms 13.54% NagaiHondaForce::GetAdhesionParameter 406ms 0.38% 14.73% 14110ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 150ms 0.14% 14.86% 13927ms 12.87% CellPropertyCollection::GetPropertiesType (inline) 107ms 0.099% 14.96% 13918ms 12.86% SimpleWntCellCycleModel::UpdateCellCyclePhase 378ms 0.35% 15.31% 12552ms 11.60% boost::numeric::ublas::vector_assign (inline) 117ms 0.11% 15.42% 12086ms 11.16% MutableVertexMesh::CheckForIntersections 3340ms 3.09% 18.51% 11515ms 10.64% __dynamic_cast 81ms 0.075% 18.58% 11398ms 10.53% AbstractCellProperty::IsSubType (inline) 65ms 0.06% 18.64% 11263ms 10.40% VertexBasedCellPopulation::GetDampingConstant 66ms 0.061% 18.70% 10647ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.045% 18.75% 10556ms 9.75% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 18.77% 10368ms 9.58% AbstractCellBasedSimulation::DoCellBirth 1289ms 1.19% 19.96% 9849ms 9.10% std::__new_allocator::allocate (inline) 2667ms 2.46% 22.42% 9372ms 8.66% boost::numeric::ublas::indexing_vector_assign 0 0% 22.42% 9312ms 8.60% std::_Rb_tree::_M_create_node (inline) 0 0% 22.42% 9310ms 8.60% std::allocator_traits::allocate (inline) 824ms 0.76% 23.18% 9042ms 8.35% VertexMesh::ElementIncludesPoint 1308ms 1.21% 24.39% 8995ms 8.31% std::_Rb_tree::_M_erase 93ms 0.086% 24.48% 8701ms 8.04% Cell::GetMutationState 791ms 0.73% 25.21% 8699ms 8.04% operator new 0 0% 25.21% 8698ms 8.04% std::_Rb_tree::_M_get_node (inline) 333ms 0.31% 25.52% 8687ms 8.03% VertexMesh::GetNextEdgeGradientOfElementAtNode 28ms 0.026% 25.54% 8578ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.54% 8212ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 212ms 0.2% 25.74% 8177ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 466ms 0.43% 26.17% 8107ms 7.49% VertexMesh::GetCentroidOfElement 0 0% 26.17% 8061ms 7.45% std::_Rb_tree::_M_drop_node (inline) 271ms 0.25% 26.42% 7859ms 7.26% std::__new_allocator::deallocate (inline) 0 0% 26.42% 7839ms 7.24% std::allocator_traits::deallocate (inline) 0 0% 26.42% 7757ms 7.17% std::_Rb_tree::_M_put_node (inline) 0 0% 26.42% 7745ms 7.15% std::set::~set (inline) 3059ms 2.83% 29.24% 7723ms 7.13% __GI___libc_malloc 2964ms 2.74% 31.98% 7640ms 7.06% __GI___libc_free 18ms 0.017% 32.00% 7287ms 6.73% MutableVertexMesh::RemoveDeletedNodesAndElements 427ms 0.39% 32.39% 7238ms 6.69% std::map::operator[] (partial-inline) 1267ms 1.17% 33.56% 7147ms 6.60% AbstractMesh::GetDistanceBetweenNodes 151ms 0.14% 33.70% 6775ms 6.26% std::_Rb_tree::_Rb_tree (partial-inline) 6740ms 6.23% 39.93% 6740ms 6.23% __strcmp_avx2 674ms 0.62% 40.55% 6416ms 5.93% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 40.57% 6383ms 5.90% std::set::set (inline) 83ms 0.077% 40.64% 6187ms 5.72% SimpleWntCellCycleModel::GetWntLevel 6123ms 5.66% 46.30% 6123ms 5.66% boost::numeric::ublas::c_vector::operator() 160ms 0.15% 46.45% 6032ms 5.57% WntConcentration::GetWntLevel 2766ms 2.56% 49.00% 5743ms 5.31% __cxxabiv1::__si_class_type_info::__do_dyncast 2415ms 2.23% 51.23% 5717ms 5.28% std::_Rb_tree::_M_lower_bound (inline) 730ms 0.67% 51.91% 5480ms 5.06% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.91% 5341ms 4.93% std::set::insert (inline) 15ms 0.014% 51.92% 5213ms 4.82% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 51.95% 5069ms 4.68% EdgeHelper::RemoveDeletedEdges 1503ms 1.39% 53.34% 4891ms 4.52% boost::numeric::ublas::c_vector::operator[] (inline) 27ms 0.025% 53.37% 4833ms 4.46% EdgeHelper::UpdateEdgesMapKey 4347ms 4.02% 57.38% 4670ms 4.31% _int_free 0 0% 57.38% 4650ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 57.38% 4650ms 4.30% std::map::lower_bound (inline) 203ms 0.19% 57.57% 4544ms 4.20% MutableElement::ResetIndex 1ms 0.00092% 57.57% 4490ms 4.15% AbstractCellBasedSimulation::DoCellRemoval (inline) 487ms 0.45% 58.02% 4487ms 4.15% std::_Rb_tree::_M_insert_ (inline) 45ms 0.042% 58.06% 4470ms 4.13% std::set_intersection (inline) 270ms 0.25% 58.31% 4425ms 4.09% std::__set_intersection 67ms 0.062% 58.37% 4120ms 3.81% AbstractCellProperty::IsType (inline) 53ms 0.049% 58.42% 3974ms 3.67% Cell::GetCellProliferativeType 122ms 0.11% 58.54% 3968ms 3.67% AbstractCellPopulation::GetCellUsingLocationIndex 3918ms 3.62% 62.15% 3918ms 3.62% boost::numeric::ublas::same_impl_ex 11ms 0.01% 62.17% 3479ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.17% 3233ms 2.99% std::insert_iterator::operator= (inline) 838ms 0.77% 62.94% 3229ms 2.98% AbstractElement::GetNodeLocation 41ms 0.038% 62.98% 3089ms 2.85% Cell::SetCellProliferativeType 2139ms 1.98% 64.95% 3004ms 2.78% _int_malloc 856ms 0.79% 65.74% 2995ms 2.77% AbstractCellProperty::IsSame 52ms 0.048% 65.79% 2950ms 2.73% CellPropertyCollection::HasProperty 46ms 0.042% 65.83% 2872ms 2.65% std::_Rb_tree::erase 0 0% 65.83% 2861ms 2.64% Cell::HasCellProperty (inline) 398ms 0.37% 66.20% 2851ms 2.63% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0018% 66.20% 2823ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 634ms 0.59% 66.79% 2812ms 2.60% boost::numeric::ublas::vector_binary::size (inline) 2731ms 2.52% 69.31% 2731ms 2.52% std::_Rb_tree::_S_right (inline) 237ms 0.22% 69.53% 2533ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 21ms 0.019% 69.55% 2526ms 2.33% Cell::GetCellData 3ms 0.0028% 69.55% 2518ms 2.33% std::_Rb_tree::_M_insert_unique 0 0% 69.55% 2490ms 2.30% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.55% 2375ms 2.19% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.55% 2366ms 2.19% AbstractCellPopulation::WriteResultsToFiles 108ms 0.1% 69.65% 2293ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 103ms 0.095% 69.75% 2273ms 2.10% VertexMesh::GetVolumeOfElement 2260ms 2.09% 71.84% 2260ms 2.09% std::_Rb_tree_increment 4ms 0.0037% 71.84% 2167ms 2.00% AbstractCellPopulation::Iterator::operator++ (inline) 212ms 0.2% 72.04% 2159ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 465ms 0.43% 72.47% 2139ms 1.98% std::type_info::operator== (inline) 35ms 0.032% 72.50% 2119ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.50% 1935ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.50% 1926ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1304ms 1.20% 73.70% 1912ms 1.77% std::_Rb_tree::equal_range (inline) 68ms 0.063% 73.77% 1852ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 73.77% 1833ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.77% 1833ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 32ms 0.03% 73.80% 1735ms 1.60% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.80% 1734ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 29ms 0.027% 73.82% 1685ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 52ms 0.048% 73.87% 1621ms 1.50% Node::RemoveElement 20ms 0.018% 73.89% 1579ms 1.46% std::set::erase (inline) 163ms 0.15% 74.04% 1522ms 1.41% CellPropertyCollection::AddProperty 113ms 0.1% 74.14% 1463ms 1.35% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.14% 1459ms 1.35% tcache_get (inline) 1459ms 1.35% 75.49% 1459ms 1.35% tcache_get_n (inline) 26ms 0.024% 75.52% 1457ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 67ms 0.062% 75.58% 1399ms 1.29% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.58% 1395ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.0028% 75.58% 1253ms 1.16% OffLatticeSimulation::ApplyBoundaries 76ms 0.07% 75.65% 1221ms 1.13% std::less::operator() (inline) 28ms 0.026% 75.68% 1177ms 1.09% CellPropertyRegistry::Get 1150ms 1.06% 76.74% 1150ms 1.06% std::_Rb_tree_insert_and_rebalance 0 0% 76.74% 1148ms 1.06% boost::numeric::ublas::norm_2 (inline) 946ms 0.87% 77.61% 1145ms 1.06% std::operator< (inline) 1140ms 1.05% 78.67% 1140ms 1.05% Node::rGetLocation 534ms 0.49% 79.16% 1139ms 1.05% boost::numeric::ublas::vector_norm_2::apply 1130ms 1.04% 80.20% 1130ms 1.04% [libchaste_cell_based.so] 0 0% 80.20% 1100ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 69ms 0.064% 80.27% 1097ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 13ms 0.012% 80.28% 1072ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 103ms 0.095% 80.37% 1051ms 0.97% std::_Rb_tree::find (inline) 0 0% 80.37% 1032ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.37% 1015ms 0.94% std::map::clear (inline) 124ms 0.11% 80.49% 1004ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.49% 1004ms 0.93% boost::shared_ptr::~shared_ptr (inline) 979ms 0.9% 81.39% 979ms 0.9% std::vector::size (inline) 6ms 0.0055% 81.40% 962ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 384ms 0.35% 81.75% 928ms 0.86% Edge::GetMapIndex 924ms 0.85% 82.61% 924ms 0.85% [libchaste_mesh.so] 16ms 0.015% 82.62% 917ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 155ms 0.14% 82.76% 891ms 0.82% boost::numeric::ublas::detail::equals 0 0% 82.76% 875ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0028% 82.77% 875ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.073% 82.84% 872ms 0.81% std::swap_ranges (inline) 1ms 0.00092% 82.84% 871ms 0.8% std::map::find (inline) 0 0% 82.84% 846ms 0.78% VertexMeshWriter::MakeVtkMesh 838ms 0.77% 83.62% 842ms 0.78% boost::detail::sp_counted_base::release 98ms 0.091% 83.71% 821ms 0.76% MutableElement::GetNodeLocalIndex 119ms 0.11% 83.82% 803ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 794ms 0.73% 84.55% 794ms 0.73% std::swap (inline) 0 0% 84.55% 793ms 0.73% std::iter_swap (inline) 435ms 0.4% 84.95% 724ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 32ms 0.03% 84.98% 715ms 0.66% Edge::AddElement 19ms 0.018% 85.00% 711ms 0.66% MutableElement::RegisterWithEdges (inline) 691ms 0.64% 85.64% 691ms 0.64% Node::GetIndex 0 0% 85.64% 691ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 85.65% 691ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.65% 688ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 123ms 0.11% 85.77% 687ms 0.63% boost::shared_ptr::shared_ptr (inline) 0 0% 85.77% 685ms 0.63% boost::numeric::ublas::norm_inf (inline) 373ms 0.34% 86.11% 685ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 19ms 0.018% 86.13% 677ms 0.63% AbstractNumericalMethod::DetectStepSizeExceptions 124ms 0.11% 86.24% 669ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.24% 669ms 0.62% std::allocator_traits::construct (inline) 89ms 0.082% 86.33% 658ms 0.61% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.33% 617ms 0.57% vtkPolygon::New 1ms 0.00092% 86.33% 616ms 0.57% vtkPolygon::vtkPolygon 0 0% 86.33% 614ms 0.57% std::_Rb_tree::_M_construct_node (inline) 4ms 0.0037% 86.33% 613ms 0.57% std::_Vector_base::_M_allocate (inline) 28ms 0.026% 86.36% 599ms 0.55% MutableElement::RegisterWithNodes (inline) 582ms 0.54% 86.90% 582ms 0.54% operator delete 26ms 0.024% 86.92% 574ms 0.53% Node::AddElement 568ms 0.52% 87.44% 568ms 0.52% boost::shared_ptr::operator-> (inline) 27ms 0.025% 87.47% 566ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.47% 566ms 0.52% boost::numeric::ublas::vector::vector (inline) 541ms 0.5% 87.97% 564ms 0.52% boost::detail::shared_count::shared_count (inline) 562ms 0.52% 88.49% 562ms 0.52% [libstdc++.so.6.0.33]