File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96004ms, 87.38% of 109865ms total Dropped 1124 nodes (cum <= 549.33ms) flat flat% sum% cum cum% 0 0% 0% 109512ms 99.68% __libc_start_call_main 0 0% 0% 109512ms 99.68% __libc_start_main_impl 0 0% 0% 109512ms 99.68% _start 0 0% 0% 109490ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109490ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109490ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109490ms 99.66% main 0 0% 0% 109449ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109449ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109449ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 109441ms 99.61% AbstractCellBasedSimulation::Solve 24ms 0.022% 0.027% 57466ms 52.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.0073% 0.035% 54267ms 49.39% ForwardEulerNumericalMethod::UpdateAllNodePositions 143ms 0.13% 0.16% 53210ms 48.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 326ms 0.3% 0.46% 41331ms 37.62% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.46% 38828ms 35.34% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.46% 23888ms 21.74% VertexBasedCellPopulation::Update 0 0% 0.46% 23754ms 21.62% MutableVertexMesh::ReMesh 14855ms 13.52% 13.98% 23585ms 21.47% Cylindrical2dVertexMesh::GetVectorFromAtoB 97ms 0.088% 14.07% 17723ms 16.13% Cell::ReadyToDivide 46ms 0.042% 14.11% 16390ms 14.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 329ms 0.3% 14.41% 15043ms 13.69% NagaiHondaForce::GetAdhesionParameter 165ms 0.15% 14.56% 14101ms 12.83% SimpleWntCellCycleModel::UpdateCellCyclePhase 430ms 0.39% 14.96% 14092ms 12.83% boost::numeric::ublas::c_vector::c_vector (partial-inline) 107ms 0.097% 15.05% 13515ms 12.30% CellPropertyCollection::GetPropertiesType (inline) 298ms 0.27% 15.32% 12652ms 11.52% boost::numeric::ublas::vector_assign (inline) 138ms 0.13% 15.45% 11784ms 10.73% MutableVertexMesh::CheckForIntersections 3403ms 3.10% 18.55% 11445ms 10.42% __dynamic_cast 74ms 0.067% 18.61% 11313ms 10.30% AbstractCellProperty::IsSubType (inline) 84ms 0.076% 18.69% 11270ms 10.26% VertexBasedCellPopulation::GetDampingConstant 62ms 0.056% 18.75% 10685ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.038% 18.79% 10593ms 9.64% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.025% 18.81% 10324ms 9.40% AbstractCellBasedSimulation::DoCellBirth 1231ms 1.12% 19.93% 9975ms 9.08% std::__new_allocator::allocate (inline) 2858ms 2.60% 22.53% 9823ms 8.94% boost::numeric::ublas::indexing_vector_assign 391ms 0.36% 22.89% 9737ms 8.86% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.89% 9504ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 22.89% 9433ms 8.59% std::allocator_traits::allocate (inline) 1273ms 1.16% 24.05% 9191ms 8.37% std::_Rb_tree::_M_erase 33ms 0.03% 24.08% 8827ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 770ms 0.7% 24.78% 8771ms 7.98% operator new 0 0% 24.78% 8747ms 7.96% std::_Rb_tree::_M_get_node (inline) 792ms 0.72% 25.50% 8631ms 7.86% VertexMesh::ElementIncludesPoint 82ms 0.075% 25.57% 8585ms 7.81% Cell::GetMutationState 0 0% 25.57% 8349ms 7.60% std::_Rb_tree::_Alloc_node::operator() (inline) 178ms 0.16% 25.74% 8314ms 7.57% std::_Rb_tree::~_Rb_tree (inline) 452ms 0.41% 26.15% 8288ms 7.54% VertexMesh::GetCentroidOfElement 0 0% 26.15% 8267ms 7.52% std::_Rb_tree::_M_drop_node (inline) 232ms 0.21% 26.36% 7976ms 7.26% std::__new_allocator::deallocate (inline) 0 0% 26.36% 7970ms 7.25% std::allocator_traits::deallocate (inline) 0 0% 26.36% 7924ms 7.21% std::set::~set (inline) 0 0% 26.36% 7920ms 7.21% std::_Rb_tree::_M_put_node (inline) 1609ms 1.46% 27.82% 7800ms 7.10% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2926ms 2.66% 30.49% 7776ms 7.08% __GI___libc_malloc 487ms 0.44% 30.93% 7693ms 7.00% std::map::operator[] (partial-inline) 15ms 0.014% 30.94% 7577ms 6.90% MutableVertexMesh::RemoveDeletedNodesAndElements 2310ms 2.10% 33.05% 7464ms 6.79% __GI___libc_free 188ms 0.17% 33.22% 7077ms 6.44% std::_Rb_tree::_Rb_tree (partial-inline) 786ms 0.72% 33.93% 6633ms 6.04% std::_Rb_tree::_M_copy (inline) 26ms 0.024% 33.96% 6616ms 6.02% std::set::set (inline) 135ms 0.12% 34.08% 6438ms 5.86% SimpleWntCellCycleModel::GetWntLevel 6265ms 5.70% 39.78% 6265ms 5.70% __strcmp_avx2 170ms 0.15% 39.94% 6182ms 5.63% WntConcentration::GetWntLevel 6012ms 5.47% 45.41% 6012ms 5.47% boost::numeric::ublas::c_vector::operator() 2537ms 2.31% 47.72% 6012ms 5.47% std::_Rb_tree::_M_lower_bound (inline) 2966ms 2.70% 50.42% 5632ms 5.13% __cxxabiv1::__si_class_type_info::__do_dyncast 756ms 0.69% 51.11% 5620ms 5.12% std::_Rb_tree::_M_clone_node (inline) 23ms 0.021% 51.13% 5466ms 4.98% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.13% 5431ms 4.94% std::set::insert (inline) 27ms 0.025% 51.15% 5248ms 4.78% EdgeHelper::RemoveDeletedEdges 2017ms 1.84% 52.99% 5209ms 4.74% boost::numeric::ublas::c_vector::operator[] (inline) 4715ms 4.29% 57.28% 5136ms 4.67% _int_free 0 0% 57.28% 4986ms 4.54% std::_Rb_tree::lower_bound (inline) 0 0% 57.28% 4986ms 4.54% std::map::lower_bound (inline) 34ms 0.031% 57.31% 4945ms 4.50% EdgeHelper::UpdateEdgesMapKey 568ms 0.52% 57.83% 4620ms 4.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.83% 4606ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 219ms 0.2% 58.03% 4569ms 4.16% std::set_intersection (inline) 190ms 0.17% 58.20% 4523ms 4.12% MutableElement::ResetIndex 246ms 0.22% 58.42% 4350ms 3.96% std::__set_intersection 130ms 0.12% 58.54% 4251ms 3.87% AbstractCellPopulation::GetCellUsingLocationIndex 4064ms 3.70% 62.24% 4064ms 3.70% boost::numeric::ublas::same_impl_ex 50ms 0.046% 62.29% 3855ms 3.51% AbstractCellProperty::IsType (inline) 44ms 0.04% 62.33% 3841ms 3.50% Cell::GetCellProliferativeType 14ms 0.013% 62.34% 3519ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.34% 3372ms 3.07% std::insert_iterator::operator= (inline) 2200ms 2.00% 64.34% 3152ms 2.87% _int_malloc 61ms 0.056% 64.40% 3102ms 2.82% Cell::SetCellProliferativeType 891ms 0.81% 65.21% 3073ms 2.80% AbstractElement::GetNodeLocation 18ms 0.016% 65.22% 2965ms 2.70% std::_Rb_tree::_M_insert_unique_ (inline) 72ms 0.066% 65.29% 2866ms 2.61% std::_Rb_tree::erase 2850ms 2.59% 67.88% 2850ms 2.59% std::_Rb_tree::_S_right (inline) 34ms 0.031% 67.91% 2741ms 2.49% CellPropertyCollection::HasProperty 760ms 0.69% 68.61% 2720ms 2.48% AbstractCellProperty::IsSame 593ms 0.54% 69.15% 2716ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 288ms 0.26% 69.41% 2689ms 2.45% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.41% 2634ms 2.40% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.41% 2630ms 2.39% Cell::HasCellProperty (inline) 0 0% 69.41% 2591ms 2.36% boost::numeric::ublas::c_vector::assign (inline) 244ms 0.22% 69.63% 2580ms 2.35% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.022% 69.65% 2483ms 2.26% Cell::GetCellData 1ms 0.00091% 69.65% 2466ms 2.24% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.65% 2426ms 2.21% AbstractCellPopulation::WriteResultsToFiles 86ms 0.078% 69.73% 2311ms 2.10% VertexMesh::GetVolumeOfElement 60ms 0.055% 69.79% 2223ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 29ms 0.026% 69.81% 2169ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 193ms 0.18% 69.99% 2131ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 7ms 0.0064% 69.99% 2123ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.0027% 70.00% 2109ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.00% 2109ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2078ms 1.89% 71.89% 2078ms 1.89% std::_Rb_tree_increment 0 0% 71.89% 1986ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 71.89% 1975ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 489ms 0.45% 72.33% 1960ms 1.78% std::type_info::operator== (inline) 72ms 0.066% 72.40% 1916ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 1227ms 1.12% 73.52% 1815ms 1.65% std::_Rb_tree::equal_range (inline) 0 0% 73.52% 1776ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 24ms 0.022% 73.54% 1635ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 44ms 0.04% 73.58% 1593ms 1.45% VertexMesh::GetSurfaceAreaOfElement 49ms 0.045% 73.62% 1486ms 1.35% Node::RemoveElement 0 0% 73.62% 1481ms 1.35% tcache_get (inline) 1481ms 1.35% 74.97% 1481ms 1.35% tcache_get_n (inline) 153ms 0.14% 75.11% 1478ms 1.35% CellPropertyCollection::AddProperty 63ms 0.057% 75.17% 1445ms 1.32% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 44ms 0.04% 75.21% 1443ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.0082% 75.22% 1442ms 1.31% std::set::erase (inline) 0 0% 75.22% 1439ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 70ms 0.064% 75.28% 1406ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.28% 1366ms 1.24% boost::numeric::ublas::norm_2 (inline) 593ms 0.54% 75.82% 1343ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 75.82% 1292ms 1.18% OffLatticeSimulation::ApplyBoundaries 1277ms 1.16% 76.98% 1277ms 1.16% [libchaste_cell_based.so] 67ms 0.061% 77.04% 1277ms 1.16% std::less::operator() (inline) 1013ms 0.92% 77.97% 1210ms 1.10% std::operator< (inline) 27ms 0.025% 77.99% 1170ms 1.06% CellPropertyRegistry::Get 83ms 0.076% 78.07% 1160ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.07% 1155ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1116ms 1.02% 79.08% 1116ms 1.02% std::_Rb_tree_insert_and_rebalance 25ms 0.023% 79.11% 1092ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.11% 1086ms 0.99% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.01% 79.12% 1086ms 0.99% boost::numeric::ublas::c_vector::swap 79ms 0.072% 79.19% 1075ms 0.98% std::swap_ranges (inline) 99ms 0.09% 79.28% 1068ms 0.97% std::_Rb_tree::find (inline) 0 0% 79.28% 1058ms 0.96% std::_Rb_tree::clear (inline) 110ms 0.1% 79.38% 1056ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.38% 1056ms 0.96% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0073% 79.38% 1047ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.38% 1044ms 0.95% std::map::clear (inline) 998ms 0.91% 80.29% 998ms 0.91% Node::rGetLocation 997ms 0.91% 81.20% 997ms 0.91% std::swap (inline) 0 0% 81.20% 996ms 0.91% std::iter_swap (inline) 18ms 0.016% 81.22% 984ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 172ms 0.16% 81.37% 961ms 0.87% boost::numeric::ublas::detail::equals 956ms 0.87% 82.24% 956ms 0.87% std::vector::size (inline) 874ms 0.8% 83.04% 904ms 0.82% boost::detail::sp_counted_base::release 164ms 0.15% 83.19% 899ms 0.82% MutableElement::GetNodeLocalIndex 0 0% 83.19% 857ms 0.78% std::map::find (inline) 1ms 0.00091% 83.19% 853ms 0.78% VertexMeshWriter::MakeVtkMesh 842ms 0.77% 83.96% 842ms 0.77% [libchaste_mesh.so] 241ms 0.22% 84.18% 821ms 0.75% std::__new_allocator::construct (inline) 0 0% 84.18% 821ms 0.75% std::allocator_traits::construct (inline) 97ms 0.088% 84.26% 807ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 420ms 0.38% 84.65% 798ms 0.73% Edge::GetMapIndex 433ms 0.39% 85.04% 774ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.04% 757ms 0.69% std::_Rb_tree::_M_construct_node (inline) 25ms 0.023% 85.06% 751ms 0.68% Edge::AddElement 18ms 0.016% 85.08% 748ms 0.68% MutableElement::RegisterWithEdges (inline) 0 0% 85.08% 743ms 0.68% boost::numeric::ublas::norm_inf (inline) 373ms 0.34% 85.42% 743ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 173ms 0.16% 85.58% 735ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 85.58% 715ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 710ms 0.65% 86.22% 710ms 0.65% Node::GetIndex 0 0% 86.22% 691ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00091% 86.22% 686ms 0.62% std::_Vector_base::_M_allocate (inline) 654ms 0.6% 86.82% 654ms 0.6% [libstdc++.so.6.0.33] 0 0% 86.82% 628ms 0.57% std::_Rb_tree::_Auto_node::_M_insert (inline) 14ms 0.013% 86.83% 628ms 0.57% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.83% 609ms 0.55% vtkPolygon::New 1ms 0.00091% 86.83% 609ms 0.55% vtkPolygon::vtkPolygon 31ms 0.028% 86.86% 586ms 0.53% MutableElement::RegisterWithNodes (inline) 41ms 0.037% 86.90% 583ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.90% 583ms 0.53% boost::numeric::ublas::vector::vector (inline) 8ms 0.0073% 86.90% 579ms 0.53% std::vector::_M_default_append (inline) 526ms 0.48% 87.38% 562ms 0.51% boost::detail::shared_count::shared_count (inline)