File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96488ms, 88.20% of 109401ms total Dropped 1145 nodes (cum <= 547ms) flat flat% sum% cum cum% 0 0% 0% 108924ms 99.56% __libc_start_call_main 0 0% 0% 108924ms 99.56% __libc_start_main_impl 0 0% 0% 108924ms 99.56% _start 0 0% 0% 108903ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108903ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108903ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108903ms 99.54% main 0 0% 0% 108863ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108863ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108863ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108856ms 99.50% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.024% 56350ms 51.51% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.037% 52871ms 48.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 119ms 0.11% 0.15% 51372ms 46.96% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.3% 0.45% 39708ms 36.30% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.45% 39476ms 36.08% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.45% 24520ms 22.41% VertexBasedCellPopulation::Update 0 0% 0.45% 24390ms 22.29% MutableVertexMesh::ReMesh 14443ms 13.20% 13.65% 22578ms 20.64% Cylindrical2dVertexMesh::GetVectorFromAtoB 124ms 0.11% 13.76% 17678ms 16.16% Cell::ReadyToDivide 72ms 0.066% 13.83% 16383ms 14.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 364ms 0.33% 14.16% 14550ms 13.30% NagaiHondaForce::GetAdhesionParameter 863ms 0.79% 14.95% 14455ms 13.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 110ms 0.1% 15.05% 14022ms 12.82% SimpleWntCellCycleModel::UpdateCellCyclePhase 135ms 0.12% 15.18% 13824ms 12.64% CellPropertyCollection::GetPropertiesType (inline) 350ms 0.32% 15.50% 12526ms 11.45% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.62% 12004ms 10.97% MutableVertexMesh::CheckForIntersections 3196ms 2.92% 18.54% 11490ms 10.50% __dynamic_cast 55ms 0.05% 18.59% 11366ms 10.39% AbstractCellProperty::IsSubType (inline) 84ms 0.077% 18.67% 11219ms 10.25% VertexBasedCellPopulation::GetDampingConstant 1198ms 1.10% 19.76% 10641ms 9.73% std::__new_allocator::allocate (inline) 82ms 0.075% 19.84% 10596ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.055% 19.89% 10478ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 19.91% 10397ms 9.50% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.91% 10129ms 9.26% std::allocator_traits::allocate (inline) 0 0% 19.91% 10042ms 9.18% std::_Rb_tree::_M_create_node (inline) 916ms 0.84% 20.75% 9562ms 8.74% operator new 0 0% 20.75% 9457ms 8.64% std::_Rb_tree::_M_get_node (inline) 2745ms 2.51% 23.26% 9290ms 8.49% boost::numeric::ublas::indexing_vector_assign 285ms 0.26% 23.52% 9123ms 8.34% VertexMesh::GetNextEdgeGradientOfElementAtNode 1379ms 1.26% 24.78% 8989ms 8.22% std::_Rb_tree::_M_erase 761ms 0.7% 25.48% 8930ms 8.16% VertexMesh::ElementIncludesPoint 82ms 0.075% 25.55% 8796ms 8.04% Cell::GetMutationState 38ms 0.035% 25.59% 8736ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.59% 8603ms 7.86% std::_Rb_tree::_Alloc_node::operator() (inline) 3412ms 3.12% 28.70% 8445ms 7.72% __GI___libc_malloc 0 0% 28.70% 8307ms 7.59% std::_Rb_tree::_M_drop_node (inline) 473ms 0.43% 29.14% 8266ms 7.56% VertexMesh::GetCentroidOfElement 244ms 0.22% 29.36% 8150ms 7.45% std::_Rb_tree::~_Rb_tree (inline) 256ms 0.23% 29.59% 8136ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 29.59% 8113ms 7.42% std::allocator_traits::deallocate (inline) 3143ms 2.87% 32.47% 8045ms 7.35% __GI___libc_free 0 0% 32.47% 8023ms 7.33% std::_Rb_tree::_M_put_node (inline) 13ms 0.012% 32.48% 7892ms 7.21% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 32.48% 7695ms 7.03% std::set::~set (inline) 479ms 0.44% 32.92% 7583ms 6.93% std::map::operator[] (partial-inline) 1332ms 1.22% 34.13% 7097ms 6.49% AbstractMesh::GetDistanceBetweenNodes 147ms 0.13% 34.27% 6851ms 6.26% std::_Rb_tree::_Rb_tree (partial-inline) 6719ms 6.14% 40.41% 6719ms 6.14% __strcmp_avx2 691ms 0.63% 41.04% 6473ms 5.92% std::_Rb_tree::_M_copy (inline) 17ms 0.016% 41.06% 6373ms 5.83% std::set::set (inline) 100ms 0.091% 41.15% 6360ms 5.81% SimpleWntCellCycleModel::GetWntLevel 168ms 0.15% 41.30% 6172ms 5.64% WntConcentration::GetWntLevel 6037ms 5.52% 46.82% 6037ms 5.52% boost::numeric::ublas::c_vector::operator() 2728ms 2.49% 49.31% 5767ms 5.27% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 49.31% 5764ms 5.27% std::set::insert (inline) 2445ms 2.23% 51.55% 5710ms 5.22% std::_Rb_tree::_M_lower_bound (inline) 719ms 0.66% 52.21% 5529ms 5.05% std::_Rb_tree::_M_clone_node (inline) 30ms 0.027% 52.23% 5461ms 4.99% MutableVertexMesh::RemoveDeletedNodes 29ms 0.027% 52.26% 5276ms 4.82% EdgeHelper::RemoveDeletedEdges 155ms 0.14% 52.40% 4987ms 4.56% MutableElement::ResetIndex 43ms 0.039% 52.44% 4978ms 4.55% EdgeHelper::UpdateEdgesMapKey 4547ms 4.16% 56.60% 4894ms 4.47% _int_free 568ms 0.52% 57.12% 4893ms 4.47% std::_Rb_tree::_M_insert_ (inline) 1441ms 1.32% 58.43% 4695ms 4.29% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 58.43% 4557ms 4.17% std::_Rb_tree::lower_bound (inline) 0 0% 58.43% 4557ms 4.17% std::map::lower_bound (inline) 0 0% 58.43% 4551ms 4.16% AbstractCellBasedSimulation::DoCellRemoval (inline) 60ms 0.055% 58.49% 4464ms 4.08% std::set_intersection (inline) 278ms 0.25% 58.74% 4404ms 4.03% std::__set_intersection 101ms 0.092% 58.83% 3929ms 3.59% AbstractCellPopulation::GetCellUsingLocationIndex 41ms 0.037% 58.87% 3921ms 3.58% Cell::GetCellProliferativeType 78ms 0.071% 58.94% 3846ms 3.52% AbstractCellProperty::IsType (inline) 3702ms 3.38% 62.33% 3702ms 3.38% boost::numeric::ublas::same_impl_ex 5ms 0.0046% 62.33% 3513ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2543ms 2.32% 64.66% 3444ms 3.15% _int_malloc 874ms 0.8% 65.46% 3412ms 3.12% AbstractElement::GetNodeLocation 0 0% 65.46% 3251ms 2.97% std::insert_iterator::operator= (inline) 45ms 0.041% 65.50% 3123ms 2.85% Cell::SetCellProliferativeType 52ms 0.048% 65.54% 3011ms 2.75% std::_Rb_tree::erase 0 0% 65.54% 2905ms 2.66% std::_Rb_tree::_M_insert_unique (inline) 6ms 0.0055% 65.55% 2859ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 766ms 0.7% 66.25% 2785ms 2.55% AbstractCellProperty::IsSame 2767ms 2.53% 68.78% 2767ms 2.53% std::_Rb_tree::_S_right (inline) 636ms 0.58% 69.36% 2704ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 56ms 0.051% 69.41% 2697ms 2.47% CellPropertyCollection::HasProperty 420ms 0.38% 69.80% 2674ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.80% 2587ms 2.36% Cell::HasCellProperty (inline) 267ms 0.24% 70.04% 2583ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.04% 2508ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 31ms 0.028% 70.07% 2492ms 2.28% std::_Rb_tree::_M_emplace_hint_unique 29ms 0.027% 70.09% 2414ms 2.21% Cell::GetCellData 0 0% 70.09% 2409ms 2.20% AbstractCellPopulation::WriteResultsToFiles 3ms 0.0027% 70.10% 2344ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 270ms 0.25% 70.34% 2338ms 2.14% AbstractCellPopulation::Iterator::IsRealCell (inline) 114ms 0.1% 70.45% 2272ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.45% 2237ms 2.04% boost::numeric::ublas::c_vector::operator-= (inline) 113ms 0.1% 70.55% 2195ms 2.01% VertexMesh::GetVolumeOfElement 2060ms 1.88% 72.43% 2060ms 1.88% std::_Rb_tree_increment 490ms 0.45% 72.88% 2019ms 1.85% std::type_info::operator== (inline) 2ms 0.0018% 72.88% 1981ms 1.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.88% 1981ms 1.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.88% 1970ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.88% 1953ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 70ms 0.064% 72.95% 1876ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 25ms 0.023% 72.97% 1772ms 1.62% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1152ms 1.05% 74.02% 1764ms 1.61% std::_Rb_tree::equal_range (inline) 0 0% 74.02% 1744ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 17ms 0.016% 74.04% 1658ms 1.52% VertexMesh::GetSurfaceAreaOfElement 19ms 0.017% 74.06% 1589ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.069% 74.13% 1580ms 1.44% Node::RemoveElement 141ms 0.13% 74.26% 1572ms 1.44% CellPropertyCollection::AddProperty 87ms 0.08% 74.33% 1567ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 11ms 0.01% 74.34% 1510ms 1.38% std::set::erase (inline) 133ms 0.12% 74.47% 1508ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.47% 1439ms 1.32% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 74.47% 1430ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.47% 1417ms 1.30% tcache_get (inline) 1417ms 1.30% 75.76% 1417ms 1.30% tcache_get_n (inline) 71ms 0.065% 75.83% 1395ms 1.28% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.83% 1321ms 1.21% OffLatticeSimulation::ApplyBoundaries 1303ms 1.19% 77.02% 1303ms 1.19% Node::rGetLocation 0 0% 77.02% 1222ms 1.12% boost::numeric::ublas::norm_2 (inline) 539ms 0.49% 77.51% 1210ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 119ms 0.11% 77.62% 1182ms 1.08% std::_Rb_tree::find (inline) 30ms 0.027% 77.65% 1177ms 1.08% CellPropertyRegistry::Get 61ms 0.056% 77.70% 1157ms 1.06% std::less::operator() (inline) 1154ms 1.05% 78.76% 1154ms 1.05% std::_Rb_tree_insert_and_rebalance 17ms 0.016% 78.77% 1148ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1139ms 1.04% 79.81% 1139ms 1.04% [libchaste_cell_based.so] 879ms 0.8% 80.62% 1096ms 1.00% std::operator< (inline) 0 0% 80.62% 1086ms 0.99% std::_Rb_tree::clear (inline) 0 0% 80.62% 1054ms 0.96% std::map::clear (inline) 21ms 0.019% 80.64% 1028ms 0.94% MutableElement::RegisterWithEdges (inline) 17ms 0.016% 80.65% 1019ms 0.93% Edge::AddElement 19ms 0.017% 80.67% 1000ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 8ms 0.0073% 80.68% 985ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 138ms 0.13% 80.80% 973ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.80% 973ms 0.89% boost::shared_ptr::~shared_ptr (inline) 158ms 0.14% 80.95% 969ms 0.89% boost::numeric::ublas::detail::equals 0 0% 80.95% 964ms 0.88% std::map::find (inline) 943ms 0.86% 81.81% 943ms 0.86% std::vector::size (inline) 0 0% 81.81% 936ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0082% 81.82% 936ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 931ms 0.85% 82.67% 931ms 0.85% [libchaste_mesh.so] 77ms 0.07% 82.74% 927ms 0.85% std::swap_ranges (inline) 401ms 0.37% 83.11% 883ms 0.81% Edge::GetMapIndex 0 0% 83.11% 856ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 83.11% 850ms 0.78% std::iter_swap (inline) 850ms 0.78% 83.88% 850ms 0.78% std::swap (inline) 130ms 0.12% 84.00% 847ms 0.77% MutableElement::GetNodeLocalIndex 801ms 0.73% 84.73% 806ms 0.74% boost::detail::sp_counted_base::release 98ms 0.09% 84.82% 775ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.82% 759ms 0.69% boost::numeric::ublas::norm_inf (inline) 368ms 0.34% 85.16% 759ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 449ms 0.41% 85.57% 758ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.57% 710ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 36ms 0.033% 85.60% 710ms 0.65% std::_Rb_tree::_M_insert_node (inline) 15ms 0.014% 85.62% 703ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.62% 700ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 695ms 0.64% 86.25% 695ms 0.64% Node::GetIndex 89ms 0.081% 86.33% 688ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 150ms 0.14% 86.47% 675ms 0.62% boost::shared_ptr::shared_ptr (inline) 0 0% 86.47% 668ms 0.61% std::_Vector_base::_M_allocate (inline) 34ms 0.031% 86.50% 645ms 0.59% MutableElement::RegisterWithNodes (inline) 101ms 0.092% 86.59% 634ms 0.58% std::__new_allocator::construct (inline) 0 0% 86.59% 634ms 0.58% std::allocator_traits::construct (inline) 0 0% 86.59% 621ms 0.57% vtkPolygon::New 0 0% 86.59% 621ms 0.57% vtkPolygon::vtkPolygon 28ms 0.026% 86.62% 604ms 0.55% Node::AddElement 597ms 0.55% 87.16% 597ms 0.55% [libstdc++.so.6.0.33] 0 0% 87.16% 587ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.16% 585ms 0.53% std::_Rb_tree::_M_construct_node (inline) 577ms 0.53% 87.69% 577ms 0.53% operator delete 552ms 0.5% 88.20% 552ms 0.5% boost::shared_ptr::operator-> (inline)