File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96550ms, 88.82% of 108701ms total Dropped 1137 nodes (cum <= 543.50ms) flat flat% sum% cum cum% 0 0% 0% 108242ms 99.58% __libc_start_call_main 0 0% 0% 108242ms 99.58% __libc_start_main_impl 0 0% 0% 108242ms 99.58% _start 0 0% 0% 108223ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108223ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108223ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108223ms 99.56% main 0 0% 0% 108183ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108183ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108183ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108175ms 99.52% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.015% 56095ms 51.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 26ms 0.024% 0.039% 52946ms 48.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 117ms 0.11% 0.15% 51345ms 47.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 346ms 0.32% 0.46% 39783ms 36.60% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.47% 39128ms 36.00% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.47% 24341ms 22.39% VertexBasedCellPopulation::Update 3ms 0.0028% 0.47% 24214ms 22.28% MutableVertexMesh::ReMesh 14495ms 13.33% 13.81% 22992ms 21.15% Cylindrical2dVertexMesh::GetVectorFromAtoB 115ms 0.11% 13.91% 17409ms 16.02% Cell::ReadyToDivide 75ms 0.069% 13.98% 16160ms 14.87% AbstractPhaseBasedCellCycleModel::ReadyToDivide 342ms 0.31% 14.30% 14624ms 13.45% NagaiHondaForce::GetAdhesionParameter 404ms 0.37% 14.67% 14186ms 13.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 165ms 0.15% 14.82% 13751ms 12.65% CellPropertyCollection::GetPropertiesType (inline) 101ms 0.093% 14.91% 13742ms 12.64% SimpleWntCellCycleModel::UpdateCellCyclePhase 395ms 0.36% 15.27% 12718ms 11.70% boost::numeric::ublas::vector_assign (inline) 145ms 0.13% 15.41% 12081ms 11.11% MutableVertexMesh::CheckForIntersections 3204ms 2.95% 18.36% 11190ms 10.29% __dynamic_cast 75ms 0.069% 18.42% 11084ms 10.20% AbstractCellProperty::IsSubType (inline) 76ms 0.07% 18.49% 11084ms 10.20% VertexBasedCellPopulation::GetDampingConstant 70ms 0.064% 18.56% 10470ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 54ms 0.05% 18.61% 10373ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.027% 18.64% 10216ms 9.40% AbstractCellBasedSimulation::DoCellBirth 1258ms 1.16% 19.79% 10064ms 9.26% std::__new_allocator::allocate (inline) 0 0% 19.79% 9570ms 8.80% std::_Rb_tree::_M_create_node (inline) 0 0% 19.79% 9532ms 8.77% std::allocator_traits::allocate (inline) 2771ms 2.55% 22.34% 9441ms 8.69% boost::numeric::ublas::indexing_vector_assign 1456ms 1.34% 23.68% 9199ms 8.46% std::_Rb_tree::_M_erase 884ms 0.81% 24.49% 8952ms 8.24% operator new 792ms 0.73% 25.22% 8926ms 8.21% VertexMesh::ElementIncludesPoint 0 0% 25.22% 8879ms 8.17% std::_Rb_tree::_M_get_node (inline) 324ms 0.3% 25.52% 8877ms 8.17% VertexMesh::GetNextEdgeGradientOfElementAtNode 74ms 0.068% 25.59% 8619ms 7.93% Cell::GetMutationState 32ms 0.029% 25.62% 8610ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.62% 8463ms 7.79% std::_Rb_tree::_Alloc_node::operator() (inline) 260ms 0.24% 25.86% 8319ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 512ms 0.47% 26.33% 8228ms 7.57% VertexMesh::GetCentroidOfElement 0 0% 26.33% 8127ms 7.48% std::_Rb_tree::_M_drop_node (inline) 251ms 0.23% 26.56% 7950ms 7.31% std::__new_allocator::deallocate (inline) 0 0% 26.56% 7918ms 7.28% std::allocator_traits::deallocate (inline) 3251ms 2.99% 29.55% 7890ms 7.26% __GI___libc_malloc 0 0% 29.55% 7849ms 7.22% std::_Rb_tree::_M_put_node (inline) 0 0% 29.55% 7827ms 7.20% std::set::~set (inline) 12ms 0.011% 29.56% 7803ms 7.18% MutableVertexMesh::RemoveDeletedNodesAndElements 2682ms 2.47% 32.03% 7783ms 7.16% __GI___libc_free 1283ms 1.18% 33.21% 7111ms 6.54% AbstractMesh::GetDistanceBetweenNodes 462ms 0.43% 33.63% 6985ms 6.43% std::map::operator[] (partial-inline) 159ms 0.15% 33.78% 6852ms 6.30% std::_Rb_tree::_Rb_tree (partial-inline) 598ms 0.55% 34.33% 6486ms 5.97% std::_Rb_tree::_M_copy (inline) 6447ms 5.93% 40.26% 6447ms 5.93% __strcmp_avx2 15ms 0.014% 40.28% 6381ms 5.87% std::set::set (inline) 95ms 0.087% 40.36% 6201ms 5.70% SimpleWntCellCycleModel::GetWntLevel 6184ms 5.69% 46.05% 6184ms 5.69% boost::numeric::ublas::c_vector::operator() 151ms 0.14% 46.19% 6022ms 5.54% WntConcentration::GetWntLevel 761ms 0.7% 46.89% 5612ms 5.16% std::_Rb_tree::_M_clone_node (inline) 2698ms 2.48% 49.37% 5517ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 2379ms 2.19% 51.56% 5511ms 5.07% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.56% 5498ms 5.06% std::set::insert (inline) 29ms 0.027% 51.59% 5368ms 4.94% MutableVertexMesh::RemoveDeletedNodes 43ms 0.04% 51.63% 5194ms 4.78% EdgeHelper::RemoveDeletedEdges 4597ms 4.23% 55.86% 5094ms 4.69% _int_free 1539ms 1.42% 57.27% 4993ms 4.59% boost::numeric::ublas::c_vector::operator[] (inline) 37ms 0.034% 57.31% 4927ms 4.53% EdgeHelper::UpdateEdgesMapKey 250ms 0.23% 57.54% 4886ms 4.49% MutableElement::ResetIndex 510ms 0.47% 58.01% 4642ms 4.27% std::_Rb_tree::_M_insert_ (inline) 1ms 0.00092% 58.01% 4559ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 58ms 0.053% 58.06% 4479ms 4.12% std::set_intersection (inline) 251ms 0.23% 58.29% 4421ms 4.07% std::__set_intersection 0 0% 58.29% 4374ms 4.02% std::_Rb_tree::lower_bound (inline) 0 0% 58.29% 4374ms 4.02% std::map::lower_bound (inline) 53ms 0.049% 58.34% 3956ms 3.64% Cell::GetCellProliferativeType 118ms 0.11% 58.45% 3921ms 3.61% AbstractCellPopulation::GetCellUsingLocationIndex 3897ms 3.59% 62.03% 3897ms 3.59% boost::numeric::ublas::same_impl_ex 56ms 0.052% 62.08% 3760ms 3.46% AbstractCellProperty::IsType (inline) 10ms 0.0092% 62.09% 3537ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.09% 3233ms 2.97% std::insert_iterator::operator= (inline) 818ms 0.75% 62.85% 3179ms 2.92% AbstractElement::GetNodeLocation 27ms 0.025% 62.87% 3090ms 2.84% std::_Rb_tree::erase 42ms 0.039% 62.91% 3088ms 2.84% Cell::SetCellProliferativeType 2105ms 1.94% 64.85% 3048ms 2.80% _int_malloc 639ms 0.59% 65.43% 2824ms 2.60% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.0037% 65.44% 2811ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 417ms 0.38% 65.82% 2777ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 702ms 0.65% 66.47% 2729ms 2.51% AbstractCellProperty::IsSame 0 0% 66.47% 2687ms 2.47% std::_Rb_tree::_M_insert_unique 2642ms 2.43% 68.90% 2642ms 2.43% std::_Rb_tree::_S_right (inline) 48ms 0.044% 68.94% 2617ms 2.41% CellPropertyCollection::HasProperty 274ms 0.25% 69.19% 2544ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 28ms 0.026% 69.22% 2518ms 2.32% Cell::GetCellData 0 0% 69.22% 2490ms 2.29% Cell::HasCellProperty (inline) 0 0% 69.22% 2453ms 2.26% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.22% 2429ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.22% 2395ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 107ms 0.098% 69.32% 2326ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 89ms 0.082% 69.40% 2315ms 2.13% VertexMesh::GetVolumeOfElement 2ms 0.0018% 69.40% 2245ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 216ms 0.2% 69.60% 2231ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 1481ms 1.36% 70.96% 2192ms 2.02% std::_Rb_tree::equal_range (inline) 2184ms 2.01% 72.97% 2184ms 2.01% std::_Rb_tree_increment 33ms 0.03% 73.00% 2103ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 493ms 0.45% 73.46% 2027ms 1.86% std::type_info::operator== (inline) 0 0% 73.46% 1998ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.46% 1981ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00092% 73.46% 1935ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.46% 1935ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 63ms 0.058% 73.52% 1812ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.52% 1779ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 73.54% 1759ms 1.62% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.023% 73.56% 1651ms 1.52% VertexMesh::GetSurfaceAreaOfElement 159ms 0.15% 73.71% 1636ms 1.51% CellPropertyCollection::AddProperty 49ms 0.045% 73.75% 1582ms 1.46% Node::RemoveElement 23ms 0.021% 73.77% 1552ms 1.43% std::set::erase (inline) 23ms 0.021% 73.80% 1506ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 120ms 0.11% 73.91% 1493ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 98ms 0.09% 74.00% 1485ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.00% 1398ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.00% 1391ms 1.28% tcache_get (inline) 1391ms 1.28% 75.28% 1391ms 1.28% tcache_get_n (inline) 2ms 0.0018% 75.28% 1226ms 1.13% OffLatticeSimulation::ApplyBoundaries 0 0% 75.28% 1210ms 1.11% boost::numeric::ublas::norm_2 (inline) 512ms 0.47% 75.75% 1205ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 73ms 0.067% 75.82% 1184ms 1.09% std::less::operator() (inline) 1156ms 1.06% 76.88% 1156ms 1.06% Node::rGetLocation 24ms 0.022% 76.90% 1152ms 1.06% CellPropertyRegistry::Get 0 0% 76.90% 1143ms 1.05% std::_Rb_tree::clear (inline) 1133ms 1.04% 77.94% 1133ms 1.04% [libchaste_cell_based.so] 1125ms 1.03% 78.98% 1125ms 1.03% std::_Rb_tree_insert_and_rebalance 0 0% 78.98% 1124ms 1.03% std::map::clear (inline) 908ms 0.84% 79.81% 1111ms 1.02% std::operator< (inline) 0 0% 79.81% 1107ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 103ms 0.095% 79.91% 1107ms 1.02% std::_Rb_tree::find (inline) 86ms 0.079% 79.99% 1057ms 0.97% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.018% 80.01% 1042ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 146ms 0.13% 80.14% 986ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.14% 986ms 0.91% boost::shared_ptr::~shared_ptr (inline) 10ms 0.0092% 80.15% 970ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 26ms 0.024% 80.17% 946ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 937ms 0.86% 81.04% 937ms 0.86% std::vector::size (inline) 0 0% 81.04% 912ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 81.04% 912ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 143ms 0.13% 81.17% 908ms 0.84% boost::numeric::ublas::detail::equals 91ms 0.084% 81.25% 908ms 0.84% std::swap_ranges (inline) 398ms 0.37% 81.62% 899ms 0.83% Edge::GetMapIndex 0 0% 81.62% 885ms 0.81% std::map::find (inline) 883ms 0.81% 82.43% 883ms 0.81% [libchaste_mesh.so] 0 0% 82.43% 852ms 0.78% VertexMeshWriter::MakeVtkMesh 815ms 0.75% 83.18% 821ms 0.76% boost::detail::sp_counted_base::release 0 0% 83.18% 817ms 0.75% std::iter_swap (inline) 817ms 0.75% 83.93% 817ms 0.75% std::swap (inline) 152ms 0.14% 84.07% 787ms 0.72% boost::shared_ptr::shared_ptr (inline) 21ms 0.019% 84.09% 785ms 0.72% MutableElement::RegisterWithEdges (inline) 34ms 0.031% 84.12% 774ms 0.71% Edge::AddElement 97ms 0.089% 84.21% 774ms 0.71% MutableElement::GetNodeLocalIndex 108ms 0.099% 84.31% 758ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 461ms 0.42% 84.74% 749ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 117ms 0.11% 84.84% 742ms 0.68% std::__new_allocator::construct (inline) 0 0% 84.84% 742ms 0.68% std::allocator_traits::construct (inline) 12ms 0.011% 84.86% 740ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 84.86% 730ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 98ms 0.09% 84.95% 728ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 84.95% 725ms 0.67% boost::numeric::ublas::norm_inf (inline) 373ms 0.34% 85.29% 725ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 719ms 0.66% 85.95% 719ms 0.66% Node::GetIndex 696ms 0.64% 86.59% 696ms 0.64% tcache_put (inline) 0 0% 86.59% 691ms 0.64% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.59% 669ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.016% 86.61% 669ms 0.62% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.61% 647ms 0.6% std::_Vector_base::_M_allocate (inline) 608ms 0.56% 87.17% 634ms 0.58% boost::detail::shared_count::shared_count (inline) 23ms 0.021% 87.19% 625ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 87.19% 612ms 0.56% vtkPolygon::New 1ms 0.00092% 87.19% 612ms 0.56% vtkPolygon::vtkPolygon 43ms 0.04% 87.23% 608ms 0.56% Node::AddElement 0 0% 87.23% 579ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 578ms 0.53% 87.76% 578ms 0.53% operator delete 566ms 0.52% 88.28% 566ms 0.52% boost::shared_ptr::operator-> (inline) 561ms 0.52% 88.80% 561ms 0.52% [libstdc++.so.6.0.33] 27ms 0.025% 88.82% 559ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.82% 559ms 0.51% boost::numeric::ublas::vector::vector (inline)