File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96756ms, 88.55% of 109273ms total Dropped 1136 nodes (cum <= 546.37ms) flat flat% sum% cum cum% 0 0% 0% 108817ms 99.58% __libc_start_call_main 0 0% 0% 108817ms 99.58% __libc_start_main_impl 0 0% 0% 108817ms 99.58% _start 0 0% 0% 108798ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108798ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108798ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108798ms 99.57% main 0 0% 0% 108759ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108759ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108759ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 9ms 0.0082% 0.0082% 108752ms 99.52% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.025% 56416ms 51.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 24ms 0.022% 0.047% 53183ms 48.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 126ms 0.12% 0.16% 51583ms 47.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 328ms 0.3% 0.46% 39883ms 36.50% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.46% 39346ms 36.01% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.47% 24419ms 22.35% VertexBasedCellPopulation::Update 4ms 0.0037% 0.47% 24282ms 22.22% MutableVertexMesh::ReMesh 14445ms 13.22% 13.69% 22827ms 20.89% Cylindrical2dVertexMesh::GetVectorFromAtoB 108ms 0.099% 13.79% 17471ms 15.99% Cell::ReadyToDivide 76ms 0.07% 13.86% 16200ms 14.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 375ms 0.34% 14.20% 14929ms 13.66% NagaiHondaForce::GetAdhesionParameter 442ms 0.4% 14.60% 14410ms 13.19% boost::numeric::ublas::c_vector::c_vector (partial-inline) 133ms 0.12% 14.73% 13957ms 12.77% CellPropertyCollection::GetPropertiesType (inline) 105ms 0.096% 14.82% 13854ms 12.68% SimpleWntCellCycleModel::UpdateCellCyclePhase 354ms 0.32% 15.15% 12904ms 11.81% boost::numeric::ublas::vector_assign (inline) 137ms 0.13% 15.27% 12099ms 11.07% MutableVertexMesh::CheckForIntersections 3366ms 3.08% 18.35% 11599ms 10.61% __dynamic_cast 61ms 0.056% 18.41% 11494ms 10.52% AbstractCellProperty::IsSubType (inline) 72ms 0.066% 18.47% 11198ms 10.25% VertexBasedCellPopulation::GetDampingConstant 86ms 0.079% 18.55% 10481ms 9.59% AbstractTargetAreaModifier::UpdateTargetAreas 1290ms 1.18% 19.73% 10417ms 9.53% std::__new_allocator::allocate (inline) 58ms 0.053% 19.79% 10365ms 9.49% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.028% 19.81% 10239ms 9.37% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.81% 9871ms 9.03% std::allocator_traits::allocate (inline) 0 0% 19.81% 9856ms 9.02% std::_Rb_tree::_M_create_node (inline) 2806ms 2.57% 22.38% 9626ms 8.81% boost::numeric::ublas::indexing_vector_assign 820ms 0.75% 23.13% 9256ms 8.47% operator new 0 0% 23.13% 9199ms 8.42% std::_Rb_tree::_M_get_node (inline) 1466ms 1.34% 24.47% 9174ms 8.40% std::_Rb_tree::_M_erase 753ms 0.69% 25.16% 8968ms 8.21% VertexMesh::ElementIncludesPoint 87ms 0.08% 25.24% 8787ms 8.04% Cell::GetMutationState 15ms 0.014% 25.26% 8784ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.26% 8709ms 7.97% std::_Rb_tree::_Alloc_node::operator() (inline) 349ms 0.32% 25.58% 8699ms 7.96% VertexMesh::GetNextEdgeGradientOfElementAtNode 478ms 0.44% 26.01% 8366ms 7.66% VertexMesh::GetCentroidOfElement 212ms 0.19% 26.21% 8293ms 7.59% std::_Rb_tree::~_Rb_tree (inline) 3428ms 3.14% 29.34% 8238ms 7.54% __GI___libc_malloc 0 0% 29.34% 8130ms 7.44% std::_Rb_tree::_M_drop_node (inline) 283ms 0.26% 29.60% 7968ms 7.29% std::__new_allocator::deallocate (inline) 0 0% 29.60% 7930ms 7.26% std::allocator_traits::deallocate (inline) 0 0% 29.60% 7839ms 7.17% std::_Rb_tree::_M_put_node (inline) 12ms 0.011% 29.61% 7812ms 7.15% MutableVertexMesh::RemoveDeletedNodesAndElements 3011ms 2.76% 32.37% 7793ms 7.13% __GI___libc_free 0 0% 32.37% 7792ms 7.13% std::set::~set (inline) 451ms 0.41% 32.78% 7123ms 6.52% std::map::operator[] (partial-inline) 151ms 0.14% 32.92% 7111ms 6.51% std::_Rb_tree::_Rb_tree (partial-inline) 1372ms 1.26% 34.18% 7008ms 6.41% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 694ms 0.64% 34.81% 6774ms 6.20% std::_Rb_tree::_M_copy (inline) 6682ms 6.11% 40.93% 6682ms 6.11% __strcmp_avx2 11ms 0.01% 40.94% 6643ms 6.08% std::set::set (inline) 133ms 0.12% 41.06% 6326ms 5.79% SimpleWntCellCycleModel::GetWntLevel 6200ms 5.67% 46.73% 6200ms 5.67% boost::numeric::ublas::c_vector::operator() 129ms 0.12% 46.85% 6111ms 5.59% WntConcentration::GetWntLevel 714ms 0.65% 47.50% 5821ms 5.33% std::_Rb_tree::_M_clone_node (inline) 2756ms 2.52% 50.03% 5781ms 5.29% __cxxabiv1::__si_class_type_info::__do_dyncast 2368ms 2.17% 52.19% 5534ms 5.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 52.19% 5405ms 4.95% std::set::insert (inline) 29ms 0.027% 52.22% 5402ms 4.94% MutableVertexMesh::RemoveDeletedNodes 40ms 0.037% 52.26% 5231ms 4.79% EdgeHelper::RemoveDeletedEdges 1533ms 1.40% 53.66% 4918ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 39ms 0.036% 53.69% 4897ms 4.48% EdgeHelper::UpdateEdgesMapKey 225ms 0.21% 53.90% 4875ms 4.46% MutableElement::ResetIndex 4442ms 4.07% 57.97% 4777ms 4.37% _int_free 1ms 0.00092% 57.97% 4676ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 492ms 0.45% 58.42% 4603ms 4.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.42% 4472ms 4.09% std::_Rb_tree::lower_bound (inline) 0 0% 58.42% 4472ms 4.09% std::map::lower_bound (inline) 56ms 0.051% 58.47% 4386ms 4.01% std::set_intersection (inline) 235ms 0.22% 58.68% 4330ms 3.96% std::__set_intersection 3926ms 3.59% 62.28% 3926ms 3.59% boost::numeric::ublas::same_impl_ex 28ms 0.026% 62.30% 3916ms 3.58% Cell::GetCellProliferativeType 120ms 0.11% 62.41% 3897ms 3.57% AbstractCellPopulation::GetCellUsingLocationIndex 67ms 0.061% 62.47% 3867ms 3.54% AbstractCellProperty::IsType (inline) 7ms 0.0064% 62.48% 3577ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 873ms 0.8% 63.28% 3351ms 3.07% AbstractElement::GetNodeLocation 0 0% 63.28% 3243ms 2.97% std::insert_iterator::operator= (inline) 41ms 0.038% 63.32% 3177ms 2.91% std::_Rb_tree::erase 2235ms 2.05% 65.36% 3159ms 2.89% _int_malloc 33ms 0.03% 65.39% 3111ms 2.85% Cell::SetCellProliferativeType 4ms 0.0037% 65.39% 2891ms 2.65% std::_Rb_tree::_M_insert_unique_ (inline) 693ms 0.63% 66.03% 2858ms 2.62% boost::numeric::ublas::vector_binary::size (inline) 714ms 0.65% 66.68% 2780ms 2.54% AbstractCellProperty::IsSame 45ms 0.041% 66.72% 2695ms 2.47% CellPropertyCollection::HasProperty 2666ms 2.44% 69.16% 2666ms 2.44% std::_Rb_tree::_S_right (inline) 422ms 0.39% 69.55% 2638ms 2.41% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.55% 2574ms 2.36% Cell::HasCellProperty (inline) 234ms 0.21% 69.76% 2559ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.00092% 69.76% 2514ms 2.30% std::_Rb_tree::_M_insert_unique 0 0% 69.76% 2488ms 2.28% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.76% 2482ms 2.27% AbstractCellPopulation::WriteResultsToFiles 22ms 0.02% 69.78% 2474ms 2.26% Cell::GetCellData 0 0% 69.78% 2474ms 2.26% boost::numeric::ublas::c_vector::assign (inline) 90ms 0.082% 69.87% 2280ms 2.09% VertexMesh::GetVolumeOfElement 102ms 0.093% 69.96% 2249ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0027% 69.96% 2162ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 228ms 0.21% 70.17% 2153ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 34ms 0.031% 70.20% 2147ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 1447ms 1.32% 71.53% 2131ms 1.95% std::_Rb_tree::equal_range (inline) 475ms 0.43% 71.96% 2066ms 1.89% std::type_info::operator== (inline) 2035ms 1.86% 73.82% 2035ms 1.86% std::_Rb_tree_increment 0 0% 73.82% 2026ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.82% 2013ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0018% 73.83% 1983ms 1.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.83% 1983ms 1.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 59ms 0.054% 73.88% 1841ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.88% 1816ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.017% 73.90% 1628ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 48ms 0.044% 73.94% 1627ms 1.49% Node::RemoveElement 23ms 0.021% 73.96% 1620ms 1.48% VertexMesh::GetSurfaceAreaOfElement 22ms 0.02% 73.98% 1594ms 1.46% std::set::erase (inline) 158ms 0.14% 74.13% 1550ms 1.42% CellPropertyCollection::AddProperty 127ms 0.12% 74.24% 1524ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 33ms 0.03% 74.27% 1469ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.27% 1449ms 1.33% tcache_get (inline) 1449ms 1.33% 75.60% 1449ms 1.33% tcache_get_n (inline) 0 0% 75.60% 1448ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 83ms 0.076% 75.68% 1422ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.68% 1271ms 1.16% OffLatticeSimulation::ApplyBoundaries 0 0% 75.68% 1256ms 1.15% boost::numeric::ublas::norm_2 (inline) 543ms 0.5% 76.17% 1243ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1204ms 1.10% 77.27% 1204ms 1.10% Node::rGetLocation 76ms 0.07% 77.34% 1203ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 67ms 0.061% 77.41% 1174ms 1.07% std::less::operator() (inline) 0 0% 77.41% 1147ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 29ms 0.027% 77.43% 1127ms 1.03% CellPropertyRegistry::Get 1127ms 1.03% 78.46% 1127ms 1.03% [libchaste_cell_based.so] 1121ms 1.03% 79.49% 1121ms 1.03% std::_Rb_tree_insert_and_rebalance 888ms 0.81% 80.30% 1107ms 1.01% std::operator< (inline) 3ms 0.0027% 80.30% 1102ms 1.01% std::_Rb_tree::clear (inline) 0 0% 80.30% 1083ms 0.99% std::map::clear (inline) 11ms 0.01% 80.31% 1075ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 103ms 0.094% 80.41% 1045ms 0.96% std::_Rb_tree::find (inline) 10ms 0.0092% 80.42% 1036ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 146ms 0.13% 80.55% 981ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.55% 981ms 0.9% boost::shared_ptr::~shared_ptr (inline) 965ms 0.88% 81.43% 965ms 0.88% [libchaste_mesh.so] 14ms 0.013% 81.45% 953ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 950ms 0.87% 82.32% 950ms 0.87% std::vector::size (inline) 157ms 0.14% 82.46% 937ms 0.86% boost::numeric::ublas::detail::equals 402ms 0.37% 82.83% 922ms 0.84% Edge::GetMapIndex 0 0% 82.83% 919ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 82.83% 919ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.079% 82.91% 916ms 0.84% std::swap_ranges (inline) 0 0% 82.91% 868ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 82.91% 830ms 0.76% std::iter_swap (inline) 830ms 0.76% 83.67% 830ms 0.76% std::swap (inline) 0 0% 83.67% 827ms 0.76% std::map::find (inline) 91ms 0.083% 83.75% 818ms 0.75% MutableElement::GetNodeLocalIndex 798ms 0.73% 84.48% 805ms 0.74% boost::detail::sp_counted_base::release 123ms 0.11% 84.60% 795ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 7ms 0.0064% 84.60% 758ms 0.69% AbstractNumericalMethod::DetectStepSizeExceptions 17ms 0.016% 84.62% 754ms 0.69% MutableElement::RegisterWithEdges (inline) 120ms 0.11% 84.73% 751ms 0.69% VertexBasedCellPopulation::CheckForStepSizeException 26ms 0.024% 84.75% 744ms 0.68% Edge::AddElement 112ms 0.1% 84.85% 737ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 84.85% 727ms 0.67% boost::numeric::ublas::norm_inf (inline) 339ms 0.31% 85.16% 727ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 719ms 0.66% 85.82% 719ms 0.66% Node::GetIndex 114ms 0.1% 85.93% 719ms 0.66% std::__new_allocator::construct (inline) 0 0% 85.93% 719ms 0.66% std::allocator_traits::construct (inline) 0 0% 85.93% 684ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.017% 85.94% 684ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.94% 683ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 392ms 0.36% 86.30% 671ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.30% 668ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.30% 657ms 0.6% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.30% 633ms 0.58% vtkPolygon::New 0 0% 86.30% 633ms 0.58% vtkPolygon::vtkPolygon 626ms 0.57% 86.88% 626ms 0.57% [libstdc++.so.6.0.33] 590ms 0.54% 87.42% 625ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 87.42% 619ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 588ms 0.54% 87.95% 588ms 0.54% operator delete 586ms 0.54% 88.49% 586ms 0.54% boost::shared_ptr::operator-> (inline) 27ms 0.025% 88.51% 573ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.51% 573ms 0.52% boost::numeric::ublas::vector::vector (inline) 27ms 0.025% 88.54% 559ms 0.51% MutableElement::RegisterWithNodes (inline) 7ms 0.0064% 88.55% 554ms 0.51% std::vector::_M_default_append (inline)