File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 79806ms, 87.99% of 90700ms total Dropped 1028 nodes (cum <= 453.50ms) flat flat% sum% cum cum% 0 0% 0% 90446ms 99.72% __libc_start_call_main 0 0% 0% 90446ms 99.72% __libc_start_main_impl 0 0% 0% 90446ms 99.72% _start 0 0% 0% 90427ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 90427ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 90427ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 90427ms 99.70% main 0 0% 0% 90398ms 99.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 90398ms 99.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 90398ms 99.67% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0055% 0.0055% 90391ms 99.66% AbstractCellBasedSimulation::Solve 9ms 0.0099% 0.015% 47552ms 52.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.024% 0.04% 44645ms 49.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 36ms 0.04% 0.079% 43721ms 48.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 444ms 0.49% 0.57% 34186ms 37.69% NagaiHondaForce::AddForceContribution 0 0% 0.57% 31323ms 34.53% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0011% 0.57% 18342ms 20.22% VertexBasedCellPopulation::Update 0 0% 0.57% 18237ms 20.11% MutableVertexMesh::ReMesh 75ms 0.083% 0.65% 15871ms 17.50% Cell::ReadyToDivide 8173ms 9.01% 9.66% 15628ms 17.23% Cylindrical2dVertexMesh::GetVectorFromAtoB 49ms 0.054% 9.72% 14961ms 16.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 85ms 0.094% 9.81% 13991ms 15.43% NagaiHondaForce::GetAdhesionParameter 107ms 0.12% 9.93% 12845ms 14.16% SimpleWntCellCycleModel::UpdateCellCyclePhase 326ms 0.36% 10.29% 12106ms 13.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 78ms 0.086% 10.37% 11732ms 12.93% CellPropertyCollection::GetPropertiesType (inline) 493ms 0.54% 10.92% 11380ms 12.55% std::__new_allocator::allocate (inline) 219ms 0.24% 11.16% 10895ms 12.01% boost::numeric::ublas::vector_assign (inline) 0 0% 11.16% 10820ms 11.93% std::allocator_traits::allocate (inline) 765ms 0.84% 12.00% 10785ms 11.89% operator new 0 0% 12.00% 10677ms 11.77% std::_Rb_tree::_M_create_node (inline) 0 0% 12.00% 10352ms 11.41% std::_Rb_tree::_M_get_node (inline) 3460ms 3.81% 15.82% 9707ms 10.70% __GI___libc_malloc 81ms 0.089% 15.91% 9645ms 10.63% AbstractCellProperty::IsSubType (inline) 2145ms 2.36% 18.27% 9560ms 10.54% __dynamic_cast 44ms 0.049% 18.32% 9456ms 10.43% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.051% 18.37% 9366ms 10.33% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 18.37% 9307ms 10.26% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.0044% 18.38% 9276ms 10.23% AbstractCellBasedSimulation::DoCellBirth 103ms 0.11% 18.49% 9241ms 10.19% VertexBasedCellPopulation::GetDampingConstant 108ms 0.12% 18.61% 8445ms 9.31% MutableVertexMesh::CheckForIntersections 0 0% 18.61% 8028ms 8.85% std::_Rb_tree::_M_drop_node (inline) 905ms 1% 19.61% 8026ms 8.85% std::_Rb_tree::_M_erase 2217ms 2.44% 22.05% 7892ms 8.70% boost::numeric::ublas::indexing_vector_assign 52ms 0.057% 22.11% 7594ms 8.37% Cell::GetMutationState 305ms 0.34% 22.44% 7555ms 8.33% std::_Rb_tree::~_Rb_tree (inline) 96ms 0.11% 22.55% 7319ms 8.07% std::__new_allocator::deallocate (inline) 0 0% 22.55% 7301ms 8.05% std::allocator_traits::deallocate (inline) 0 0% 22.55% 7235ms 7.98% std::_Rb_tree::_M_put_node (inline) 0 0% 22.55% 7202ms 7.94% std::set::~set (inline) 48ms 0.053% 22.60% 7175ms 7.91% VertexBasedCellPopulation::GetLocationOfCellCentre 1920ms 2.12% 24.72% 7124ms 7.85% __GI___libc_free 0 0% 24.72% 6899ms 7.61% std::set::insert (inline) 640ms 0.71% 25.43% 6879ms 7.58% VertexMesh::GetCentroidOfElement 359ms 0.4% 25.82% 6651ms 7.33% VertexMesh::GetNextEdgeGradientOfElementAtNode 468ms 0.52% 26.34% 6444ms 7.10% std::map::operator[] (partial-inline) 841ms 0.93% 27.26% 6338ms 6.99% std::_Rb_tree::_M_insert_ (inline) 456ms 0.5% 27.77% 6302ms 6.95% VertexMesh::ElementIncludesPoint 14ms 0.015% 27.78% 6292ms 6.94% MutableVertexMesh::RemoveDeletedNodesAndElements 5992ms 6.61% 34.39% 5992ms 6.61% __strcmp_evex 93ms 0.1% 34.49% 5817ms 6.41% std::_Rb_tree::_Rb_tree (partial-inline) 5628ms 6.21% 40.70% 5628ms 6.21% boost::numeric::ublas::c_vector::operator() 601ms 0.66% 41.36% 5508ms 6.07% std::_Rb_tree::_M_copy (inline) 50ms 0.055% 41.41% 5475ms 6.04% std::set_intersection (inline) 127ms 0.14% 41.55% 5461ms 6.02% SimpleWntCellCycleModel::GetWntLevel 9ms 0.0099% 41.56% 5435ms 5.99% std::set::set (inline) 238ms 0.26% 41.83% 5425ms 5.98% std::__set_intersection 855ms 0.94% 42.77% 5334ms 5.88% AbstractMesh::GetDistanceBetweenNodes 117ms 0.13% 42.90% 5214ms 5.75% WntConcentration::GetWntLevel 4527ms 4.99% 47.89% 5147ms 5.67% _int_free 2108ms 2.32% 50.21% 4795ms 5.29% __cxxabiv1::__si_class_type_info::__do_dyncast 520ms 0.57% 50.79% 4737ms 5.22% std::_Rb_tree::_M_clone_node (inline) 551ms 0.61% 51.39% 4597ms 5.07% boost::numeric::ublas::c_vector::operator[] (inline) 3750ms 4.13% 55.53% 4520ms 4.98% _int_malloc 19ms 0.021% 55.55% 4431ms 4.89% MutableVertexMesh::RemoveDeletedNodes 42ms 0.046% 55.60% 4301ms 4.74% EdgeHelper::RemoveDeletedEdges 0 0% 55.60% 4247ms 4.68% std::insert_iterator::operator= (inline) 1848ms 2.04% 57.63% 4189ms 4.62% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.014% 57.65% 4074ms 4.49% EdgeHelper::UpdateEdgesMapKey 0 0% 57.65% 3986ms 4.39% std::_Rb_tree::_M_insert_unique_ (inline) 28ms 0.031% 57.68% 3887ms 4.29% Cell::GetCellProliferativeType 115ms 0.13% 57.81% 3851ms 4.25% MutableElement::ResetIndex 3848ms 4.24% 62.05% 3848ms 4.24% boost::numeric::ublas::same_impl_ex 1ms 0.0011% 62.05% 3699ms 4.08% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 62.05% 3672ms 4.05% std::_Rb_tree::lower_bound (inline) 0 0% 62.05% 3672ms 4.05% std::map::lower_bound (inline) 54ms 0.06% 62.11% 3381ms 3.73% AbstractCellPopulation::GetCellUsingLocationIndex 38ms 0.042% 62.15% 2931ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0011% 62.15% 2913ms 3.21% std::_Rb_tree::_M_insert_unique 123ms 0.14% 62.29% 2907ms 3.21% AbstractCellProperty::IsType (inline) 101ms 0.11% 62.40% 2864ms 3.16% Cell::SetCellProliferativeType 2839ms 3.13% 65.53% 2839ms 3.13% [libchaste_cell_based.so] 128ms 0.14% 65.67% 2592ms 2.86% boost::detail::shared_count::~shared_count (inline) 0 0% 65.67% 2592ms 2.86% boost::shared_ptr::~shared_ptr (inline) 646ms 0.71% 66.38% 2567ms 2.83% AbstractElement::GetNodeLocation 2406ms 2.65% 69.04% 2416ms 2.66% boost::detail::sp_counted_base::release 156ms 0.17% 69.21% 2271ms 2.50% boost::numeric::ublas::vector_binary::size (inline) 24ms 0.026% 69.23% 2269ms 2.50% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0055% 69.24% 2226ms 2.45% AbstractCellPopulation::Iterator::operator++ (inline) 160ms 0.18% 69.42% 2222ms 2.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.42% 2168ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 42ms 0.046% 69.46% 2159ms 2.38% std::_Rb_tree::erase 19ms 0.021% 69.48% 2137ms 2.36% Cell::GetCellData 0 0% 69.48% 2061ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 278ms 0.31% 69.79% 2053ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 35ms 0.039% 69.83% 2042ms 2.25% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.83% 2035ms 2.24% AbstractCellPopulation::WriteResultsToFiles 1987ms 2.19% 72.02% 1987ms 2.19% [libchaste_mesh.so] 265ms 0.29% 72.31% 1975ms 2.18% VertexMesh::GetAreaGradientOfElementAtNode 37ms 0.041% 72.35% 1938ms 2.14% CellPropertyCollection::HasProperty 1889ms 2.08% 74.43% 1889ms 2.08% std::_Rb_tree::_S_right (inline) 0 0% 74.43% 1887ms 2.08% Cell::HasCellProperty (inline) 334ms 0.37% 74.80% 1849ms 2.04% AbstractCellProperty::IsSame 111ms 0.12% 74.93% 1721ms 1.90% CellPropertyCollection::AddProperty 24ms 0.026% 74.95% 1694ms 1.87% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.95% 1663ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0022% 74.95% 1652ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 88ms 0.097% 75.05% 1552ms 1.71% VertexMesh::GetVolumeOfElement 296ms 0.33% 75.38% 1536ms 1.69% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 3ms 0.0033% 75.38% 1526ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.38% 1526ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 175ms 0.19% 75.57% 1515ms 1.67% std::type_info::operator== (inline) 0 0% 75.57% 1496ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 51ms 0.056% 75.63% 1466ms 1.62% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 75.63% 1370ms 1.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 48ms 0.053% 75.68% 1328ms 1.46% std::_Rb_tree::_M_erase_aux (partial-inline) 68ms 0.075% 75.76% 1325ms 1.46% VertexMesh::GetSurfaceAreaOfElement 2ms 0.0022% 75.76% 1323ms 1.46% tcache_get (inline) 1321ms 1.46% 77.22% 1321ms 1.46% tcache_get_n (inline) 0 0% 77.22% 1265ms 1.39% boost::numeric::ublas::vector_binary::operator() (inline) 52ms 0.057% 77.27% 1251ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 77.27% 1225ms 1.35% OffLatticeSimulation::ApplyBoundaries 1202ms 1.33% 78.60% 1202ms 1.33% std::_Rb_tree_increment 48ms 0.053% 78.65% 1097ms 1.21% CellPropertyRegistry::Get 39ms 0.043% 78.69% 1062ms 1.17% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 86ms 0.095% 78.79% 1034ms 1.14% boost::numeric::ublas::vector_reference::operator() (inline) 13ms 0.014% 78.80% 991ms 1.09% MutableElement::RegisterWithEdges (inline) 36ms 0.04% 78.84% 989ms 1.09% Node::RemoveElement 41ms 0.045% 78.89% 984ms 1.08% Edge::AddElement 15ms 0.017% 78.91% 969ms 1.07% boost::numeric::ublas::detail::expression_type_check (inline) 3ms 0.0033% 78.91% 956ms 1.05% std::set::erase (inline) 580ms 0.64% 79.55% 949ms 1.05% std::_Rb_tree::equal_range (inline) 0 0% 79.55% 942ms 1.04% CellPropertyCollection::~CellPropertyCollection (inline) 936ms 1.03% 80.58% 936ms 1.03% [libstdc++.so.6.0.33] 146ms 0.16% 80.74% 924ms 1.02% boost::numeric::ublas::detail::equals 0 0% 80.74% 885ms 0.98% boost::numeric::ublas::norm_2 (inline) 331ms 0.36% 81.11% 858ms 0.95% boost::numeric::ublas::vector_norm_2::apply 836ms 0.92% 82.03% 836ms 0.92% std::_Rb_tree_insert_and_rebalance 0 0% 82.03% 821ms 0.91% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.012% 82.04% 821ms 0.91% boost::numeric::ublas::c_vector::swap (inline) 149ms 0.16% 82.20% 810ms 0.89% std::swap_ranges (inline) 0 0% 82.20% 798ms 0.88% std::__new_allocator::destroy (inline) 0 0% 82.20% 798ms 0.88% std::allocator_traits::destroy (inline) 797ms 0.88% 83.08% 797ms 0.88% Node::rGetLocation 1ms 0.0011% 83.08% 794ms 0.88% VertexMeshWriter::MakeVtkMesh 0 0% 83.08% 794ms 0.88% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.08% 783ms 0.86% std::_Rb_tree::clear (inline) 0 0% 83.08% 753ms 0.83% std::map::clear (inline) 569ms 0.63% 83.71% 741ms 0.82% CellPropertyCollection::GetProperty 6ms 0.0066% 83.72% 739ms 0.81% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 712ms 0.79% 84.50% 712ms 0.79% tcache_put (inline) 347ms 0.38% 84.89% 680ms 0.75% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 42ms 0.046% 84.93% 667ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.93% 661ms 0.73% std::iter_swap (inline) 661ms 0.73% 85.66% 661ms 0.73% std::swap (inline) 0 0% 85.66% 651ms 0.72% boost::numeric::ublas::norm_inf (inline) 259ms 0.29% 85.95% 651ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 50ms 0.055% 86.00% 646ms 0.71% std::less::operator() (inline) 78ms 0.086% 86.09% 606ms 0.67% MutableElement::GetNodeLocalIndex 95ms 0.1% 86.19% 606ms 0.67% std::_Rb_tree::find (inline) 448ms 0.49% 86.69% 596ms 0.66% std::operator< (inline) 0 0% 86.69% 573ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.018% 86.70% 573ms 0.63% std::_Rb_tree::_M_insert_node (inline) 6ms 0.0066% 86.71% 566ms 0.62% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.71% 566ms 0.62% boost::numeric::ublas::vector::vector (inline) 1ms 0.0011% 86.71% 557ms 0.61% vtkPolygon::New 4ms 0.0044% 86.72% 556ms 0.61% vtkPolygon::vtkPolygon 543ms 0.6% 87.31% 543ms 0.6% std::vector::size (inline) 533ms 0.59% 87.90% 533ms 0.59% Node::GetIndex 21ms 0.023% 87.93% 512ms 0.56% MutableElement::RegisterWithNodes (inline) 2ms 0.0022% 87.93% 504ms 0.56% std::map::find (inline) 53ms 0.058% 87.99% 475ms 0.52% Node::AddElement 3ms 0.0033% 87.99% 466ms 0.51% std::_Vector_base::_M_allocate (inline)