File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95341ms, 88.51% of 107723ms total Dropped 1098 nodes (cum <= 538.62ms) flat flat% sum% cum cum% 0 0% 0% 107467ms 99.76% __libc_start_call_main 0 0% 0% 107467ms 99.76% __libc_start_main_impl 0 0% 0% 107467ms 99.76% _start 0 0% 0% 107446ms 99.74% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107446ms 99.74% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107446ms 99.74% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107446ms 99.74% main 0 0% 0% 107406ms 99.71% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107406ms 99.71% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107406ms 99.71% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107398ms 99.70% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.014% 56719ms 52.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 24ms 0.022% 0.036% 53217ms 49.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 72ms 0.067% 0.1% 52113ms 48.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 389ms 0.36% 0.46% 40473ms 37.57% NagaiHondaForce::AddForceContribution 0 0% 0.46% 37387ms 34.71% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.47% 22199ms 20.61% VertexBasedCellPopulation::Update 1ms 0.00093% 0.47% 22078ms 20.50% MutableVertexMesh::ReMesh 97ms 0.09% 0.56% 18015ms 16.72% Cell::ReadyToDivide 8992ms 8.35% 8.90% 17655ms 16.39% Cylindrical2dVertexMesh::GetVectorFromAtoB 25ms 0.023% 8.93% 16931ms 15.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 115ms 0.11% 9.03% 16930ms 15.72% NagaiHondaForce::GetAdhesionParameter 85ms 0.079% 9.11% 14560ms 13.52% SimpleWntCellCycleModel::UpdateCellCyclePhase 848ms 0.79% 9.90% 14022ms 13.02% std::__new_allocator::allocate (inline) 438ms 0.41% 10.31% 13836ms 12.84% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.31% 13554ms 12.58% std::allocator_traits::allocate (inline) 0 0% 10.31% 13346ms 12.39% std::_Rb_tree::_M_create_node (inline) 81ms 0.075% 10.38% 13242ms 12.29% CellPropertyCollection::GetPropertiesType (inline) 817ms 0.76% 11.14% 13068ms 12.13% operator new 0 0% 11.14% 12958ms 12.03% std::_Rb_tree::_M_get_node (inline) 287ms 0.27% 11.41% 12346ms 11.46% boost::numeric::ublas::vector_assign (inline) 4044ms 3.75% 15.16% 11879ms 11.03% __GI___libc_malloc 0 0% 15.16% 11526ms 10.70% std::_Rb_tree::_Alloc_node::operator() (inline) 87ms 0.081% 15.24% 11277ms 10.47% VertexBasedCellPopulation::GetDampingConstant 101ms 0.094% 15.33% 10898ms 10.12% AbstractCellProperty::IsSubType (inline) 2701ms 2.51% 17.84% 10827ms 10.05% __dynamic_cast 46ms 0.043% 17.88% 10814ms 10.04% AbstractTargetAreaModifier::UpdateTargetAreas 6ms 0.0056% 17.89% 10754ms 9.98% AbstractCellBasedSimulation::DoCellBirth 49ms 0.045% 17.94% 10724ms 9.96% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 148ms 0.14% 18.07% 9916ms 9.21% MutableVertexMesh::CheckForIntersections 1019ms 0.95% 19.02% 9413ms 8.74% std::_Rb_tree::_M_erase 0 0% 19.02% 9399ms 8.73% std::_Rb_tree::_M_drop_node (inline) 493ms 0.46% 19.48% 8956ms 8.31% std::map::operator[] (partial-inline) 2572ms 2.39% 21.86% 8938ms 8.30% boost::numeric::ublas::indexing_vector_assign 348ms 0.32% 22.19% 8867ms 8.23% std::_Rb_tree::~_Rb_tree (inline) 119ms 0.11% 22.30% 8522ms 7.91% std::__new_allocator::deallocate (inline) 0 0% 22.30% 8498ms 7.89% std::allocator_traits::deallocate (inline) 0 0% 22.30% 8480ms 7.87% std::set::~set (inline) 63ms 0.058% 22.36% 8469ms 7.86% Cell::GetMutationState 0 0% 22.36% 8441ms 7.84% std::_Rb_tree::_M_put_node (inline) 50ms 0.046% 22.40% 8382ms 7.78% VertexBasedCellPopulation::GetLocationOfCellCentre 2047ms 1.90% 24.30% 8203ms 7.61% __GI___libc_free 0 0% 24.30% 8092ms 7.51% std::set::insert (inline) 10ms 0.0093% 24.31% 7845ms 7.28% MutableVertexMesh::RemoveDeletedNodesAndElements 436ms 0.4% 24.72% 7802ms 7.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 576ms 0.53% 25.25% 7796ms 7.24% VertexMesh::GetCentroidOfElement 177ms 0.16% 25.42% 7471ms 6.94% std::_Rb_tree::_Rb_tree (partial-inline) 916ms 0.85% 26.27% 7468ms 6.93% std::_Rb_tree::_M_insert_ (inline) 520ms 0.48% 26.75% 7292ms 6.77% VertexMesh::ElementIncludesPoint 715ms 0.66% 27.41% 7103ms 6.59% std::_Rb_tree::_M_copy (inline) 7ms 0.0065% 27.42% 7008ms 6.51% std::set::set (inline) 6495ms 6.03% 33.45% 6495ms 6.03% boost::numeric::ublas::c_vector::operator() 53ms 0.049% 33.50% 6477ms 6.01% std::set_intersection (inline) 140ms 0.13% 33.63% 6424ms 5.96% SimpleWntCellCycleModel::GetWntLevel 269ms 0.25% 33.88% 6424ms 5.96% std::__set_intersection 6384ms 5.93% 39.80% 6384ms 5.93% __strcmp_evex 2510ms 2.33% 42.13% 6362ms 5.91% std::_Rb_tree::_M_lower_bound (inline) 689ms 0.64% 42.77% 6187ms 5.74% std::_Rb_tree::_M_clone_node (inline) 129ms 0.12% 42.89% 6137ms 5.70% WntConcentration::GetWntLevel 5345ms 4.96% 47.86% 6108ms 5.67% _int_free 956ms 0.89% 48.74% 5991ms 5.56% AbstractMesh::GetDistanceBetweenNodes 31ms 0.029% 48.77% 5732ms 5.32% MutableVertexMesh::RemoveDeletedNodes 4710ms 4.37% 53.14% 5628ms 5.22% _int_malloc 55ms 0.051% 53.19% 5590ms 5.19% EdgeHelper::RemoveDeletedEdges 0 0% 53.19% 5470ms 5.08% std::_Rb_tree::lower_bound (inline) 0 0% 53.19% 5470ms 5.08% std::map::lower_bound (inline) 20ms 0.019% 53.21% 5311ms 4.93% EdgeHelper::UpdateEdgesMapKey 603ms 0.56% 53.77% 5307ms 4.93% boost::numeric::ublas::c_vector::operator[] (inline) 2486ms 2.31% 56.08% 5252ms 4.88% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.08% 5143ms 4.77% std::insert_iterator::operator= (inline) 0 0% 56.08% 4832ms 4.49% std::_Rb_tree::_M_insert_unique_ (inline) 115ms 0.11% 56.19% 4719ms 4.38% MutableElement::ResetIndex 48ms 0.045% 56.23% 4615ms 4.28% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.23% 4425ms 4.11% AbstractCellBasedSimulation::DoCellRemoval (inline) 23ms 0.021% 56.25% 4424ms 4.11% Cell::GetCellProliferativeType 4388ms 4.07% 60.33% 4388ms 4.07% boost::numeric::ublas::same_impl_ex 50ms 0.046% 60.37% 3456ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 172ms 0.16% 60.53% 3428ms 3.18% AbstractCellProperty::IsType (inline) 3409ms 3.16% 63.70% 3409ms 3.16% [libchaste_cell_based.so] 120ms 0.11% 63.81% 3301ms 3.06% Cell::SetCellProliferativeType 3287ms 3.05% 66.86% 3287ms 3.05% std::_Rb_tree::_S_right (inline) 1ms 0.00093% 66.86% 3260ms 3.03% std::_Rb_tree::_M_insert_unique 144ms 0.13% 66.99% 3203ms 2.97% boost::detail::shared_count::~shared_count (inline) 0 0% 66.99% 3203ms 2.97% boost::shared_ptr::~shared_ptr (inline) 2981ms 2.77% 69.76% 2989ms 2.77% boost::detail::sp_counted_base::release 39ms 0.036% 69.80% 2952ms 2.74% std::_Rb_tree::_M_emplace_hint_unique 847ms 0.79% 70.58% 2942ms 2.73% AbstractElement::GetNodeLocation 213ms 0.2% 70.78% 2938ms 2.73% AbstractCellPopulation::Iterator::IsRealCell 3ms 0.0028% 70.79% 2933ms 2.72% AbstractCellPopulation::Iterator::operator++ (inline) 48ms 0.045% 70.83% 2672ms 2.48% std::_Rb_tree::erase 0 0% 70.83% 2623ms 2.43% boost::numeric::ublas::c_vector::assign (inline) 137ms 0.13% 70.96% 2581ms 2.40% boost::numeric::ublas::vector_binary::size (inline) 8ms 0.0074% 70.96% 2536ms 2.35% Cell::GetCellData 313ms 0.29% 71.25% 2475ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.25% 2440ms 2.27% AbstractCellPopulation::WriteResultsToFiles 42ms 0.039% 71.29% 2350ms 2.18% CellPropertyCollection::HasProperty 0 0% 71.29% 2336ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 58ms 0.054% 71.35% 2318ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.35% 2293ms 2.13% Cell::HasCellProperty (inline) 39ms 0.036% 71.38% 2289ms 2.12% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2277ms 2.11% 73.50% 2277ms 2.11% [libchaste_mesh.so] 250ms 0.23% 73.73% 2200ms 2.04% VertexMesh::GetAreaGradientOfElementAtNode 461ms 0.43% 74.16% 2120ms 1.97% AbstractCellProperty::IsSame 340ms 0.32% 74.47% 2076ms 1.93% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.47% 2003ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 74.48% 1997ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 96ms 0.089% 74.56% 1847ms 1.71% VertexMesh::GetVolumeOfElement 0 0% 74.56% 1820ms 1.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.0028% 74.57% 1816ms 1.69% tcache_get (inline) 0 0% 74.57% 1813ms 1.68% VertexMeshWriter::WriteVtkUsingMesh 1813ms 1.68% 76.25% 1813ms 1.68% tcache_get_n (inline) 154ms 0.14% 76.39% 1741ms 1.62% CellPropertyCollection::AddProperty 6ms 0.0056% 76.40% 1717ms 1.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.40% 1717ms 1.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 73ms 0.068% 76.47% 1703ms 1.58% AbstractCellPopulation::GetLocationIndexUsingCell 172ms 0.16% 76.63% 1659ms 1.54% std::type_info::operator== (inline) 66ms 0.061% 76.69% 1646ms 1.53% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 76.69% 1538ms 1.43% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 76.69% 1509ms 1.40% OffLatticeSimulation::ApplyBoundaries 1498ms 1.39% 78.08% 1498ms 1.39% std::_Rb_tree_increment 61ms 0.057% 78.13% 1480ms 1.37% std::_Rb_tree::_M_erase_aux (partial-inline) 65ms 0.06% 78.20% 1460ms 1.36% VertexMesh::GetSurfaceAreaOfElement 57ms 0.053% 78.25% 1382ms 1.28% boost::numeric::ublas::c_vector::operator= (inline) 810ms 0.75% 79.00% 1308ms 1.21% std::_Rb_tree::equal_range (inline) 45ms 0.042% 79.04% 1305ms 1.21% Node::RemoveElement 57ms 0.053% 79.09% 1302ms 1.21% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 3ms 0.0028% 79.10% 1263ms 1.17% std::set::erase (inline) 131ms 0.12% 79.22% 1237ms 1.15% boost::numeric::ublas::vector_reference::operator() (inline) 17ms 0.016% 79.23% 1229ms 1.14% MutableElement::RegisterWithEdges (inline) 41ms 0.038% 79.27% 1223ms 1.14% Edge::AddElement 0 0% 79.27% 1154ms 1.07% CellPropertyCollection::~CellPropertyCollection (inline) 71ms 0.066% 79.34% 1153ms 1.07% CellPropertyRegistry::Get 1084ms 1.01% 80.34% 1084ms 1.01% std::_Rb_tree_insert_and_rebalance 1075ms 1% 81.34% 1075ms 1% [libstdc++.so.6.0.33] 27ms 0.025% 81.37% 1063ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.37% 1006ms 0.93% boost::numeric::ublas::norm_2 (inline) 184ms 0.17% 81.54% 1002ms 0.93% boost::numeric::ublas::detail::equals 112ms 0.1% 81.64% 972ms 0.9% std::_Rb_tree::find (inline) 378ms 0.35% 81.99% 968ms 0.9% boost::numeric::ublas::vector_norm_2::apply 0 0% 81.99% 961ms 0.89% std::__new_allocator::destroy (inline) 0 0% 81.99% 961ms 0.89% std::allocator_traits::destroy (inline) 0 0% 81.99% 960ms 0.89% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.0019% 82.00% 942ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 82.00% 941ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0019% 82.00% 941ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 181ms 0.17% 82.17% 939ms 0.87% std::swap_ranges (inline) 16ms 0.015% 82.18% 934ms 0.87% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 50ms 0.046% 82.23% 904ms 0.84% std::__copy_move::__copy_m (inline) 0 0% 82.23% 904ms 0.84% std::__copy_move_a (inline) 0 0% 82.23% 904ms 0.84% std::__copy_move_a1 (inline) 0 0% 82.23% 904ms 0.84% std::__copy_move_a2 (inline) 0 0% 82.23% 904ms 0.84% std::copy (inline) 1ms 0.00093% 82.23% 901ms 0.84% std::_Rb_tree::clear (inline) 880ms 0.82% 83.04% 880ms 0.82% tcache_put (inline) 873ms 0.81% 83.85% 873ms 0.81% Node::rGetLocation 0 0% 83.85% 873ms 0.81% std::map::clear (inline) 850ms 0.79% 84.64% 850ms 0.79% __memcpy_avx512_unaligned_erms 71ms 0.066% 84.71% 837ms 0.78% std::less::operator() (inline) 2ms 0.0019% 84.71% 832ms 0.77% std::map::find (inline) 647ms 0.6% 85.31% 820ms 0.76% CellPropertyCollection::GetProperty 587ms 0.54% 85.86% 766ms 0.71% std::operator< (inline) 0 0% 85.86% 758ms 0.7% std::iter_swap (inline) 758ms 0.7% 86.56% 758ms 0.7% std::swap (inline) 360ms 0.33% 86.90% 750ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.90% 736ms 0.68% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.023% 86.92% 736ms 0.68% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.92% 724ms 0.67% boost::numeric::ublas::norm_inf (inline) 298ms 0.28% 87.19% 724ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 713ms 0.66% 87.86% 713ms 0.66% std::vector::size (inline) 0 0% 87.86% 697ms 0.65% vtkPolygon::New 0 0% 87.86% 697ms 0.65% vtkPolygon::vtkPolygon 61ms 0.057% 87.91% 674ms 0.63% MutableElement::GetNodeLocalIndex 21ms 0.019% 87.93% 623ms 0.58% MutableElement::RegisterWithNodes (inline) 40ms 0.037% 87.97% 598ms 0.56% Node::AddElement 1ms 0.00093% 87.97% 595ms 0.55% std::_Vector_base::_M_allocate (inline) 576ms 0.53% 88.51% 576ms 0.53% Node::GetIndex