File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94514ms, 87.92% of 107506ms total Dropped 1081 nodes (cum <= 537.53ms) flat flat% sum% cum cum% 0 0% 0% 106992ms 99.52% __libc_start_call_main 0 0% 0% 106992ms 99.52% __libc_start_main_impl 0 0% 0% 106992ms 99.52% _start 0 0% 0% 106975ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106975ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106975ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106975ms 99.51% main 0 0% 0% 106940ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106940ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106940ms 99.47% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 106933ms 99.47% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.02% 55648ms 51.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 25ms 0.023% 0.043% 52487ms 48.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 126ms 0.12% 0.16% 51476ms 47.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 354ms 0.33% 0.49% 39946ms 37.16% NagaiHondaForce::AddForceContribution 2ms 0.0019% 0.49% 38553ms 35.86% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.49% 23843ms 22.18% VertexBasedCellPopulation::Update 0 0% 0.49% 23719ms 22.06% MutableVertexMesh::ReMesh 14594ms 13.58% 14.07% 22980ms 21.38% Cylindrical2dVertexMesh::GetVectorFromAtoB 94ms 0.087% 14.15% 17465ms 16.25% Cell::ReadyToDivide 70ms 0.065% 14.22% 16261ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 326ms 0.3% 14.52% 15023ms 13.97% NagaiHondaForce::GetAdhesionParameter 393ms 0.37% 14.89% 14501ms 13.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 127ms 0.12% 15.01% 13832ms 12.87% SimpleWntCellCycleModel::UpdateCellCyclePhase 124ms 0.12% 15.12% 13313ms 12.38% CellPropertyCollection::GetPropertiesType (inline) 341ms 0.32% 15.44% 12998ms 12.09% boost::numeric::ublas::vector_assign (inline) 150ms 0.14% 15.58% 11989ms 11.15% MutableVertexMesh::CheckForIntersections 3159ms 2.94% 18.52% 11039ms 10.27% __dynamic_cast 67ms 0.062% 18.58% 11038ms 10.27% VertexBasedCellPopulation::GetDampingConstant 101ms 0.094% 18.67% 10904ms 10.14% AbstractCellProperty::IsSubType (inline) 76ms 0.071% 18.74% 10336ms 9.61% AbstractTargetAreaModifier::UpdateTargetAreas 18ms 0.017% 18.76% 10252ms 9.54% AbstractCellBasedSimulation::DoCellBirth 54ms 0.05% 18.81% 10243ms 9.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1201ms 1.12% 19.93% 9876ms 9.19% std::__new_allocator::allocate (inline) 2674ms 2.49% 22.41% 9585ms 8.92% boost::numeric::ublas::indexing_vector_assign 0 0% 22.41% 9350ms 8.70% std::_Rb_tree::_M_create_node (inline) 0 0% 22.41% 9330ms 8.68% std::allocator_traits::allocate (inline) 1422ms 1.32% 23.74% 9235ms 8.59% std::_Rb_tree::_M_erase 357ms 0.33% 24.07% 8975ms 8.35% VertexMesh::GetNextEdgeGradientOfElementAtNode 818ms 0.76% 24.83% 8850ms 8.23% VertexMesh::ElementIncludesPoint 814ms 0.76% 25.59% 8768ms 8.16% operator new 30ms 0.028% 25.62% 8726ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.62% 8712ms 8.10% std::_Rb_tree::_M_get_node (inline) 73ms 0.068% 25.68% 8569ms 7.97% Cell::GetMutationState 217ms 0.2% 25.89% 8461ms 7.87% std::_Rb_tree::~_Rb_tree (inline) 439ms 0.41% 26.29% 8303ms 7.72% VertexMesh::GetCentroidOfElement 0 0% 26.29% 8145ms 7.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.29% 8124ms 7.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.29% 8022ms 7.46% std::set::~set (inline) 234ms 0.22% 26.51% 7916ms 7.36% std::__new_allocator::deallocate (inline) 0 0% 26.51% 7877ms 7.33% std::allocator_traits::deallocate (inline) 0 0% 26.51% 7836ms 7.29% std::_Rb_tree::_M_put_node (inline) 3214ms 2.99% 29.50% 7833ms 7.29% __GI___libc_free 3112ms 2.89% 32.40% 7749ms 7.21% __GI___libc_malloc 9ms 0.0084% 32.40% 7359ms 6.85% MutableVertexMesh::RemoveDeletedNodesAndElements 488ms 0.45% 32.86% 7295ms 6.79% std::map::operator[] (partial-inline) 1329ms 1.24% 34.09% 7226ms 6.72% AbstractMesh::GetDistanceBetweenNodes 138ms 0.13% 34.22% 6743ms 6.27% std::_Rb_tree::_Rb_tree (partial-inline) 708ms 0.66% 34.88% 6364ms 5.92% std::_Rb_tree::_M_copy (inline) 105ms 0.098% 34.98% 6354ms 5.91% SimpleWntCellCycleModel::GetWntLevel 9ms 0.0084% 34.99% 6338ms 5.90% std::set::set (inline) 6210ms 5.78% 40.76% 6210ms 5.78% __strcmp_avx2 145ms 0.13% 40.90% 6177ms 5.75% WntConcentration::GetWntLevel 6066ms 5.64% 46.54% 6066ms 5.64% boost::numeric::ublas::c_vector::operator() 2405ms 2.24% 48.78% 5654ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 0 0% 48.78% 5478ms 5.10% std::set::insert (inline) 2679ms 2.49% 51.27% 5399ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 708ms 0.66% 51.93% 5384ms 5.01% std::_Rb_tree::_M_clone_node (inline) 23ms 0.021% 51.95% 5329ms 4.96% MutableVertexMesh::RemoveDeletedNodes 32ms 0.03% 51.98% 5140ms 4.78% EdgeHelper::RemoveDeletedEdges 39ms 0.036% 52.02% 4881ms 4.54% EdgeHelper::UpdateEdgesMapKey 1461ms 1.36% 53.37% 4712ms 4.38% boost::numeric::ublas::c_vector::operator[] (inline) 57ms 0.053% 53.43% 4665ms 4.34% std::set_intersection (inline) 274ms 0.25% 53.68% 4608ms 4.29% std::__set_intersection 4279ms 3.98% 57.66% 4605ms 4.28% _int_free 614ms 0.57% 58.23% 4589ms 4.27% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.23% 4535ms 4.22% std::_Rb_tree::lower_bound (inline) 0 0% 58.23% 4535ms 4.22% std::map::lower_bound (inline) 217ms 0.2% 58.44% 4504ms 4.19% MutableElement::ResetIndex 0 0% 58.44% 4444ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 33ms 0.031% 58.47% 3988ms 3.71% Cell::GetCellProliferativeType 3922ms 3.65% 62.11% 3922ms 3.65% boost::numeric::ublas::same_impl_ex 102ms 0.095% 62.21% 3866ms 3.60% AbstractCellPopulation::GetCellUsingLocationIndex 61ms 0.057% 62.27% 3562ms 3.31% AbstractCellProperty::IsType (inline) 12ms 0.011% 62.28% 3451ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.28% 3322ms 3.09% std::insert_iterator::operator= (inline) 43ms 0.04% 62.32% 3201ms 2.98% Cell::SetCellProliferativeType 711ms 0.66% 62.98% 3016ms 2.81% AbstractElement::GetNodeLocation 2142ms 1.99% 64.97% 2977ms 2.77% _int_malloc 7ms 0.0065% 64.98% 2953ms 2.75% std::_Rb_tree::_M_insert_unique_ (inline) 567ms 0.53% 65.51% 2783ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 39ms 0.036% 65.54% 2771ms 2.58% std::_Rb_tree::erase 464ms 0.43% 65.97% 2746ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 2734ms 2.54% 68.52% 2734ms 2.54% std::_Rb_tree::_S_right (inline) 713ms 0.66% 69.18% 2530ms 2.35% AbstractCellProperty::IsSame 2ms 0.0019% 69.18% 2525ms 2.35% std::_Rb_tree::_M_insert_unique 269ms 0.25% 69.43% 2500ms 2.33% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.43% 2479ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 50ms 0.047% 69.48% 2454ms 2.28% CellPropertyCollection::HasProperty 0 0% 69.48% 2386ms 2.22% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.48% 2371ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.48% 2344ms 2.18% Cell::HasCellProperty (inline) 146ms 0.14% 69.61% 2340ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 28ms 0.026% 69.64% 2241ms 2.08% Cell::GetCellData 48ms 0.045% 69.68% 2231ms 2.08% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00093% 69.69% 2229ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 105ms 0.098% 69.78% 2188ms 2.04% VertexMesh::GetVolumeOfElement 204ms 0.19% 69.97% 2186ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 2106ms 1.96% 71.93% 2106ms 1.96% std::_Rb_tree_increment 0 0% 71.93% 1947ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.93% 1936ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.93% 1936ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.00093% 71.93% 1931ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 55ms 0.051% 71.98% 1852ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 432ms 0.4% 72.39% 1817ms 1.69% std::type_info::operator== (inline) 1255ms 1.17% 73.55% 1813ms 1.69% std::_Rb_tree::equal_range (inline) 0 0% 73.55% 1742ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.028% 73.58% 1682ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.02% 73.60% 1664ms 1.55% VertexMesh::GetSurfaceAreaOfElement 176ms 0.16% 73.76% 1529ms 1.42% CellPropertyCollection::AddProperty 27ms 0.025% 73.79% 1513ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 126ms 0.12% 73.91% 1497ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 86ms 0.08% 73.99% 1472ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 51ms 0.047% 74.03% 1468ms 1.37% Node::RemoveElement 0 0% 74.03% 1458ms 1.36% tcache_get (inline) 1458ms 1.36% 75.39% 1458ms 1.36% tcache_get_n (inline) 24ms 0.022% 75.41% 1435ms 1.33% std::set::erase (inline) 0 0% 75.41% 1431ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0019% 75.41% 1278ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 75.41% 1229ms 1.14% boost::numeric::ublas::norm_2 (inline) 0 0% 75.41% 1226ms 1.14% std::_Rb_tree::_Auto_node::_Auto_node (inline) 545ms 0.51% 75.92% 1221ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1156ms 1.08% 77.00% 1156ms 1.08% std::_Rb_tree_insert_and_rebalance 76ms 0.071% 77.07% 1132ms 1.05% std::less::operator() (inline) 1114ms 1.04% 78.10% 1114ms 1.04% Node::rGetLocation 87ms 0.081% 78.18% 1112ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 84ms 0.078% 78.26% 1096ms 1.02% std::_Rb_tree::find (inline) 1094ms 1.02% 79.28% 1094ms 1.02% [libchaste_cell_based.so] 13ms 0.012% 79.29% 1077ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 870ms 0.81% 80.10% 1056ms 0.98% std::operator< (inline) 24ms 0.022% 80.12% 1055ms 0.98% CellPropertyRegistry::Get 24ms 0.022% 80.15% 1047ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 236ms 0.22% 80.37% 1014ms 0.94% boost::numeric::ublas::detail::equals 1ms 0.00093% 80.37% 994ms 0.92% std::_Rb_tree::clear (inline) 0 0% 80.37% 980ms 0.91% std::map::clear (inline) 159ms 0.15% 80.51% 954ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.51% 954ms 0.89% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0084% 80.52% 944ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 944ms 0.88% 81.40% 944ms 0.88% [libchaste_mesh.so] 918ms 0.85% 82.25% 918ms 0.85% std::vector::size (inline) 0 0% 82.25% 887ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.00093% 82.26% 887ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 352ms 0.33% 82.58% 886ms 0.82% Edge::GetMapIndex 89ms 0.083% 82.67% 886ms 0.82% std::swap_ranges (inline) 0 0% 82.67% 881ms 0.82% std::map::find (inline) 2ms 0.0019% 82.67% 848ms 0.79% VertexMeshWriter::MakeVtkMesh 175ms 0.16% 82.83% 843ms 0.78% boost::shared_ptr::shared_ptr (inline) 105ms 0.098% 82.93% 826ms 0.77% MutableElement::GetNodeLocalIndex 0 0% 82.93% 799ms 0.74% CellPropertyCollection::~CellPropertyCollection (inline) 798ms 0.74% 83.67% 798ms 0.74% std::swap (inline) 0 0% 83.67% 797ms 0.74% std::iter_swap (inline) 767ms 0.71% 84.38% 773ms 0.72% boost::detail::sp_counted_base::release 25ms 0.023% 84.41% 771ms 0.72% MutableElement::RegisterWithEdges (inline) 38ms 0.035% 84.44% 767ms 0.71% Edge::AddElement 113ms 0.11% 84.55% 764ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 740ms 0.69% 85.24% 740ms 0.69% Node::GetIndex 462ms 0.43% 85.67% 731ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.67% 707ms 0.66% boost::numeric::ublas::norm_inf (inline) 376ms 0.35% 86.02% 707ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.02% 694ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.04% 694ms 0.65% std::_Rb_tree::_M_insert_node (inline) 94ms 0.087% 86.13% 687ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.13% 687ms 0.64% std::allocator_traits::construct (inline) 641ms 0.6% 86.72% 668ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 86.72% 638ms 0.59% std::_Rb_tree::_M_construct_node (inline) 623ms 0.58% 87.30% 623ms 0.58% [libstdc++.so.6.0.33] 0 0% 87.30% 614ms 0.57% std::_Vector_base::_M_allocate (inline) 36ms 0.033% 87.33% 613ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 87.33% 605ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.00093% 87.34% 590ms 0.55% vtkPolygon::New 2ms 0.0019% 87.34% 588ms 0.55% vtkPolygon::vtkPolygon 23ms 0.021% 87.36% 569ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.36% 569ms 0.53% boost::numeric::ublas::vector::vector (inline) 34ms 0.032% 87.39% 568ms 0.53% Node::AddElement 564ms 0.52% 87.92% 564ms 0.52% boost::shared_ptr::operator-> (inline)