File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95355ms, 88.10% of 108235ms total Dropped 1126 nodes (cum <= 541.17ms) flat flat% sum% cum cum% 0 0% 0% 107762ms 99.56% __libc_start_call_main 0 0% 0% 107762ms 99.56% __libc_start_main_impl 0 0% 0% 107762ms 99.56% _start 0 0% 0% 107744ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107744ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107744ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107744ms 99.55% main 0 0% 0% 107703ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107703ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107703ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107695ms 99.50% AbstractCellBasedSimulation::Solve 7ms 0.0065% 0.0092% 55909ms 51.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 23ms 0.021% 0.03% 52739ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 110ms 0.1% 0.13% 51707ms 47.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 421ms 0.39% 0.52% 40234ms 37.17% NagaiHondaForce::AddForceContribution 0 0% 0.52% 39052ms 36.08% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.52% 24282ms 22.43% VertexBasedCellPopulation::Update 0 0% 0.52% 24141ms 22.30% MutableVertexMesh::ReMesh 14680ms 13.56% 14.08% 23296ms 21.52% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.07% 14.15% 17285ms 15.97% Cell::ReadyToDivide 121ms 0.11% 14.27% 16144ms 14.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 319ms 0.29% 14.56% 14986ms 13.85% NagaiHondaForce::GetAdhesionParameter 451ms 0.42% 14.98% 14531ms 13.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 153ms 0.14% 15.12% 13725ms 12.68% SimpleWntCellCycleModel::UpdateCellCyclePhase 126ms 0.12% 15.24% 13279ms 12.27% CellPropertyCollection::GetPropertiesType (inline) 382ms 0.35% 15.59% 12922ms 11.94% boost::numeric::ublas::vector_assign (inline) 139ms 0.13% 15.72% 12074ms 11.16% MutableVertexMesh::CheckForIntersections 3020ms 2.79% 18.51% 11111ms 10.27% __dynamic_cast 97ms 0.09% 18.60% 11027ms 10.19% AbstractCellProperty::IsSubType (inline) 72ms 0.067% 18.66% 10961ms 10.13% VertexBasedCellPopulation::GetDampingConstant 80ms 0.074% 18.74% 10271ms 9.49% AbstractTargetAreaModifier::UpdateTargetAreas 56ms 0.052% 18.79% 10163ms 9.39% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.026% 18.81% 10155ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1232ms 1.14% 19.95% 9870ms 9.12% std::__new_allocator::allocate (inline) 2703ms 2.50% 22.45% 9625ms 8.89% boost::numeric::ublas::indexing_vector_assign 1405ms 1.30% 23.75% 9339ms 8.63% std::_Rb_tree::_M_erase 0 0% 23.75% 9324ms 8.61% std::_Rb_tree::_M_create_node (inline) 0 0% 23.75% 9297ms 8.59% std::allocator_traits::allocate (inline) 380ms 0.35% 24.10% 9125ms 8.43% VertexMesh::GetNextEdgeGradientOfElementAtNode 810ms 0.75% 24.85% 8959ms 8.28% VertexMesh::ElementIncludesPoint 25ms 0.023% 24.87% 8908ms 8.23% VertexBasedCellPopulation::GetLocationOfCellCentre 852ms 0.79% 25.66% 8756ms 8.09% operator new 0 0% 25.66% 8648ms 7.99% std::_Rb_tree::_M_get_node (inline) 516ms 0.48% 26.13% 8498ms 7.85% VertexMesh::GetCentroidOfElement 224ms 0.21% 26.34% 8469ms 7.82% std::_Rb_tree::~_Rb_tree (inline) 76ms 0.07% 26.41% 8391ms 7.75% Cell::GetMutationState 0 0% 26.41% 8303ms 7.67% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.41% 8223ms 7.60% std::_Rb_tree::_Alloc_node::operator() (inline) 258ms 0.24% 26.65% 8053ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 26.65% 8018ms 7.41% std::allocator_traits::deallocate (inline) 0 0% 26.65% 8011ms 7.40% std::set::~set (inline) 0 0% 26.65% 7964ms 7.36% std::_Rb_tree::_M_put_node (inline) 3074ms 2.84% 29.49% 7885ms 7.29% __GI___libc_free 3059ms 2.83% 32.32% 7726ms 7.14% __GI___libc_malloc 13ms 0.012% 32.33% 7600ms 7.02% MutableVertexMesh::RemoveDeletedNodesAndElements 466ms 0.43% 32.76% 7329ms 6.77% std::map::operator[] (partial-inline) 1265ms 1.17% 33.93% 7263ms 6.71% AbstractMesh::GetDistanceBetweenNodes 136ms 0.13% 34.05% 6770ms 6.25% std::_Rb_tree::_Rb_tree (partial-inline) 6457ms 5.97% 40.02% 6457ms 5.97% __strcmp_avx2 618ms 0.57% 40.59% 6440ms 5.95% std::_Rb_tree::_M_copy (inline) 92ms 0.085% 40.68% 6392ms 5.91% SimpleWntCellCycleModel::GetWntLevel 6365ms 5.88% 46.56% 6365ms 5.88% boost::numeric::ublas::c_vector::operator() 11ms 0.01% 46.57% 6323ms 5.84% std::set::set (inline) 135ms 0.12% 46.69% 6208ms 5.74% WntConcentration::GetWntLevel 2451ms 2.26% 48.96% 5745ms 5.31% std::_Rb_tree::_M_lower_bound (inline) 2669ms 2.47% 51.42% 5654ms 5.22% __cxxabiv1::__si_class_type_info::__do_dyncast 808ms 0.75% 52.17% 5530ms 5.11% std::_Rb_tree::_M_clone_node (inline) 30ms 0.028% 52.20% 5487ms 5.07% MutableVertexMesh::RemoveDeletedNodes 0 0% 52.20% 5351ms 4.94% std::set::insert (inline) 39ms 0.036% 52.23% 5332ms 4.93% EdgeHelper::RemoveDeletedEdges 35ms 0.032% 52.26% 5050ms 4.67% EdgeHelper::UpdateEdgesMapKey 1443ms 1.33% 53.60% 4870ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 4468ms 4.13% 57.73% 4803ms 4.44% _int_free 208ms 0.19% 57.92% 4654ms 4.30% MutableElement::ResetIndex 0 0% 57.92% 4653ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 57.92% 4653ms 4.30% std::map::lower_bound (inline) 1ms 0.00092% 57.92% 4608ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 55ms 0.051% 57.97% 4543ms 4.20% std::set_intersection (inline) 483ms 0.45% 58.42% 4506ms 4.16% std::_Rb_tree::_M_insert_ (inline) 295ms 0.27% 58.69% 4488ms 4.15% std::__set_intersection 4070ms 3.76% 62.45% 4070ms 3.76% boost::numeric::ublas::same_impl_ex 124ms 0.11% 62.56% 3964ms 3.66% AbstractCellPopulation::GetCellUsingLocationIndex 37ms 0.034% 62.60% 3908ms 3.61% Cell::GetCellProliferativeType 6ms 0.0055% 62.60% 3580ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 65ms 0.06% 62.66% 3534ms 3.27% AbstractCellProperty::IsType (inline) 0 0% 62.66% 3281ms 3.03% std::insert_iterator::operator= (inline) 751ms 0.69% 63.36% 3158ms 2.92% AbstractElement::GetNodeLocation 60ms 0.055% 63.41% 3149ms 2.91% Cell::SetCellProliferativeType 2253ms 2.08% 65.49% 3138ms 2.90% _int_malloc 40ms 0.037% 65.53% 2941ms 2.72% std::_Rb_tree::erase 6ms 0.0055% 65.54% 2927ms 2.70% std::_Rb_tree::_M_insert_unique_ (inline) 571ms 0.53% 66.06% 2853ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 2718ms 2.51% 68.57% 2718ms 2.51% std::_Rb_tree::_S_right (inline) 488ms 0.45% 69.03% 2618ms 2.42% std::_Rb_tree_const_iterator::operator++ (inline) 669ms 0.62% 69.64% 2526ms 2.33% AbstractCellProperty::IsSame 0 0% 69.64% 2490ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.64% 2437ms 2.25% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0018% 69.65% 2424ms 2.24% std::_Rb_tree::_M_insert_unique 0 0% 69.65% 2409ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 241ms 0.22% 69.87% 2395ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 35ms 0.032% 69.90% 2385ms 2.20% CellPropertyCollection::HasProperty 28ms 0.026% 69.93% 2318ms 2.14% Cell::GetCellData 113ms 0.1% 70.03% 2276ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.03% 2275ms 2.10% Cell::HasCellProperty (inline) 92ms 0.085% 70.12% 2260ms 2.09% VertexMesh::GetVolumeOfElement 1ms 0.00092% 70.12% 2180ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 195ms 0.18% 70.30% 2156ms 1.99% AbstractCellPopulation::Iterator::IsRealCell 47ms 0.043% 70.34% 2155ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.34% 2008ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.34% 1997ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1953ms 1.80% 72.14% 1953ms 1.80% std::_Rb_tree_increment 2ms 0.0018% 72.15% 1926ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.15% 1926ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1328ms 1.23% 73.37% 1911ms 1.77% std::_Rb_tree::equal_range (inline) 84ms 0.078% 73.45% 1873ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 414ms 0.38% 73.83% 1857ms 1.72% std::type_info::operator== (inline) 0 0% 73.83% 1801ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.018% 73.85% 1678ms 1.55% VertexMesh::GetSurfaceAreaOfElement 27ms 0.025% 73.88% 1647ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 124ms 0.11% 73.99% 1589ms 1.47% boost::numeric::ublas::vector_reference::operator() (inline) 45ms 0.042% 74.03% 1533ms 1.42% Node::RemoveElement 15ms 0.014% 74.05% 1501ms 1.39% std::set::erase (inline) 0 0% 74.05% 1466ms 1.35% boost::numeric::ublas::vector_binary::operator() (inline) 30ms 0.028% 74.07% 1456ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 177ms 0.16% 74.24% 1430ms 1.32% CellPropertyCollection::AddProperty 71ms 0.066% 74.30% 1403ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.30% 1352ms 1.25% tcache_get (inline) 1352ms 1.25% 75.55% 1352ms 1.25% tcache_get_n (inline) 1ms 0.00092% 75.55% 1265ms 1.17% OffLatticeSimulation::ApplyBoundaries 0 0% 75.55% 1229ms 1.14% boost::numeric::ublas::norm_2 (inline) 527ms 0.49% 76.04% 1220ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 83ms 0.077% 76.12% 1191ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 1190ms 1.10% 77.22% 1190ms 1.10% Node::rGetLocation 78ms 0.072% 77.29% 1184ms 1.09% std::less::operator() (inline) 1152ms 1.06% 78.35% 1152ms 1.06% std::_Rb_tree_insert_and_rebalance 907ms 0.84% 79.19% 1106ms 1.02% std::operator< (inline) 0 0% 79.19% 1101ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.19% 1095ms 1.01% std::_Rb_tree::clear (inline) 89ms 0.082% 79.27% 1086ms 1.00% std::_Rb_tree::find (inline) 0 0% 79.27% 1075ms 0.99% std::map::clear (inline) 18ms 0.017% 79.29% 1062ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 16ms 0.015% 79.30% 1059ms 0.98% CellPropertyRegistry::Get 1056ms 0.98% 80.28% 1056ms 0.98% [libchaste_cell_based.so] 1017ms 0.94% 81.22% 1017ms 0.94% std::vector::size (inline) 152ms 0.14% 81.36% 998ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.36% 998ms 0.92% boost::shared_ptr::~shared_ptr (inline) 7ms 0.0065% 81.37% 971ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.37% 970ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 81.37% 970ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 92ms 0.085% 81.46% 965ms 0.89% std::swap_ranges (inline) 960ms 0.89% 82.34% 960ms 0.89% [libchaste_mesh.so] 371ms 0.34% 82.69% 956ms 0.88% Edge::GetMapIndex 27ms 0.025% 82.71% 914ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 138ms 0.13% 82.84% 879ms 0.81% boost::numeric::ublas::detail::equals 874ms 0.81% 83.65% 874ms 0.81% std::swap (inline) 0 0% 83.65% 873ms 0.81% std::iter_swap (inline) 0 0% 83.65% 863ms 0.8% std::map::find (inline) 1ms 0.00092% 83.65% 847ms 0.78% VertexMeshWriter::MakeVtkMesh 822ms 0.76% 84.41% 827ms 0.76% boost::detail::sp_counted_base::release 115ms 0.11% 84.51% 821ms 0.76% MutableElement::GetNodeLocalIndex 169ms 0.16% 84.67% 796ms 0.74% boost::shared_ptr::shared_ptr (inline) 30ms 0.028% 84.70% 787ms 0.73% MutableElement::RegisterWithEdges (inline) 131ms 0.12% 84.82% 770ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.026% 84.84% 765ms 0.71% Edge::AddElement 455ms 0.42% 85.26% 749ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 117ms 0.11% 85.37% 743ms 0.69% std::__new_allocator::construct (inline) 0 0% 85.37% 743ms 0.69% std::allocator_traits::construct (inline) 739ms 0.68% 86.05% 739ms 0.68% Node::GetIndex 0 0% 86.05% 722ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.05% 713ms 0.66% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.07% 713ms 0.66% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.07% 697ms 0.64% boost::numeric::ublas::norm_inf (inline) 345ms 0.32% 86.39% 697ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.39% 676ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.39% 648ms 0.6% std::_Vector_base::_M_allocate (inline) 596ms 0.55% 86.94% 627ms 0.58% boost::detail::shared_count::shared_count (inline) 1ms 0.00092% 86.94% 602ms 0.56% vtkPolygon::New 1ms 0.00092% 86.95% 601ms 0.56% vtkPolygon::vtkPolygon 26ms 0.024% 86.97% 596ms 0.55% MutableElement::RegisterWithNodes (inline) 22ms 0.02% 86.99% 595ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.99% 595ms 0.55% boost::numeric::ublas::vector::vector (inline) 580ms 0.54% 87.53% 580ms 0.54% operator delete 575ms 0.53% 88.06% 575ms 0.53% [libstdc++.so.6.0.33] 32ms 0.03% 88.09% 559ms 0.52% Node::AddElement 0 0% 88.09% 554ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 15ms 0.014% 88.10% 548ms 0.51% std::vector::_M_default_append (inline)