File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96942ms, 87.65% of 110603ms total Dropped 1131 nodes (cum <= 553.01ms) flat flat% sum% cum cum% 0 0% 0% 110258ms 99.69% __libc_start_call_main 0 0% 0% 110258ms 99.69% __libc_start_main_impl 0 0% 0% 110258ms 99.69% _start 0 0% 0% 110236ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110236ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110236ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110236ms 99.67% main 0 0% 0% 110194ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110194ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110194ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 110186ms 99.62% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.017% 56215ms 50.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.0063% 0.024% 52884ms 47.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 148ms 0.13% 0.16% 51838ms 46.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0018% 0.16% 40669ms 36.77% AbstractCellBasedSimulation::UpdateCellPopulation 289ms 0.26% 0.42% 39703ms 35.90% NagaiHondaForce::AddForceContribution 0 0% 0.42% 25729ms 23.26% VertexBasedCellPopulation::Update 0 0% 0.42% 25575ms 23.12% MutableVertexMesh::ReMesh 14883ms 13.46% 13.88% 23460ms 21.21% Cylindrical2dVertexMesh::GetVectorFromAtoB 94ms 0.085% 13.96% 17667ms 15.97% Cell::ReadyToDivide 82ms 0.074% 14.04% 16267ms 14.71% AbstractPhaseBasedCellCycleModel::ReadyToDivide 326ms 0.29% 14.33% 14324ms 12.95% NagaiHondaForce::GetAdhesionParameter 167ms 0.15% 14.48% 13964ms 12.63% SimpleWntCellCycleModel::UpdateCellCyclePhase 467ms 0.42% 14.90% 13865ms 12.54% boost::numeric::ublas::c_vector::c_vector (partial-inline) 116ms 0.1% 15.01% 13697ms 12.38% CellPropertyCollection::GetPropertiesType (inline) 133ms 0.12% 15.13% 13244ms 11.97% MutableVertexMesh::CheckForIntersections 290ms 0.26% 15.39% 12415ms 11.22% boost::numeric::ublas::vector_assign (inline) 3423ms 3.09% 18.49% 11604ms 10.49% __dynamic_cast 85ms 0.077% 18.56% 11517ms 10.41% VertexBasedCellPopulation::GetDampingConstant 71ms 0.064% 18.63% 11485ms 10.38% AbstractCellProperty::IsSubType (inline) 75ms 0.068% 18.69% 10733ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 55ms 0.05% 18.74% 10629ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 19ms 0.017% 18.76% 10262ms 9.28% AbstractCellBasedSimulation::DoCellBirth 837ms 0.76% 19.52% 10173ms 9.20% VertexMesh::ElementIncludesPoint 1341ms 1.21% 20.73% 9927ms 8.98% std::__new_allocator::allocate (inline) 0 0% 20.73% 9506ms 8.59% std::_Rb_tree::_M_create_node (inline) 0 0% 20.73% 9421ms 8.52% std::allocator_traits::allocate (inline) 2866ms 2.59% 23.32% 9325ms 8.43% boost::numeric::ublas::indexing_vector_assign 357ms 0.32% 23.64% 9308ms 8.42% VertexMesh::GetNextEdgeGradientOfElementAtNode 1327ms 1.20% 24.84% 8951ms 8.09% std::_Rb_tree::_M_erase 25ms 0.023% 24.87% 8800ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.87% 8712ms 7.88% std::_Rb_tree::_M_get_node (inline) 89ms 0.08% 24.95% 8626ms 7.80% Cell::GetMutationState 786ms 0.71% 25.66% 8583ms 7.76% operator new 0 0% 25.66% 8379ms 7.58% std::_Rb_tree::_Alloc_node::operator() (inline) 463ms 0.42% 26.08% 8361ms 7.56% VertexMesh::GetCentroidOfElement 243ms 0.22% 26.30% 8017ms 7.25% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.30% 7974ms 7.21% std::_Rb_tree::_M_drop_node (inline) 18ms 0.016% 26.31% 7946ms 7.18% MutableVertexMesh::RemoveDeletedNodesAndElements 231ms 0.21% 26.52% 7728ms 6.99% std::__new_allocator::deallocate (inline) 481ms 0.43% 26.96% 7726ms 6.99% std::map::operator[] (partial-inline) 0 0% 26.96% 7723ms 6.98% std::allocator_traits::deallocate (inline) 0 0% 26.96% 7657ms 6.92% std::_Rb_tree::_M_put_node (inline) 0 0% 26.96% 7602ms 6.87% std::set::~set (inline) 2826ms 2.56% 29.51% 7570ms 6.84% __GI___libc_malloc 1390ms 1.26% 30.77% 7469ms 6.75% AbstractMesh::GetDistanceBetweenNodes 217ms 0.2% 30.96% 7237ms 6.54% std::_Rb_tree::_Rb_tree (partial-inline) 2299ms 2.08% 33.04% 7213ms 6.52% __GI___libc_free 34ms 0.031% 33.07% 6746ms 6.10% std::set::set (inline) 785ms 0.71% 33.78% 6740ms 6.09% std::_Rb_tree::_M_copy (inline) 6569ms 5.94% 39.72% 6569ms 5.94% __strcmp_avx2 118ms 0.11% 39.83% 6355ms 5.75% SimpleWntCellCycleModel::GetWntLevel 6191ms 5.60% 45.43% 6191ms 5.60% boost::numeric::ublas::c_vector::operator() 175ms 0.16% 45.59% 6152ms 5.56% WntConcentration::GetWntLevel 2413ms 2.18% 47.77% 6008ms 5.43% std::_Rb_tree::_M_lower_bound (inline) 826ms 0.75% 48.51% 5701ms 5.15% std::_Rb_tree::_M_clone_node (inline) 30ms 0.027% 48.54% 5571ms 5.04% MutableVertexMesh::RemoveDeletedNodes 43ms 0.039% 48.58% 5387ms 4.87% EdgeHelper::RemoveDeletedEdges 0 0% 48.58% 5384ms 4.87% std::set::insert (inline) 2809ms 2.54% 51.12% 5367ms 4.85% __cxxabiv1::__si_class_type_info::__do_dyncast 1941ms 1.75% 52.87% 5365ms 4.85% boost::numeric::ublas::c_vector::operator[] (inline) 39ms 0.035% 52.91% 5018ms 4.54% EdgeHelper::UpdateEdgesMapKey 0 0% 52.91% 5016ms 4.54% std::_Rb_tree::lower_bound (inline) 0 0% 52.91% 5016ms 4.54% std::map::lower_bound (inline) 4432ms 4.01% 56.92% 4892ms 4.42% _int_free 210ms 0.19% 57.11% 4822ms 4.36% MutableElement::ResetIndex 1ms 0.0009% 57.11% 4667ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 149ms 0.13% 57.24% 4594ms 4.15% AbstractCellPopulation::GetCellUsingLocationIndex 526ms 0.48% 57.72% 4534ms 4.10% std::_Rb_tree::_M_insert_ (inline) 120ms 0.11% 57.83% 4220ms 3.82% std::set_intersection (inline) 229ms 0.21% 58.03% 4100ms 3.71% std::__set_intersection 45ms 0.041% 58.07% 3866ms 3.50% Cell::GetCellProliferativeType 62ms 0.056% 58.13% 3845ms 3.48% AbstractCellProperty::IsType (inline) 3668ms 3.32% 61.45% 3668ms 3.32% boost::numeric::ublas::same_impl_ex 13ms 0.012% 61.46% 3519ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2244ms 2.03% 63.49% 3215ms 2.91% _int_malloc 0 0% 63.49% 3179ms 2.87% std::insert_iterator::operator= (inline) 76ms 0.069% 63.56% 3060ms 2.77% std::_Rb_tree::erase 83ms 0.075% 63.63% 3036ms 2.74% Cell::SetCellProliferativeType 3022ms 2.73% 66.36% 3022ms 2.73% std::_Rb_tree::_S_right (inline) 797ms 0.72% 67.08% 2967ms 2.68% AbstractElement::GetNodeLocation 23ms 0.021% 67.10% 2829ms 2.56% CellPropertyCollection::HasProperty 12ms 0.011% 67.12% 2758ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 67.12% 2754ms 2.49% Cell::HasCellProperty (inline) 768ms 0.69% 67.81% 2740ms 2.48% AbstractCellProperty::IsSame 238ms 0.22% 68.03% 2672ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 5ms 0.0045% 68.03% 2626ms 2.37% std::_Rb_tree::_M_insert_unique 0 0% 68.03% 2618ms 2.37% boost::numeric::ublas::c_vector::operator-= (inline) 231ms 0.21% 68.24% 2571ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.24% 2554ms 2.31% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.24% 2534ms 2.29% AbstractCellPopulation::WriteResultsToFiles 615ms 0.56% 68.79% 2524ms 2.28% boost::numeric::ublas::vector_binary::size (inline) 26ms 0.024% 68.82% 2522ms 2.28% Cell::GetCellData 89ms 0.08% 68.90% 2281ms 2.06% VertexMesh::GetVolumeOfElement 56ms 0.051% 68.95% 2201ms 1.99% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 42ms 0.038% 68.99% 2180ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0027% 68.99% 2122ms 1.92% AbstractCellPopulation::Iterator::operator++ (inline) 184ms 0.17% 69.16% 2118ms 1.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 2117ms 1.91% 71.07% 2117ms 1.91% std::_Rb_tree_increment 103ms 0.093% 71.16% 2070ms 1.87% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 71.16% 2068ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0009% 71.16% 2057ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.16% 2057ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0018% 71.17% 2053ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1287ms 1.16% 72.33% 1990ms 1.80% std::_Rb_tree::equal_range (inline) 491ms 0.44% 72.77% 1972ms 1.78% std::type_info::operator== (inline) 1ms 0.0009% 72.77% 1863ms 1.68% VertexMeshWriter::WriteVtkUsingMesh 73ms 0.066% 72.84% 1862ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 38ms 0.034% 72.88% 1658ms 1.50% VertexMesh::GetSurfaceAreaOfElement 21ms 0.019% 72.89% 1634ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1562ms 1.41% 74.31% 1562ms 1.41% __memcpy_avx_unaligned_erms 52ms 0.047% 74.35% 1529ms 1.38% std::__copy_move::__copy_m (inline) 0 0% 74.35% 1529ms 1.38% std::__copy_move_a (inline) 0 0% 74.35% 1529ms 1.38% std::__copy_move_a1 (inline) 0 0% 74.35% 1529ms 1.38% std::__copy_move_a2 (inline) 0 0% 74.35% 1529ms 1.38% std::copy (inline) 36ms 0.033% 74.39% 1509ms 1.36% Node::RemoveElement 12ms 0.011% 74.40% 1478ms 1.34% std::set::erase (inline) 146ms 0.13% 74.53% 1474ms 1.33% CellPropertyCollection::AddProperty 37ms 0.033% 74.56% 1469ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 84ms 0.076% 74.64% 1446ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 3ms 0.0027% 74.64% 1354ms 1.22% OffLatticeSimulation::ApplyBoundaries 0 0% 74.64% 1346ms 1.22% tcache_get (inline) 1346ms 1.22% 75.86% 1346ms 1.22% tcache_get_n (inline) 67ms 0.061% 75.92% 1329ms 1.20% std::less::operator() (inline) 1302ms 1.18% 77.10% 1302ms 1.18% [libchaste_cell_based.so] 61ms 0.055% 77.15% 1271ms 1.15% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 77.15% 1269ms 1.15% boost::numeric::ublas::norm_2 (inline) 1028ms 0.93% 78.08% 1262ms 1.14% std::operator< (inline) 576ms 0.52% 78.60% 1260ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 78.60% 1249ms 1.13% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 78.60% 1181ms 1.07% std::_Rb_tree::clear (inline) 74ms 0.067% 78.67% 1159ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.67% 1156ms 1.05% std::map::clear (inline) 11ms 0.0099% 78.68% 1143ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.68% 1127ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 23ms 0.021% 78.70% 1121ms 1.01% CellPropertyRegistry::Get 0 0% 78.70% 1121ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0081% 78.71% 1121ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 3ms 0.0027% 78.71% 1114ms 1.01% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 86ms 0.078% 78.79% 1112ms 1.01% std::swap_ranges (inline) 1108ms 1.00% 79.79% 1108ms 1.00% std::_Rb_tree_insert_and_rebalance 1027ms 0.93% 80.72% 1027ms 0.93% std::swap (inline) 0 0% 80.72% 1026ms 0.93% std::iter_swap (inline) 13ms 0.012% 80.73% 1023ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 133ms 0.12% 80.85% 1017ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.85% 1017ms 0.92% boost::shared_ptr::~shared_ptr (inline) 94ms 0.085% 80.93% 1011ms 0.91% std::_Rb_tree::find (inline) 158ms 0.14% 81.08% 1000ms 0.9% boost::numeric::ublas::detail::equals 951ms 0.86% 81.94% 951ms 0.86% Node::rGetLocation 898ms 0.81% 82.75% 898ms 0.81% std::vector::size (inline) 207ms 0.19% 82.94% 879ms 0.79% std::__new_allocator::construct (inline) 0 0% 82.94% 879ms 0.79% std::allocator_traits::construct (inline) 1ms 0.0009% 82.94% 879ms 0.79% std::map::find (inline) 0 0% 82.94% 870ms 0.79% VertexMeshWriter::MakeVtkMesh 811ms 0.73% 83.67% 845ms 0.76% boost::detail::sp_counted_base::release 209ms 0.19% 83.86% 819ms 0.74% boost::shared_ptr::shared_ptr (inline) 20ms 0.018% 83.88% 814ms 0.74% MutableElement::RegisterWithEdges (inline) 23ms 0.021% 83.90% 811ms 0.73% Edge::AddElement 403ms 0.36% 84.26% 801ms 0.72% Edge::GetMapIndex 0 0% 84.26% 794ms 0.72% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.26% 788ms 0.71% boost::numeric::ublas::norm_inf (inline) 386ms 0.35% 84.61% 788ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 759ms 0.69% 85.30% 759ms 0.69% [libchaste_mesh.so] 743ms 0.67% 85.97% 743ms 0.67% [libstdc++.so.6.0.33] 420ms 0.38% 86.35% 728ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.35% 724ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.35% 709ms 0.64% std::_Vector_base::_M_allocate (inline) 0 0% 86.35% 684ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.35% 683ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.37% 683ms 0.62% std::_Rb_tree::_M_insert_node (inline) 653ms 0.59% 86.96% 653ms 0.59% Node::GetIndex 132ms 0.12% 87.08% 621ms 0.56% MutableElement::GetNodeLocalIndex 25ms 0.023% 87.10% 619ms 0.56% MutableElement::RegisterWithNodes (inline) 575ms 0.52% 87.62% 610ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 87.62% 610ms 0.55% vtkPolygon::New 2ms 0.0018% 87.62% 609ms 0.55% vtkPolygon::vtkPolygon 23ms 0.021% 87.64% 606ms 0.55% Node::AddElement 5ms 0.0045% 87.65% 576ms 0.52% std::vector::_M_default_append (inline)