File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95655ms, 87.49% of 109327ms total Dropped 1131 nodes (cum <= 546.63ms) flat flat% sum% cum cum% 0 0% 0% 108945ms 99.65% __libc_start_call_main 0 0% 0% 108945ms 99.65% __libc_start_main_impl 0 0% 0% 108945ms 99.65% _start 0 0% 0% 108922ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108922ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108922ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108922ms 99.63% main 0 0% 0% 108877ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108877ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108877ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 108869ms 99.58% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.025% 56527ms 51.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.038% 53099ms 48.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 153ms 0.14% 0.18% 52015ms 47.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 304ms 0.28% 0.46% 40227ms 36.80% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.46% 39119ms 35.78% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.46% 24015ms 21.97% VertexBasedCellPopulation::Update 2ms 0.0018% 0.46% 23882ms 21.84% MutableVertexMesh::ReMesh 14581ms 13.34% 13.80% 23093ms 21.12% Cylindrical2dVertexMesh::GetVectorFromAtoB 97ms 0.089% 13.89% 17984ms 16.45% Cell::ReadyToDivide 62ms 0.057% 13.94% 16659ms 15.24% AbstractPhaseBasedCellCycleModel::ReadyToDivide 340ms 0.31% 14.26% 14710ms 13.46% NagaiHondaForce::GetAdhesionParameter 168ms 0.15% 14.41% 14293ms 13.07% SimpleWntCellCycleModel::UpdateCellCyclePhase 489ms 0.45% 14.86% 14084ms 12.88% boost::numeric::ublas::c_vector::c_vector (partial-inline) 115ms 0.11% 14.96% 13641ms 12.48% CellPropertyCollection::GetPropertiesType (inline) 299ms 0.27% 15.24% 12535ms 11.47% boost::numeric::ublas::vector_assign (inline) 153ms 0.14% 15.37% 11873ms 10.86% MutableVertexMesh::CheckForIntersections 3369ms 3.08% 18.46% 11756ms 10.75% __dynamic_cast 74ms 0.068% 18.52% 11660ms 10.67% AbstractCellProperty::IsSubType (inline) 88ms 0.08% 18.60% 11175ms 10.22% VertexBasedCellPopulation::GetDampingConstant 53ms 0.048% 18.65% 10700ms 9.79% AbstractTargetAreaModifier::UpdateTargetAreas 43ms 0.039% 18.69% 10625ms 9.72% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.027% 18.72% 10327ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1375ms 1.26% 19.98% 9892ms 9.05% std::__new_allocator::allocate (inline) 2913ms 2.66% 22.64% 9498ms 8.69% boost::numeric::ublas::indexing_vector_assign 402ms 0.37% 23.01% 9441ms 8.64% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.01% 9399ms 8.60% std::_Rb_tree::_M_create_node (inline) 0 0% 23.01% 9319ms 8.52% std::allocator_traits::allocate (inline) 1218ms 1.11% 24.12% 8922ms 8.16% std::_Rb_tree::_M_erase 849ms 0.78% 24.90% 8687ms 7.95% VertexMesh::ElementIncludesPoint 29ms 0.027% 24.93% 8655ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.93% 8586ms 7.85% std::_Rb_tree::_M_get_node (inline) 85ms 0.078% 25.00% 8561ms 7.83% Cell::GetMutationState 798ms 0.73% 25.73% 8553ms 7.82% operator new 0 0% 25.73% 8354ms 7.64% std::_Rb_tree::_Alloc_node::operator() (inline) 453ms 0.41% 26.15% 8276ms 7.57% VertexMesh::GetCentroidOfElement 0 0% 26.15% 8084ms 7.39% std::_Rb_tree::_M_drop_node (inline) 210ms 0.19% 26.34% 8071ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 245ms 0.22% 26.56% 7823ms 7.16% std::__new_allocator::deallocate (inline) 0 0% 26.56% 7809ms 7.14% std::allocator_traits::deallocate (inline) 22ms 0.02% 26.58% 7789ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.58% 7749ms 7.09% std::_Rb_tree::_M_put_node (inline) 0 0% 26.58% 7660ms 7.01% std::set::~set (inline) 2931ms 2.68% 29.27% 7552ms 6.91% __GI___libc_malloc 1395ms 1.28% 30.54% 7488ms 6.85% AbstractMesh::GetDistanceBetweenNodes 2471ms 2.26% 32.80% 7393ms 6.76% __GI___libc_free 248ms 0.23% 33.03% 7372ms 6.74% std::_Rb_tree::_Rb_tree (partial-inline) 494ms 0.45% 33.48% 7268ms 6.65% std::map::operator[] (partial-inline) 780ms 0.71% 34.19% 6843ms 6.26% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.21% 6811ms 6.23% std::set::set (inline) 6764ms 6.19% 40.40% 6764ms 6.19% __strcmp_avx2 145ms 0.13% 40.53% 6235ms 5.70% SimpleWntCellCycleModel::GetWntLevel 6075ms 5.56% 46.08% 6075ms 5.56% boost::numeric::ublas::c_vector::operator() 176ms 0.16% 46.25% 6027ms 5.51% WntConcentration::GetWntLevel 802ms 0.73% 46.98% 5787ms 5.29% std::_Rb_tree::_M_clone_node (inline) 2973ms 2.72% 49.70% 5746ms 5.26% __cxxabiv1::__si_class_type_info::__do_dyncast 2424ms 2.22% 51.92% 5632ms 5.15% std::_Rb_tree::_M_lower_bound (inline) 1994ms 1.82% 53.74% 5230ms 4.78% boost::numeric::ublas::c_vector::operator[] (inline) 20ms 0.018% 53.76% 5229ms 4.78% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.76% 5164ms 4.72% std::set::insert (inline) 36ms 0.033% 53.79% 5030ms 4.60% EdgeHelper::RemoveDeletedEdges 4458ms 4.08% 57.87% 4910ms 4.49% _int_free 195ms 0.18% 58.05% 4826ms 4.41% MutableElement::ResetIndex 0 0% 58.05% 4761ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 37ms 0.034% 58.08% 4663ms 4.27% EdgeHelper::UpdateEdgesMapKey 0 0% 58.08% 4608ms 4.21% std::_Rb_tree::lower_bound (inline) 0 0% 58.08% 4608ms 4.21% std::map::lower_bound (inline) 305ms 0.28% 58.36% 4538ms 4.15% std::set_intersection (inline) 155ms 0.14% 58.50% 4364ms 3.99% AbstractCellPopulation::GetCellUsingLocationIndex 469ms 0.43% 58.93% 4334ms 3.96% std::_Rb_tree::_M_insert_ (inline) 234ms 0.21% 59.14% 4233ms 3.87% std::__set_intersection 23ms 0.021% 59.17% 4049ms 3.70% Cell::GetCellProliferativeType 64ms 0.059% 59.22% 3924ms 3.59% AbstractCellProperty::IsType (inline) 3778ms 3.46% 62.68% 3778ms 3.46% boost::numeric::ublas::same_impl_ex 12ms 0.011% 62.69% 3591ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 72ms 0.066% 62.76% 3278ms 3.00% Cell::SetCellProliferativeType 0 0% 62.76% 3224ms 2.95% std::insert_iterator::operator= (inline) 66ms 0.06% 62.82% 3137ms 2.87% std::_Rb_tree::erase 2146ms 1.96% 64.78% 3131ms 2.86% _int_malloc 861ms 0.79% 65.57% 3058ms 2.80% AbstractElement::GetNodeLocation 41ms 0.038% 65.61% 2846ms 2.60% CellPropertyCollection::HasProperty 7ms 0.0064% 65.61% 2839ms 2.60% std::_Rb_tree::_M_insert_unique_ (inline) 719ms 0.66% 66.27% 2819ms 2.58% AbstractCellProperty::IsSame 0 0% 66.27% 2757ms 2.52% Cell::HasCellProperty (inline) 2682ms 2.45% 68.72% 2682ms 2.45% std::_Rb_tree::_S_right (inline) 0 0% 68.72% 2619ms 2.40% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.72% 2605ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 232ms 0.21% 68.93% 2567ms 2.35% VertexMesh::GetAreaGradientOfElementAtNode 641ms 0.59% 69.52% 2550ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 271ms 0.25% 69.77% 2513ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.77% 2476ms 2.26% AbstractCellPopulation::WriteResultsToFiles 33ms 0.03% 69.80% 2401ms 2.20% Cell::GetCellData 2ms 0.0018% 69.80% 2325ms 2.13% std::_Rb_tree::_M_insert_unique 54ms 0.049% 69.85% 2288ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 103ms 0.094% 69.94% 2285ms 2.09% VertexMesh::GetVolumeOfElement 10ms 0.0091% 69.95% 2126ms 1.94% AbstractCellPopulation::Iterator::operator++ (inline) 172ms 0.16% 70.11% 2106ms 1.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 43ms 0.039% 70.15% 2104ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 502ms 0.46% 70.61% 2100ms 1.92% std::type_info::operator== (inline) 3ms 0.0027% 70.61% 2096ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.61% 2096ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.61% 2026ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 1348ms 1.23% 71.85% 2022ms 1.85% std::_Rb_tree::equal_range (inline) 2ms 0.0018% 71.85% 2015ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1989ms 1.82% 73.67% 1989ms 1.82% std::_Rb_tree_increment 79ms 0.072% 73.74% 1878ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.74% 1811ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.016% 73.75% 1625ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 43ms 0.039% 73.79% 1572ms 1.44% VertexMesh::GetSurfaceAreaOfElement 53ms 0.048% 73.84% 1502ms 1.37% Node::RemoveElement 102ms 0.093% 73.94% 1462ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 33ms 0.03% 73.97% 1453ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.01% 73.98% 1451ms 1.33% std::set::erase (inline) 62ms 0.057% 74.03% 1425ms 1.30% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.03% 1368ms 1.25% boost::numeric::ublas::norm_2 (inline) 590ms 0.54% 74.57% 1352ms 1.24% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 74.57% 1351ms 1.24% OffLatticeSimulation::ApplyBoundaries 0 0% 74.57% 1330ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 1323ms 1.21% 75.78% 1323ms 1.21% [libchaste_cell_based.so] 133ms 0.12% 75.91% 1311ms 1.20% CellPropertyCollection::AddProperty 0 0% 75.91% 1272ms 1.16% tcache_get (inline) 1272ms 1.16% 77.07% 1272ms 1.16% tcache_get_n (inline) 71ms 0.065% 77.13% 1245ms 1.14% std::_Rb_tree::_M_erase_aux (partial-inline) 83ms 0.076% 77.21% 1238ms 1.13% std::less::operator() (inline) 44ms 0.04% 77.25% 1213ms 1.11% CellPropertyRegistry::Get 23ms 0.021% 77.27% 1173ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 944ms 0.86% 78.14% 1155ms 1.06% std::operator< (inline) 10ms 0.0091% 78.14% 1125ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1084ms 0.99% 79.14% 1084ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 79.14% 1067ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0082% 79.14% 1067ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 111ms 0.1% 79.25% 1066ms 0.98% std::_Rb_tree::find (inline) 0 0% 79.25% 1065ms 0.97% std::_Rb_tree::clear (inline) 91ms 0.083% 79.33% 1058ms 0.97% std::swap_ranges (inline) 0 0% 79.33% 1052ms 0.96% std::map::clear (inline) 0 0% 79.33% 1045ms 0.96% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.012% 79.34% 997ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 975ms 0.89% 80.23% 975ms 0.89% Node::rGetLocation 139ms 0.13% 80.36% 972ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.36% 972ms 0.89% boost::shared_ptr::~shared_ptr (inline) 180ms 0.16% 80.52% 971ms 0.89% boost::numeric::ublas::detail::equals 968ms 0.89% 81.41% 968ms 0.89% std::swap (inline) 0 0% 81.41% 967ms 0.88% std::iter_swap (inline) 0 0% 81.41% 903ms 0.83% std::map::find (inline) 264ms 0.24% 81.65% 901ms 0.82% std::__new_allocator::construct (inline) 0 0% 81.65% 901ms 0.82% std::allocator_traits::construct (inline) 3ms 0.0027% 81.65% 852ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 81.65% 813ms 0.74% std::_Rb_tree::_M_construct_node (inline) 811ms 0.74% 82.40% 811ms 0.74% std::vector::size (inline) 810ms 0.74% 83.14% 810ms 0.74% [libchaste_mesh.so] 760ms 0.7% 83.83% 794ms 0.73% boost::detail::sp_counted_base::release 29ms 0.027% 83.86% 772ms 0.71% Edge::AddElement 21ms 0.019% 83.88% 772ms 0.71% MutableElement::RegisterWithEdges (inline) 0 0% 83.88% 769ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 83ms 0.076% 83.95% 767ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 431ms 0.39% 84.35% 762ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 183ms 0.17% 84.52% 752ms 0.69% boost::shared_ptr::shared_ptr (inline) 2ms 0.0018% 84.52% 733ms 0.67% std::_Vector_base::_M_allocate (inline) 412ms 0.38% 84.89% 729ms 0.67% Edge::GetMapIndex 0 0% 84.89% 728ms 0.67% boost::numeric::ublas::norm_inf (inline) 405ms 0.37% 85.26% 728ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 144ms 0.13% 85.40% 691ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 85.40% 682ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.023% 85.42% 682ms 0.62% std::_Rb_tree::_M_insert_node (inline) 678ms 0.62% 86.04% 678ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.04% 673ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 10ms 0.0091% 86.05% 630ms 0.58% std::vector::_M_default_append (inline) 1ms 0.00091% 86.05% 626ms 0.57% vtkPolygon::New 0 0% 86.05% 625ms 0.57% vtkPolygon::vtkPolygon 32ms 0.029% 86.08% 605ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.08% 605ms 0.55% boost::numeric::ublas::vector::vector (inline) 0 0% 86.08% 586ms 0.54% std::map::map (inline) 36ms 0.033% 86.11% 583ms 0.53% MutableElement::RegisterWithNodes (inline) 537ms 0.49% 86.60% 569ms 0.52% boost::detail::shared_count::shared_count (inline) 567ms 0.52% 87.12% 567ms 0.52% Node::GetIndex 408ms 0.37% 87.49% 564ms 0.52% malloc_consolidate