File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97233ms, 88.62% of 109716ms total Dropped 1122 nodes (cum <= 548.58ms) flat flat% sum% cum cum% 0 0% 0% 109230ms 99.56% __libc_start_call_main 0 0% 0% 109230ms 99.56% __libc_start_main_impl 0 0% 0% 109230ms 99.56% _start 0 0% 0% 109209ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109209ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109209ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109209ms 99.54% main 0 0% 0% 109169ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109169ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109169ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109161ms 99.49% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.015% 56662ms 51.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.026% 53466ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 137ms 0.12% 0.15% 51925ms 47.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 337ms 0.31% 0.46% 39869ms 36.34% NagaiHondaForce::AddForceContribution 0 0% 0.46% 39360ms 35.87% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.46% 24328ms 22.17% VertexBasedCellPopulation::Update 1ms 0.00091% 0.46% 24191ms 22.05% MutableVertexMesh::ReMesh 14545ms 13.26% 13.72% 22894ms 20.87% Cylindrical2dVertexMesh::GetVectorFromAtoB 114ms 0.1% 13.82% 17694ms 16.13% Cell::ReadyToDivide 80ms 0.073% 13.89% 16386ms 14.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 329ms 0.3% 14.19% 14713ms 13.41% NagaiHondaForce::GetAdhesionParameter 433ms 0.39% 14.59% 14420ms 13.14% boost::numeric::ublas::c_vector::c_vector (partial-inline) 148ms 0.13% 14.72% 14033ms 12.79% CellPropertyCollection::GetPropertiesType (inline) 125ms 0.11% 14.84% 13918ms 12.69% SimpleWntCellCycleModel::UpdateCellCyclePhase 409ms 0.37% 15.21% 12835ms 11.70% boost::numeric::ublas::vector_assign (inline) 125ms 0.11% 15.33% 12040ms 10.97% MutableVertexMesh::CheckForIntersections 3443ms 3.14% 18.46% 11546ms 10.52% __dynamic_cast 66ms 0.06% 18.52% 11532ms 10.51% VertexBasedCellPopulation::GetDampingConstant 60ms 0.055% 18.58% 11425ms 10.41% AbstractCellProperty::IsSubType (inline) 83ms 0.076% 18.65% 10673ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.056% 18.71% 10570ms 9.63% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 38ms 0.035% 18.74% 10411ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1394ms 1.27% 20.01% 10288ms 9.38% std::__new_allocator::allocate (inline) 0 0% 20.01% 9782ms 8.92% std::_Rb_tree::_M_create_node (inline) 0 0% 20.01% 9750ms 8.89% std::allocator_traits::allocate (inline) 2628ms 2.40% 22.41% 9552ms 8.71% boost::numeric::ublas::indexing_vector_assign 0 0% 22.41% 9085ms 8.28% std::_Rb_tree::_M_get_node (inline) 799ms 0.73% 23.14% 9029ms 8.23% operator new 1444ms 1.32% 24.45% 9029ms 8.23% std::_Rb_tree::_M_erase 795ms 0.72% 25.18% 8868ms 8.08% VertexMesh::ElementIncludesPoint 25ms 0.023% 25.20% 8836ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 340ms 0.31% 25.51% 8752ms 7.98% VertexMesh::GetNextEdgeGradientOfElementAtNode 76ms 0.069% 25.58% 8735ms 7.96% Cell::GetMutationState 0 0% 25.58% 8577ms 7.82% std::_Rb_tree::_Alloc_node::operator() (inline) 477ms 0.43% 26.02% 8324ms 7.59% VertexMesh::GetCentroidOfElement 240ms 0.22% 26.23% 8207ms 7.48% std::_Rb_tree::~_Rb_tree (inline) 3253ms 2.96% 29.20% 8061ms 7.35% __GI___libc_malloc 0 0% 29.20% 7845ms 7.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.20% 7716ms 7.03% std::set::~set (inline) 20ms 0.018% 29.22% 7606ms 6.93% MutableVertexMesh::RemoveDeletedNodesAndElements 195ms 0.18% 29.39% 7603ms 6.93% std::__new_allocator::deallocate (inline) 0 0% 29.39% 7580ms 6.91% std::allocator_traits::deallocate (inline) 0 0% 29.39% 7505ms 6.84% std::_Rb_tree::_M_put_node (inline) 480ms 0.44% 29.83% 7504ms 6.84% std::map::operator[] (partial-inline) 3410ms 3.11% 32.94% 7503ms 6.84% __GI___libc_free 1405ms 1.28% 34.22% 7171ms 6.54% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 153ms 0.14% 34.36% 7023ms 6.40% std::_Rb_tree::_Rb_tree (partial-inline) 612ms 0.56% 34.92% 6655ms 6.07% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.93% 6605ms 6.02% std::set::set (inline) 6520ms 5.94% 40.88% 6520ms 5.94% __strcmp_avx2 95ms 0.087% 40.96% 6392ms 5.83% SimpleWntCellCycleModel::GetWntLevel 180ms 0.16% 41.13% 6211ms 5.66% WntConcentration::GetWntLevel 6114ms 5.57% 46.70% 6114ms 5.57% boost::numeric::ublas::c_vector::operator() 2499ms 2.28% 48.98% 6108ms 5.57% std::_Rb_tree::_M_lower_bound (inline) 844ms 0.77% 49.75% 5753ms 5.24% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.75% 5642ms 5.14% std::set::insert (inline) 2759ms 2.51% 52.26% 5621ms 5.12% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.019% 52.28% 5406ms 4.93% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 52.31% 5260ms 4.79% EdgeHelper::RemoveDeletedEdges 48ms 0.044% 52.36% 5014ms 4.57% EdgeHelper::UpdateEdgesMapKey 0 0% 52.36% 4855ms 4.43% std::_Rb_tree::lower_bound (inline) 0 0% 52.36% 4855ms 4.43% std::map::lower_bound (inline) 547ms 0.5% 52.85% 4764ms 4.34% std::_Rb_tree::_M_insert_ (inline) 212ms 0.19% 53.05% 4748ms 4.33% MutableElement::ResetIndex 1522ms 1.39% 54.44% 4748ms 4.33% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.00091% 54.44% 4612ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 82ms 0.075% 54.51% 4537ms 4.14% std::set_intersection (inline) 264ms 0.24% 54.75% 4455ms 4.06% std::__set_intersection 116ms 0.11% 54.86% 4285ms 3.91% AbstractCellPopulation::GetCellUsingLocationIndex 3765ms 3.43% 58.29% 4085ms 3.72% _int_free 41ms 0.037% 58.33% 4026ms 3.67% Cell::GetCellProliferativeType 4021ms 3.66% 61.99% 4021ms 3.66% boost::numeric::ublas::same_impl_ex 69ms 0.063% 62.05% 3839ms 3.50% AbstractCellProperty::IsType (inline) 5ms 0.0046% 62.06% 3539ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.06% 3309ms 3.02% std::insert_iterator::operator= (inline) 833ms 0.76% 62.82% 3251ms 2.96% AbstractElement::GetNodeLocation 2271ms 2.07% 64.89% 3170ms 2.89% _int_malloc 34ms 0.031% 64.92% 3151ms 2.87% Cell::SetCellProliferativeType 3044ms 2.77% 67.69% 3044ms 2.77% std::_Rb_tree::_S_right (inline) 43ms 0.039% 67.73% 2983ms 2.72% std::_Rb_tree::erase 4ms 0.0036% 67.74% 2938ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 661ms 0.6% 68.34% 2882ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 750ms 0.68% 69.02% 2811ms 2.56% AbstractCellProperty::IsSame 380ms 0.35% 69.37% 2751ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 36ms 0.033% 69.40% 2739ms 2.50% CellPropertyCollection::HasProperty 0 0% 69.40% 2704ms 2.46% std::_Rb_tree::_M_insert_unique 0 0% 69.40% 2644ms 2.41% Cell::HasCellProperty (inline) 23ms 0.021% 69.42% 2525ms 2.30% Cell::GetCellData 220ms 0.2% 69.62% 2500ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.62% 2469ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.62% 2458ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.62% 2440ms 2.22% AbstractCellPopulation::WriteResultsToFiles 120ms 0.11% 69.73% 2364ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0027% 69.73% 2291ms 2.09% AbstractCellPopulation::Iterator::operator++ (inline) 242ms 0.22% 69.96% 2278ms 2.08% AbstractCellPopulation::Iterator::IsRealCell (inline) 94ms 0.086% 70.04% 2230ms 2.03% VertexMesh::GetVolumeOfElement 2192ms 2.00% 72.04% 2192ms 2.00% std::_Rb_tree_increment 40ms 0.036% 72.08% 2117ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 494ms 0.45% 72.53% 2061ms 1.88% std::type_info::operator== (inline) 1410ms 1.29% 73.81% 2059ms 1.88% std::_Rb_tree::equal_range (inline) 2ms 0.0018% 73.81% 2004ms 1.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.81% 2004ms 1.83% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.81% 2003ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.81% 1991ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 88ms 0.08% 73.89% 1920ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 31ms 0.028% 73.92% 1794ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.92% 1787ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 73.94% 1681ms 1.53% VertexMesh::GetSurfaceAreaOfElement 23ms 0.021% 73.96% 1633ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 156ms 0.14% 74.10% 1605ms 1.46% CellPropertyCollection::AddProperty 35ms 0.032% 74.13% 1588ms 1.45% Node::RemoveElement 24ms 0.022% 74.16% 1571ms 1.43% std::set::erase (inline) 80ms 0.073% 74.23% 1566ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 119ms 0.11% 74.34% 1566ms 1.43% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.34% 1459ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.34% 1459ms 1.33% tcache_get (inline) 1459ms 1.33% 75.67% 1459ms 1.33% tcache_get_n (inline) 2ms 0.0018% 75.67% 1297ms 1.18% OffLatticeSimulation::ApplyBoundaries 0 0% 75.67% 1270ms 1.16% boost::numeric::ublas::norm_2 (inline) 64ms 0.058% 75.73% 1258ms 1.15% std::less::operator() (inline) 564ms 0.51% 76.24% 1256ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 98ms 0.089% 76.33% 1231ms 1.12% std::_Rb_tree::find (inline) 0 0% 76.33% 1205ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1001ms 0.91% 77.24% 1194ms 1.09% std::operator< (inline) 1145ms 1.04% 78.29% 1145ms 1.04% Node::rGetLocation 21ms 0.019% 78.31% 1108ms 1.01% CellPropertyRegistry::Get 16ms 0.015% 78.32% 1107ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1099ms 1.00% 79.32% 1099ms 1.00% [libchaste_cell_based.so] 85ms 0.077% 79.40% 1085ms 0.99% std::_Rb_tree::_M_erase_aux (partial-inline) 1077ms 0.98% 80.38% 1077ms 0.98% std::_Rb_tree_insert_and_rebalance 1ms 0.00091% 80.38% 1066ms 0.97% std::_Rb_tree::clear (inline) 0 0% 80.38% 1051ms 0.96% std::map::clear (inline) 1ms 0.00091% 80.38% 1018ms 0.93% std::map::find (inline) 8ms 0.0073% 80.39% 1011ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.027% 80.42% 990ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 401ms 0.37% 80.78% 979ms 0.89% Edge::GetMapIndex 141ms 0.13% 80.91% 971ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.91% 971ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.91% 970ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 80.92% 970ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 77ms 0.07% 80.99% 965ms 0.88% std::swap_ranges (inline) 176ms 0.16% 81.15% 953ms 0.87% boost::numeric::ublas::detail::equals 946ms 0.86% 82.01% 946ms 0.86% std::vector::size (inline) 938ms 0.85% 82.86% 938ms 0.85% [libchaste_mesh.so] 889ms 0.81% 83.67% 889ms 0.81% std::swap (inline) 0 0% 83.67% 888ms 0.81% std::iter_swap (inline) 1ms 0.00091% 83.68% 868ms 0.79% VertexMeshWriter::MakeVtkMesh 122ms 0.11% 83.79% 846ms 0.77% MutableElement::GetNodeLocalIndex 791ms 0.72% 84.51% 795ms 0.72% boost::detail::sp_counted_base::release 20ms 0.018% 84.53% 766ms 0.7% MutableElement::RegisterWithEdges (inline) 100ms 0.091% 84.62% 764ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 753ms 0.69% 85.30% 753ms 0.69% Node::GetIndex 25ms 0.023% 85.33% 752ms 0.69% Edge::AddElement 123ms 0.11% 85.44% 747ms 0.68% std::__new_allocator::construct (inline) 0 0% 85.44% 747ms 0.68% std::allocator_traits::construct (inline) 134ms 0.12% 85.56% 736ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 85.56% 734ms 0.67% boost::numeric::ublas::norm_inf (inline) 367ms 0.33% 85.89% 734ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 456ms 0.42% 86.31% 724ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 8ms 0.0073% 86.32% 699ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 86.32% 697ms 0.64% std::_Rb_tree::_M_construct_node (inline) 104ms 0.095% 86.41% 691ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.41% 685ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 31ms 0.028% 86.44% 664ms 0.61% MutableElement::RegisterWithNodes (inline) 1ms 0.00091% 86.44% 661ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.44% 642ms 0.59% vtkPolygon::New 3ms 0.0027% 86.44% 642ms 0.59% vtkPolygon::vtkPolygon 22ms 0.02% 86.46% 623ms 0.57% Node::AddElement 608ms 0.55% 87.02% 608ms 0.55% operator delete 0 0% 87.02% 605ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 575ms 0.52% 87.54% 602ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 87.54% 601ms 0.55% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 87.56% 601ms 0.55% std::_Rb_tree::_M_insert_node (inline) 595ms 0.54% 88.11% 595ms 0.54% boost::shared_ptr::operator-> (inline) 16ms 0.015% 88.12% 554ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.12% 554ms 0.5% boost::numeric::ublas::vector::vector (inline) 551ms 0.5% 88.62% 551ms 0.5% [libstdc++.so.6.0.33]