File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 53050ms, 88.64% of 59847ms total Dropped 922 nodes (cum <= 299.24ms) flat flat% sum% cum cum% 0 0% 0% 59540ms 99.49% __libc_start_call_main 0 0% 0% 59540ms 99.49% __libc_start_main_impl 0 0% 0% 59540ms 99.49% _start 0 0% 0% 59526ms 99.46% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 59526ms 99.46% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 59526ms 99.46% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 59526ms 99.46% main 0 0% 0% 59496ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 59496ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 59496ms 99.41% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0033% 0.0033% 59492ms 99.41% AbstractCellBasedSimulation::Solve 8ms 0.013% 0.017% 31315ms 52.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.015% 0.032% 29188ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 51ms 0.085% 0.12% 28433ms 47.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 150ms 0.25% 0.37% 21675ms 36.22% NagaiHondaForce::AddForceContribution 0 0% 0.37% 21027ms 35.13% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.37% 12744ms 21.29% VertexBasedCellPopulation::Update 0 0% 0.37% 12667ms 21.17% MutableVertexMesh::ReMesh 6384ms 10.67% 11.03% 10940ms 18.28% Cylindrical2dVertexMesh::GetVectorFromAtoB 35ms 0.058% 11.09% 9726ms 16.25% Cell::ReadyToDivide 18ms 0.03% 11.12% 9097ms 15.20% AbstractPhaseBasedCellCycleModel::ReadyToDivide 57ms 0.095% 11.22% 8626ms 14.41% NagaiHondaForce::GetAdhesionParameter 34ms 0.057% 11.28% 7867ms 13.15% SimpleWntCellCycleModel::UpdateCellCyclePhase 166ms 0.28% 11.55% 7400ms 12.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 49ms 0.082% 11.63% 6865ms 11.47% CellPropertyCollection::GetPropertiesType (inline) 201ms 0.34% 11.97% 6530ms 10.91% boost::numeric::ublas::vector_assign (inline) 503ms 0.84% 12.81% 6519ms 10.89% std::__new_allocator::allocate (inline) 25ms 0.042% 12.85% 6506ms 10.87% VertexBasedCellPopulation::GetDampingConstant 0 0% 12.85% 6293ms 10.52% std::allocator_traits::allocate (inline) 0 0% 12.85% 6141ms 10.26% std::_Rb_tree::_M_create_node (inline) 561ms 0.94% 13.79% 6060ms 10.13% operator new 78ms 0.13% 13.92% 6031ms 10.08% MutableVertexMesh::CheckForIntersections 0 0% 13.92% 5948ms 9.94% std::_Rb_tree::_M_get_node (inline) 24ms 0.04% 13.96% 5785ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 2ms 0.0033% 13.96% 5762ms 9.63% AbstractCellBasedSimulation::DoCellBirth 18ms 0.03% 13.99% 5733ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1377ms 2.30% 16.29% 5705ms 9.53% __dynamic_cast 41ms 0.069% 16.36% 5704ms 9.53% AbstractCellProperty::IsSubType (inline) 568ms 0.95% 17.31% 5609ms 9.37% std::_Rb_tree::_M_erase 0 0% 17.31% 5513ms 9.21% std::_Rb_tree::_M_drop_node (inline) 2343ms 3.91% 21.23% 5387ms 9.00% __GI___libc_malloc 0 0% 21.23% 5355ms 8.95% std::_Rb_tree::_Alloc_node::operator() (inline) 261ms 0.44% 21.66% 5318ms 8.89% std::_Rb_tree::~_Rb_tree (inline) 0 0% 21.66% 5049ms 8.44% std::set::~set (inline) 1559ms 2.60% 24.27% 4890ms 8.17% boost::numeric::ublas::indexing_vector_assign 74ms 0.12% 24.39% 4804ms 8.03% std::__new_allocator::deallocate (inline) 0 0% 24.39% 4804ms 8.03% std::allocator_traits::deallocate (inline) 0 0% 24.39% 4769ms 7.97% std::_Rb_tree::_M_put_node (inline) 35ms 0.058% 24.45% 4661ms 7.79% Cell::GetMutationState 274ms 0.46% 24.91% 4647ms 7.76% std::map::operator[] (partial-inline) 192ms 0.32% 25.23% 4544ms 7.59% VertexMesh::GetNextEdgeGradientOfElementAtNode 811ms 1.36% 26.58% 4480ms 7.49% __GI___libc_free 25ms 0.042% 26.63% 4478ms 7.48% VertexBasedCellPopulation::GetLocationOfCellCentre 14ms 0.023% 26.65% 4381ms 7.32% MutableVertexMesh::RemoveDeletedNodesAndElements 480ms 0.8% 27.45% 4363ms 7.29% VertexMesh::ElementIncludesPoint 357ms 0.6% 28.05% 4177ms 6.98% VertexMesh::GetCentroidOfElement 0 0% 28.05% 3971ms 6.64% std::set::insert (inline) 821ms 1.37% 29.42% 3866ms 6.46% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 96ms 0.16% 29.58% 3710ms 6.20% std::_Rb_tree::_Rb_tree (partial-inline) 3465ms 5.79% 35.37% 3646ms 6.09% _int_free 544ms 0.91% 36.28% 3544ms 5.92% std::_Rb_tree::_M_insert_ (inline) 419ms 0.7% 36.98% 3519ms 5.88% std::_Rb_tree::_M_copy (inline) 5ms 0.0084% 36.99% 3493ms 5.84% std::set::set (inline) 82ms 0.14% 37.12% 3410ms 5.70% SimpleWntCellCycleModel::GetWntLevel 3407ms 5.69% 42.82% 3407ms 5.69% boost::numeric::ublas::c_vector::operator() 1588ms 2.65% 45.47% 3367ms 5.63% std::_Rb_tree::_M_lower_bound (inline) 110ms 0.18% 45.65% 3248ms 5.43% WntConcentration::GetWntLevel 55ms 0.092% 45.75% 3182ms 5.32% std::set_intersection (inline) 3157ms 5.28% 51.02% 3157ms 5.28% __strcmp_evex 146ms 0.24% 51.27% 3127ms 5.22% std::__set_intersection 1877ms 3.14% 54.40% 3099ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.012% 54.41% 3069ms 5.13% MutableVertexMesh::RemoveDeletedNodes 391ms 0.65% 55.07% 2976ms 4.97% std::_Rb_tree::_M_clone_node (inline) 21ms 0.035% 55.10% 2972ms 4.97% EdgeHelper::RemoveDeletedEdges 0 0% 55.10% 2910ms 4.86% std::_Rb_tree::lower_bound (inline) 0 0% 55.10% 2910ms 4.86% std::map::lower_bound (inline) 37ms 0.062% 55.16% 2829ms 4.73% EdgeHelper::UpdateEdgesMapKey 68ms 0.11% 55.28% 2788ms 4.66% AbstractCellPopulation::GetCellUsingLocationIndex 781ms 1.30% 56.58% 2754ms 4.60% boost::numeric::ublas::c_vector::operator[] (inline) 65ms 0.11% 56.69% 2651ms 4.43% MutableElement::ResetIndex 1ms 0.0017% 56.69% 2515ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 56.69% 2459ms 4.11% std::insert_iterator::operator= (inline) 30ms 0.05% 56.74% 2370ms 3.96% Cell::GetCellProliferativeType 1814ms 3.03% 59.77% 2268ms 3.79% _int_malloc 3ms 0.005% 59.78% 2251ms 3.76% std::_Rb_tree::_M_insert_unique_ (inline) 2248ms 3.76% 63.54% 2248ms 3.76% boost::numeric::ublas::same_impl_ex 73ms 0.12% 63.66% 2229ms 3.72% boost::detail::shared_count::~shared_count (inline) 0 0% 63.66% 2229ms 3.72% boost::shared_ptr::~shared_ptr (inline) 2124ms 3.55% 67.21% 2129ms 3.56% boost::detail::sp_counted_base::release 45ms 0.075% 67.28% 1958ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 55ms 0.092% 67.37% 1946ms 3.25% AbstractCellProperty::IsType (inline) 58ms 0.097% 67.47% 1925ms 3.22% Cell::SetCellProliferativeType 0 0% 67.47% 1720ms 2.87% std::_Rb_tree::_M_insert_unique 422ms 0.71% 68.18% 1645ms 2.75% AbstractElement::GetNodeLocation 28ms 0.047% 68.22% 1582ms 2.64% std::_Rb_tree::erase 0 0% 68.22% 1573ms 2.63% boost::numeric::ublas::c_vector::assign (inline) 119ms 0.2% 68.42% 1558ms 2.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.42% 1556ms 2.60% AbstractCellPopulation::Iterator::operator++ (inline) 288ms 0.48% 68.90% 1491ms 2.49% boost::numeric::ublas::vector_binary::size (inline) 118ms 0.2% 69.10% 1462ms 2.44% VertexMesh::GetAreaGradientOfElementAtNode 21ms 0.035% 69.13% 1445ms 2.41% std::_Rb_tree::_M_emplace_hint_unique 28ms 0.047% 69.18% 1431ms 2.39% CellPropertyCollection::HasProperty 0 0% 69.18% 1395ms 2.33% Cell::HasCellProperty (inline) 1395ms 2.33% 71.51% 1395ms 2.33% std::_Rb_tree::_S_right (inline) 0 0% 71.51% 1358ms 2.27% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0017% 71.51% 1358ms 2.27% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.51% 1358ms 2.27% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 275ms 0.46% 71.97% 1357ms 2.27% AbstractCellProperty::IsSame 249ms 0.42% 72.39% 1313ms 2.19% std::_Rb_tree_const_iterator::operator++ (inline) 16ms 0.027% 72.42% 1272ms 2.13% Cell::GetCellData 21ms 0.035% 72.45% 1206ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.012% 72.46% 1166ms 1.95% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.46% 1129ms 1.89% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 72.46% 1122ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0017% 72.46% 1120ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 135ms 0.23% 72.69% 1082ms 1.81% std::type_info::operator== (inline) 67ms 0.11% 72.80% 1075ms 1.80% VertexMesh::GetVolumeOfElement 189ms 0.32% 73.12% 1028ms 1.72% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.12% 1023ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 82ms 0.14% 73.26% 962ms 1.61% CellPropertyCollection::AddProperty 52ms 0.087% 73.34% 939ms 1.57% boost::numeric::ublas::vector_reference::operator() (inline) 936ms 1.56% 74.91% 936ms 1.56% std::_Rb_tree_increment 23ms 0.038% 74.94% 915ms 1.53% VertexMesh::GetSurfaceAreaOfElement 1ms 0.0017% 74.95% 891ms 1.49% OffLatticeSimulation::ApplyBoundaries 22ms 0.037% 74.98% 879ms 1.47% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.98% 865ms 1.45% boost::numeric::ublas::norm_2 (inline) 349ms 0.58% 75.57% 859ms 1.44% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 53ms 0.089% 75.65% 859ms 1.44% std::_Rb_tree::_M_erase_aux (partial-inline) 40ms 0.067% 75.72% 853ms 1.43% Node::RemoveElement 834ms 1.39% 77.11% 834ms 1.39% [libchaste_cell_based.so] 8ms 0.013% 77.13% 817ms 1.37% std::set::erase (inline) 18ms 0.03% 77.16% 815ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 505ms 0.84% 78.00% 806ms 1.35% std::_Rb_tree::equal_range (inline) 0 0% 78.00% 786ms 1.31% std::_Rb_tree::_Auto_node::_Auto_node (inline) 29ms 0.048% 78.05% 767ms 1.28% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.05% 757ms 1.26% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 78.05% 746ms 1.25% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.05% 746ms 1.25% std::__new_allocator::destroy (inline) 0 0% 78.05% 746ms 1.25% std::allocator_traits::destroy (inline) 727ms 1.21% 79.27% 727ms 1.21% [libchaste_mesh.so] 40ms 0.067% 79.33% 679ms 1.13% std::less::operator() (inline) 0 0% 79.33% 670ms 1.12% boost::numeric::ublas::vector_binary::operator() (inline) 558ms 0.93% 80.26% 639ms 1.07% std::operator< (inline) 10ms 0.017% 80.28% 621ms 1.04% CellPropertyRegistry::Get 1ms 0.0017% 80.28% 619ms 1.03% tcache_get (inline) 5ms 0.0084% 80.29% 618ms 1.03% boost::numeric::ublas::detail::expression_type_check (inline) 618ms 1.03% 81.32% 618ms 1.03% tcache_get_n (inline) 14ms 0.023% 81.35% 601ms 1.00% Edge::AddElement 68ms 0.11% 81.46% 597ms 1% boost::numeric::ublas::detail::equals 597ms 1% 82.46% 597ms 1% std::_Rb_tree_insert_and_rebalance 5ms 0.0084% 82.47% 586ms 0.98% MutableElement::RegisterWithEdges (inline) 511ms 0.85% 83.32% 584ms 0.98% CellPropertyCollection::GetProperty 580ms 0.97% 84.29% 580ms 0.97% [libstdc++.so.6.0.33] 0 0% 84.29% 555ms 0.93% std::_Rb_tree::clear (inline) 1ms 0.0017% 84.29% 547ms 0.91% VertexMeshWriter::MakeVtkMesh 0 0% 84.29% 544ms 0.91% std::map::clear (inline) 1ms 0.0017% 84.29% 541ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 84.29% 541ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 18ms 0.03% 84.32% 541ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 109ms 0.18% 84.51% 523ms 0.87% std::swap_ranges (inline) 0 0% 84.51% 493ms 0.82% boost::numeric::ublas::norm_inf (inline) 209ms 0.35% 84.85% 493ms 0.82% boost::numeric::ublas::vector_norm_inf::apply (inline) 88ms 0.15% 85.00% 484ms 0.81% MutableElement::GetNodeLocalIndex 52ms 0.087% 85.09% 470ms 0.79% std::_Rb_tree::find (inline) 230ms 0.38% 85.47% 468ms 0.78% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 35ms 0.058% 85.53% 462ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 462ms 0.77% 86.30% 462ms 0.77% std::vector::size (inline) 213ms 0.36% 86.66% 418ms 0.7% Edge::GetMapIndex 0 0% 86.66% 414ms 0.69% std::iter_swap (inline) 414ms 0.69% 87.35% 414ms 0.69% std::swap (inline) 0 0% 87.35% 407ms 0.68% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.027% 87.38% 407ms 0.68% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.38% 399ms 0.67% vtkPolygon::New 0 0% 87.38% 399ms 0.67% vtkPolygon::vtkPolygon 0 0% 87.38% 397ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 9ms 0.015% 87.39% 394ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 83ms 0.14% 87.53% 385ms 0.64% VertexBasedCellPopulation::CheckForStepSizeException (partial-inline) 0 0% 87.53% 376ms 0.63% std::map::find (inline) 1ms 0.0017% 87.53% 344ms 0.57% std::_Vector_base::_M_allocate (inline) 19ms 0.032% 87.56% 334ms 0.56% MutableElement::RegisterWithNodes (inline) 313ms 0.52% 88.09% 313ms 0.52% Node::GetIndex 25ms 0.042% 88.13% 311ms 0.52% Node::AddElement 307ms 0.51% 88.64% 307ms 0.51% Node::rGetLocation 0 0% 88.64% 300ms 0.5% vtkCell::vtkCell