File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 72891ms, 87.05% of 83731ms total Dropped 1093 nodes (cum <= 418.65ms) flat flat% sum% cum cum% 0 0% 0% 83422ms 99.63% __libc_start_call_main 0 0% 0% 83422ms 99.63% __libc_start_main_impl 0 0% 0% 83422ms 99.63% _start 0 0% 0% 83402ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 83402ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 83402ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 83402ms 99.61% main 0 0% 0% 83362ms 99.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 83362ms 99.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 83362ms 99.56% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0036% 0.0036% 83355ms 99.55% AbstractCellBasedSimulation::Solve 13ms 0.016% 0.019% 43818ms 52.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.011% 0.03% 41276ms 49.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 104ms 0.12% 0.15% 40055ms 47.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 238ms 0.28% 0.44% 30785ms 36.77% NagaiHondaForce::AddForceContribution 1ms 0.0012% 0.44% 29473ms 35.20% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.44% 18098ms 21.61% VertexBasedCellPopulation::Update 11292ms 13.49% 13.93% 18026ms 21.53% Cylindrical2dVertexMesh::GetVectorFromAtoB 0 0% 13.93% 17969ms 21.46% MutableVertexMesh::ReMesh 50ms 0.06% 13.99% 13419ms 16.03% Cell::ReadyToDivide 40ms 0.048% 14.03% 12464ms 14.89% AbstractPhaseBasedCellCycleModel::ReadyToDivide 298ms 0.36% 14.39% 11088ms 13.24% NagaiHondaForce::GetAdhesionParameter 100ms 0.12% 14.51% 10708ms 12.79% SimpleWntCellCycleModel::UpdateCellCyclePhase 79ms 0.094% 14.60% 10669ms 12.74% CellPropertyCollection::GetPropertiesType (inline) 347ms 0.41% 15.02% 10602ms 12.66% boost::numeric::ublas::c_vector::c_vector (partial-inline) 212ms 0.25% 15.27% 9492ms 11.34% boost::numeric::ublas::vector_assign (inline) 2320ms 2.77% 18.04% 9260ms 11.06% __dynamic_cast 20ms 0.024% 18.06% 9163ms 10.94% AbstractCellProperty::IsSubType (inline) 94ms 0.11% 18.18% 9157ms 10.94% MutableVertexMesh::CheckForIntersections 73ms 0.087% 18.26% 8854ms 10.57% VertexBasedCellPopulation::GetDampingConstant 53ms 0.063% 18.33% 8117ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.05% 18.38% 8048ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.027% 18.41% 7780ms 9.29% AbstractCellBasedSimulation::DoCellBirth 887ms 1.06% 19.46% 7475ms 8.93% std::__new_allocator::allocate (inline) 326ms 0.39% 19.85% 7358ms 8.79% VertexMesh::GetNextEdgeGradientOfElementAtNode 2174ms 2.60% 22.45% 7271ms 8.68% boost::numeric::ublas::indexing_vector_assign 0 0% 22.45% 7077ms 8.45% std::_Rb_tree::_M_create_node (inline) 0 0% 22.45% 7070ms 8.44% std::allocator_traits::allocate (inline) 898ms 1.07% 23.52% 6921ms 8.27% std::_Rb_tree::_M_erase 696ms 0.83% 24.35% 6660ms 7.95% VertexMesh::ElementIncludesPoint 68ms 0.081% 24.44% 6654ms 7.95% Cell::GetMutationState 583ms 0.7% 25.13% 6647ms 7.94% operator new 32ms 0.038% 25.17% 6565ms 7.84% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.17% 6521ms 7.79% std::_Rb_tree::_M_get_node (inline) 0 0% 25.17% 6319ms 7.55% std::_Rb_tree::_M_drop_node (inline) 358ms 0.43% 25.60% 6300ms 7.52% VertexMesh::GetCentroidOfElement 0 0% 25.60% 6239ms 7.45% std::_Rb_tree::_Alloc_node::operator() (inline) 129ms 0.15% 25.75% 6222ms 7.43% std::_Rb_tree::~_Rb_tree (inline) 185ms 0.22% 25.97% 6092ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 25.97% 6078ms 7.26% std::allocator_traits::deallocate (inline) 0 0% 25.97% 6035ms 7.21% std::_Rb_tree::_M_put_node (inline) 0 0% 25.97% 5933ms 7.09% std::set::~set (inline) 2295ms 2.74% 28.71% 5900ms 7.05% __GI___libc_malloc 1074ms 1.28% 30.00% 5858ms 7.00% AbstractMesh::GetDistanceBetweenNodes 2016ms 2.41% 32.40% 5670ms 6.77% __GI___libc_free 5652ms 6.75% 39.15% 5652ms 6.75% __strcmp_evex 12ms 0.014% 39.17% 5579ms 6.66% MutableVertexMesh::RemoveDeletedNodesAndElements 154ms 0.18% 39.35% 5500ms 6.57% std::_Rb_tree::_Rb_tree (partial-inline) 337ms 0.4% 39.75% 5423ms 6.48% std::map::operator[] (partial-inline) 604ms 0.72% 40.48% 5116ms 6.11% std::_Rb_tree::_M_copy (inline) 18ms 0.021% 40.50% 5104ms 6.10% std::set::set (inline) 2262ms 2.70% 43.20% 4822ms 5.76% __cxxabiv1::__si_class_type_info::__do_dyncast 119ms 0.14% 43.34% 4791ms 5.72% SimpleWntCellCycleModel::GetWntLevel 4789ms 5.72% 49.06% 4789ms 5.72% boost::numeric::ublas::c_vector::operator() 138ms 0.16% 49.23% 4615ms 5.51% WntConcentration::GetWntLevel 573ms 0.68% 49.91% 4285ms 5.12% std::_Rb_tree::_M_clone_node (inline) 1578ms 1.88% 51.79% 4186ms 5.00% boost::numeric::ublas::c_vector::operator[] (inline) 1843ms 2.20% 54.00% 4162ms 4.97% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.014% 54.01% 3900ms 4.66% MutableVertexMesh::RemoveDeletedNodes 0 0% 54.01% 3886ms 4.64% std::set::insert (inline) 26ms 0.031% 54.04% 3763ms 4.49% EdgeHelper::RemoveDeletedEdges 3299ms 3.94% 57.98% 3634ms 4.34% _int_free 2ms 0.0024% 57.98% 3584ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 33ms 0.039% 58.02% 3545ms 4.23% EdgeHelper::UpdateEdgesMapKey 0 0% 58.02% 3444ms 4.11% std::_Rb_tree::lower_bound (inline) 0 0% 58.02% 3444ms 4.11% std::map::lower_bound (inline) 139ms 0.17% 58.19% 3407ms 4.07% MutableElement::ResetIndex 358ms 0.43% 58.62% 3249ms 3.88% std::_Rb_tree::_M_insert_ (inline) 83ms 0.099% 58.72% 3228ms 3.86% std::set_intersection (inline) 19ms 0.023% 58.74% 3215ms 3.84% Cell::GetCellProliferativeType 176ms 0.21% 58.95% 3145ms 3.76% std::__set_intersection 98ms 0.12% 59.07% 3097ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 44ms 0.053% 59.12% 3078ms 3.68% AbstractCellProperty::IsType (inline) 2970ms 3.55% 62.66% 2970ms 3.55% boost::numeric::ublas::same_impl_ex 9ms 0.011% 62.68% 2689ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.038% 62.71% 2534ms 3.03% Cell::SetCellProliferativeType 1676ms 2.00% 64.72% 2445ms 2.92% _int_malloc 0 0% 64.72% 2427ms 2.90% std::insert_iterator::operator= (inline) 721ms 0.86% 65.58% 2349ms 2.81% AbstractElement::GetNodeLocation 50ms 0.06% 65.64% 2178ms 2.60% std::_Rb_tree::erase 6ms 0.0072% 65.64% 2095ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 182ms 0.22% 65.86% 2094ms 2.50% VertexMesh::GetAreaGradientOfElementAtNode 533ms 0.64% 66.50% 2093ms 2.50% AbstractCellProperty::IsSame 443ms 0.53% 67.03% 2030ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 17ms 0.02% 67.05% 2012ms 2.40% CellPropertyCollection::HasProperty 0 0% 67.05% 1992ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 28ms 0.033% 67.08% 1977ms 2.36% Cell::GetCellData 1945ms 2.32% 69.40% 1945ms 2.32% std::_Rb_tree::_S_right (inline) 0 0% 69.40% 1942ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.40% 1939ms 2.32% Cell::HasCellProperty (inline) 0 0% 69.40% 1926ms 2.30% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0024% 69.41% 1791ms 2.14% std::_Rb_tree::_M_insert_unique (inline) 185ms 0.22% 69.63% 1782ms 2.13% std::_Rb_tree_const_iterator::operator++ (inline) 65ms 0.078% 69.70% 1758ms 2.10% VertexMesh::GetVolumeOfElement 39ms 0.047% 69.75% 1703ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0024% 69.75% 1673ms 2.00% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.75% 1673ms 2.00% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0012% 69.75% 1618ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 141ms 0.17% 69.92% 1616ms 1.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 35ms 0.042% 69.96% 1598ms 1.91% std::_Rb_tree::_M_emplace_hint_unique 0 0% 69.96% 1568ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.96% 1564ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 366ms 0.44% 70.40% 1560ms 1.86% std::type_info::operator== (inline) 1470ms 1.76% 72.16% 1470ms 1.76% std::_Rb_tree_increment 48ms 0.057% 72.21% 1445ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.0012% 72.22% 1400ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 856ms 1.02% 73.24% 1320ms 1.58% std::_Rb_tree::equal_range (inline) 24ms 0.029% 73.27% 1279ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.03% 73.30% 1233ms 1.47% VertexMesh::GetSurfaceAreaOfElement 37ms 0.044% 73.34% 1108ms 1.32% AbstractCellPopulation::GetLocationIndexUsingCell 40ms 0.048% 73.39% 1094ms 1.31% Node::RemoveElement 55ms 0.066% 73.45% 1091ms 1.30% boost::numeric::ublas::vector_reference::operator() (inline) 68ms 0.081% 73.54% 1088ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 2ms 0.0024% 73.54% 1055ms 1.26% std::set::erase (inline) 106ms 0.13% 73.66% 1054ms 1.26% CellPropertyCollection::AddProperty 0 0% 73.66% 1033ms 1.23% boost::numeric::ublas::norm_2 (inline) 1ms 0.0012% 73.67% 1023ms 1.22% OffLatticeSimulation::ApplyBoundaries 0 0% 73.67% 1023ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 432ms 0.52% 74.18% 1023ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 74.18% 1000ms 1.19% tcache_get (inline) 1000ms 1.19% 75.38% 1000ms 1.19% tcache_get_n (inline) 981ms 1.17% 76.55% 981ms 1.17% [libchaste_cell_based.so] 74ms 0.088% 76.64% 944ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 18ms 0.021% 76.66% 880ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 55ms 0.066% 76.72% 877ms 1.05% std::less::operator() (inline) 2ms 0.0024% 76.73% 854ms 1.02% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 126ms 0.15% 76.88% 848ms 1.01% boost::detail::shared_count::~shared_count (inline) 0 0% 76.88% 848ms 1.01% boost::shared_ptr::~shared_ptr (inline) 17ms 0.02% 76.90% 840ms 1.00% CellPropertyRegistry::Get 0 0% 76.90% 838ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0012% 76.90% 838ms 1.00% std::_Rb_tree::clear (inline) 645ms 0.77% 77.67% 822ms 0.98% std::operator< (inline) 0 0% 77.67% 818ms 0.98% std::map::clear (inline) 5ms 0.006% 77.67% 817ms 0.98% boost::numeric::ublas::detail::expression_type_check (inline) 137ms 0.16% 77.84% 797ms 0.95% boost::numeric::ublas::detail::equals 0 0% 77.84% 796ms 0.95% boost::numeric::ublas::c_vector::assign_temporary (inline) 19ms 0.023% 77.86% 796ms 0.95% boost::numeric::ublas::c_vector::swap (inline) 785ms 0.94% 78.80% 785ms 0.94% std::_Rb_tree_insert_and_rebalance 49ms 0.059% 78.86% 777ms 0.93% std::swap_ranges (inline) 88ms 0.11% 78.96% 774ms 0.92% std::_Rb_tree::find (inline) 762ms 0.91% 79.87% 762ms 0.91% Node::rGetLocation 0 0% 79.87% 728ms 0.87% std::iter_swap (inline) 728ms 0.87% 80.74% 728ms 0.87% std::swap (inline) 677ms 0.81% 81.55% 696ms 0.83% boost::detail::sp_counted_base::release 1ms 0.0012% 81.55% 676ms 0.81% VertexMeshWriter::MakeVtkMesh 95ms 0.11% 81.66% 647ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 15ms 0.018% 81.68% 640ms 0.76% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 81.68% 640ms 0.76% boost::numeric::ublas::norm_inf (inline) 292ms 0.35% 82.03% 640ms 0.76% boost::numeric::ublas::vector_norm_inf::apply (inline) 127ms 0.15% 82.18% 639ms 0.76% boost::shared_ptr::shared_ptr (inline) 636ms 0.76% 82.94% 636ms 0.76% std::vector::size (inline) 0 0% 82.94% 635ms 0.76% std::map::find (inline) 115ms 0.14% 83.08% 625ms 0.75% VertexBasedCellPopulation::CheckForStepSizeException 168ms 0.2% 83.28% 605ms 0.72% std::__new_allocator::construct (inline) 0 0% 83.28% 605ms 0.72% std::allocator_traits::construct (inline) 601ms 0.72% 84.00% 601ms 0.72% [libchaste_mesh.so] 19ms 0.023% 84.02% 573ms 0.68% Edge::AddElement 11ms 0.013% 84.03% 570ms 0.68% MutableElement::RegisterWithEdges (inline) 0 0% 84.03% 564ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 309ms 0.37% 84.40% 563ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.40% 556ms 0.66% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.40% 551ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 550ms 0.66% 85.06% 550ms 0.66% [libstdc++.so.6.0.33] 0 0% 85.06% 547ms 0.65% std::_Vector_base::_M_allocate (inline) 309ms 0.37% 85.43% 546ms 0.65% Edge::GetMapIndex 495ms 0.59% 86.02% 511ms 0.61% boost::detail::shared_count::shared_count (inline) 105ms 0.13% 86.14% 509ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 86.14% 492ms 0.59% vtkPolygon::New 0 0% 86.14% 492ms 0.59% vtkPolygon::vtkPolygon 0 0% 86.14% 482ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.023% 86.17% 482ms 0.58% std::_Rb_tree::_M_insert_node (inline) 256ms 0.31% 86.47% 469ms 0.56% CellPropertyCollection::GetProperty 3ms 0.0036% 86.48% 460ms 0.55% std::vector::_M_default_append (inline) 441ms 0.53% 87.00% 441ms 0.53% Node::GetIndex 19ms 0.023% 87.03% 424ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.03% 424ms 0.51% boost::numeric::ublas::vector::vector (inline) 23ms 0.027% 87.05% 421ms 0.5% MutableElement::RegisterWithNodes (inline) 0 0% 87.05% 420ms 0.5% std::map::map (inline)