File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95554ms, 87.82% of 108801ms total Dropped 1148 nodes (cum <= 544ms) flat flat% sum% cum cum% 0 0% 0% 108426ms 99.66% __libc_start_call_main 0 0% 0% 108426ms 99.66% __libc_start_main_impl 0 0% 0% 108426ms 99.66% _start 0 0% 0% 108406ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108406ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108406ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108406ms 99.64% main 0 0% 0% 108364ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108364ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108364ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108356ms 99.59% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.018% 56212ms 51.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.032% 52997ms 48.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 115ms 0.11% 0.14% 51871ms 47.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 327ms 0.3% 0.44% 39973ms 36.74% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.44% 39004ms 35.85% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.44% 23829ms 21.90% VertexBasedCellPopulation::Update 1ms 0.00092% 0.44% 23663ms 21.75% MutableVertexMesh::ReMesh 14637ms 13.45% 13.90% 23369ms 21.48% Cylindrical2dVertexMesh::GetVectorFromAtoB 82ms 0.075% 13.97% 17936ms 16.49% Cell::ReadyToDivide 62ms 0.057% 14.03% 16725ms 15.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 309ms 0.28% 14.31% 14513ms 13.34% NagaiHondaForce::GetAdhesionParameter 160ms 0.15% 14.46% 14264ms 13.11% SimpleWntCellCycleModel::UpdateCellCyclePhase 458ms 0.42% 14.88% 14118ms 12.98% boost::numeric::ublas::c_vector::c_vector (partial-inline) 147ms 0.14% 15.02% 13688ms 12.58% CellPropertyCollection::GetPropertiesType (inline) 348ms 0.32% 15.34% 12596ms 11.58% boost::numeric::ublas::vector_assign (inline) 139ms 0.13% 15.46% 11800ms 10.85% MutableVertexMesh::CheckForIntersections 3351ms 3.08% 18.54% 11737ms 10.79% __dynamic_cast 86ms 0.079% 18.62% 11637ms 10.70% AbstractCellProperty::IsSubType (inline) 74ms 0.068% 18.69% 11285ms 10.37% VertexBasedCellPopulation::GetDampingConstant 72ms 0.066% 18.76% 10654ms 9.79% AbstractTargetAreaModifier::UpdateTargetAreas 32ms 0.029% 18.79% 10560ms 9.71% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.026% 18.81% 10519ms 9.67% AbstractCellBasedSimulation::DoCellBirth 1337ms 1.23% 20.04% 9833ms 9.04% std::__new_allocator::allocate (inline) 342ms 0.31% 20.36% 9461ms 8.70% VertexMesh::GetNextEdgeGradientOfElementAtNode 2922ms 2.69% 23.04% 9411ms 8.65% boost::numeric::ublas::indexing_vector_assign 0 0% 23.04% 9261ms 8.51% std::_Rb_tree::_M_create_node (inline) 0 0% 23.04% 9232ms 8.49% std::allocator_traits::allocate (inline) 1257ms 1.16% 24.20% 8983ms 8.26% std::_Rb_tree::_M_erase 35ms 0.032% 24.23% 8860ms 8.14% VertexBasedCellPopulation::GetLocationOfCellCentre 886ms 0.81% 25.04% 8649ms 7.95% VertexMesh::ElementIncludesPoint 97ms 0.089% 25.13% 8603ms 7.91% Cell::GetMutationState 762ms 0.7% 25.83% 8530ms 7.84% operator new 0 0% 25.83% 8521ms 7.83% std::_Rb_tree::_M_get_node (inline) 466ms 0.43% 26.26% 8470ms 7.78% VertexMesh::GetCentroidOfElement 254ms 0.23% 26.49% 8205ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.49% 8126ms 7.47% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.49% 8017ms 7.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.49% 7814ms 7.18% std::set::~set (inline) 214ms 0.2% 26.69% 7770ms 7.14% std::__new_allocator::deallocate (inline) 0 0% 26.69% 7759ms 7.13% std::allocator_traits::deallocate (inline) 0 0% 26.69% 7702ms 7.08% std::_Rb_tree::_M_put_node (inline) 2870ms 2.64% 29.33% 7592ms 6.98% __GI___libc_malloc 24ms 0.022% 29.35% 7542ms 6.93% MutableVertexMesh::RemoveDeletedNodesAndElements 1481ms 1.36% 30.71% 7524ms 6.92% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 477ms 0.44% 31.15% 7522ms 6.91% std::map::operator[] (partial-inline) 2243ms 2.06% 33.21% 7330ms 6.74% __GI___libc_free 181ms 0.17% 33.38% 7086ms 6.51% std::_Rb_tree::_Rb_tree (partial-inline) 6735ms 6.19% 39.57% 6735ms 6.19% __strcmp_avx2 727ms 0.67% 40.24% 6664ms 6.12% std::_Rb_tree::_M_copy (inline) 22ms 0.02% 40.26% 6564ms 6.03% std::set::set (inline) 183ms 0.17% 40.43% 6408ms 5.89% SimpleWntCellCycleModel::GetWntLevel 165ms 0.15% 40.58% 6136ms 5.64% WntConcentration::GetWntLevel 6089ms 5.60% 46.17% 6089ms 5.60% boost::numeric::ublas::c_vector::operator() 2879ms 2.65% 48.82% 5862ms 5.39% __cxxabiv1::__si_class_type_info::__do_dyncast 2416ms 2.22% 51.04% 5702ms 5.24% std::_Rb_tree::_M_lower_bound (inline) 800ms 0.74% 51.78% 5664ms 5.21% std::_Rb_tree::_M_clone_node (inline) 2022ms 1.86% 53.63% 5343ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 20ms 0.018% 53.65% 5218ms 4.80% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.65% 5210ms 4.79% std::set::insert (inline) 4596ms 4.22% 57.88% 5069ms 4.66% _int_free 27ms 0.025% 57.90% 5046ms 4.64% EdgeHelper::RemoveDeletedEdges 0 0% 57.90% 4762ms 4.38% std::_Rb_tree::lower_bound (inline) 0 0% 57.90% 4762ms 4.38% std::map::lower_bound (inline) 35ms 0.032% 57.93% 4733ms 4.35% EdgeHelper::UpdateEdgesMapKey 206ms 0.19% 58.12% 4657ms 4.28% MutableElement::ResetIndex 0 0% 58.12% 4640ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 125ms 0.11% 58.24% 4326ms 3.98% std::set_intersection (inline) 508ms 0.47% 58.70% 4322ms 3.97% std::_Rb_tree::_M_insert_ (inline) 131ms 0.12% 58.82% 4277ms 3.93% AbstractCellPopulation::GetCellUsingLocationIndex 242ms 0.22% 59.05% 4201ms 3.86% std::__set_intersection 39ms 0.036% 59.08% 4169ms 3.83% Cell::GetCellProliferativeType 3807ms 3.50% 62.58% 3807ms 3.50% boost::numeric::ublas::same_impl_ex 45ms 0.041% 62.62% 3619ms 3.33% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.63% 3581ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 66ms 0.061% 62.69% 3372ms 3.10% Cell::SetCellProliferativeType 0 0% 62.69% 3206ms 2.95% std::insert_iterator::operator= (inline) 2183ms 2.01% 64.70% 3121ms 2.87% _int_malloc 941ms 0.86% 65.57% 3103ms 2.85% AbstractElement::GetNodeLocation 68ms 0.062% 65.63% 2994ms 2.75% std::_Rb_tree::erase 2ms 0.0018% 65.63% 2813ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 2701ms 2.48% 68.11% 2701ms 2.48% std::_Rb_tree::_S_right (inline) 205ms 0.19% 68.30% 2651ms 2.44% VertexMesh::GetAreaGradientOfElementAtNode 641ms 0.59% 68.89% 2632ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 27ms 0.025% 68.91% 2533ms 2.33% CellPropertyCollection::HasProperty 618ms 0.57% 69.48% 2525ms 2.32% AbstractCellProperty::IsSame 0 0% 69.48% 2518ms 2.31% boost::numeric::ublas::c_vector::assign (inline) 275ms 0.25% 69.74% 2490ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.74% 2464ms 2.26% Cell::HasCellProperty (inline) 0 0% 69.74% 2458ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.74% 2442ms 2.24% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0018% 69.74% 2397ms 2.20% std::_Rb_tree::_M_insert_unique 22ms 0.02% 69.76% 2389ms 2.20% Cell::GetCellData 67ms 0.062% 69.82% 2386ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 85ms 0.078% 69.90% 2319ms 2.13% VertexMesh::GetVolumeOfElement 33ms 0.03% 69.93% 2221ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 9ms 0.0083% 69.94% 2127ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 149ms 0.14% 70.07% 2115ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.00092% 70.07% 2113ms 1.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.07% 2113ms 1.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.07% 2000ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 70.08% 1990ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1334ms 1.23% 71.30% 1963ms 1.80% std::_Rb_tree::equal_range (inline) 1957ms 1.80% 73.10% 1957ms 1.80% std::_Rb_tree_increment 69ms 0.063% 73.16% 1918ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 433ms 0.4% 73.56% 1907ms 1.75% std::type_info::operator== (inline) 1ms 0.00092% 73.56% 1798ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 37ms 0.034% 73.60% 1612ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.036% 73.63% 1592ms 1.46% VertexMesh::GetSurfaceAreaOfElement 43ms 0.04% 73.67% 1508ms 1.39% Node::RemoveElement 10ms 0.0092% 73.68% 1468ms 1.35% std::set::erase (inline) 39ms 0.036% 73.72% 1441ms 1.32% AbstractCellPopulation::GetLocationIndexUsingCell 78ms 0.072% 73.79% 1411ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.79% 1406ms 1.29% tcache_get (inline) 1406ms 1.29% 75.08% 1406ms 1.29% tcache_get_n (inline) 144ms 0.13% 75.21% 1384ms 1.27% CellPropertyCollection::AddProperty 57ms 0.052% 75.27% 1372ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 1370ms 1.26% 76.53% 1370ms 1.26% [libchaste_cell_based.so] 0 0% 76.53% 1339ms 1.23% boost::numeric::ublas::norm_2 (inline) 608ms 0.56% 77.08% 1329ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.08% 1290ms 1.19% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 77.09% 1259ms 1.16% OffLatticeSimulation::ApplyBoundaries 76ms 0.07% 77.16% 1253ms 1.15% std::less::operator() (inline) 79ms 0.073% 77.23% 1248ms 1.15% std::_Rb_tree::_M_erase_aux (partial-inline) 1183ms 1.09% 78.32% 1183ms 1.09% std::_Rb_tree_insert_and_rebalance 938ms 0.86% 79.18% 1177ms 1.08% std::operator< (inline) 0 0% 79.18% 1135ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 17ms 0.016% 79.19% 1134ms 1.04% CellPropertyRegistry::Get 13ms 0.012% 79.21% 1105ms 1.02% boost::numeric::ublas::detail::expression_type_check (inline) 227ms 0.21% 79.41% 1077ms 0.99% boost::numeric::ublas::detail::equals 0 0% 79.41% 1065ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0083% 79.42% 1065ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 13ms 0.012% 79.43% 1063ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 80ms 0.074% 79.51% 1056ms 0.97% std::swap_ranges (inline) 0 0% 79.51% 1036ms 0.95% std::_Rb_tree::clear (inline) 5ms 0.0046% 79.51% 1031ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.51% 1019ms 0.94% std::map::clear (inline) 137ms 0.13% 79.64% 1008ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 79.64% 1008ms 0.93% boost::shared_ptr::~shared_ptr (inline) 92ms 0.085% 79.72% 981ms 0.9% std::_Rb_tree::find (inline) 0 0% 79.72% 976ms 0.9% std::iter_swap (inline) 976ms 0.9% 80.62% 976ms 0.9% std::swap (inline) 975ms 0.9% 81.52% 975ms 0.9% Node::rGetLocation 1ms 0.00092% 81.52% 876ms 0.81% VertexMeshWriter::MakeVtkMesh 842ms 0.77% 82.29% 842ms 0.77% std::vector::size (inline) 841ms 0.77% 83.06% 841ms 0.77% [libchaste_mesh.so] 0 0% 83.06% 837ms 0.77% CellPropertyCollection::~CellPropertyCollection (inline) 479ms 0.44% 83.50% 836ms 0.77% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 81ms 0.074% 83.58% 835ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.58% 831ms 0.76% std::map::find (inline) 782ms 0.72% 84.30% 826ms 0.76% boost::detail::sp_counted_base::release 237ms 0.22% 84.51% 792ms 0.73% std::__new_allocator::construct (inline) 0 0% 84.51% 792ms 0.73% std::allocator_traits::construct (inline) 0 0% 84.51% 774ms 0.71% boost::numeric::ublas::norm_inf (inline) 413ms 0.38% 84.89% 774ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 204ms 0.19% 85.08% 760ms 0.7% boost::shared_ptr::shared_ptr (inline) 22ms 0.02% 85.10% 747ms 0.69% MutableElement::RegisterWithEdges (inline) 0 0% 85.10% 740ms 0.68% std::_Rb_tree::_M_construct_node (inline) 20ms 0.018% 85.12% 732ms 0.67% Edge::AddElement 345ms 0.32% 85.44% 720ms 0.66% Edge::GetMapIndex 0 0% 85.44% 707ms 0.65% std::_Vector_base::_M_allocate (inline) 0 0% 85.44% 705ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.44% 705ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 85.46% 705ms 0.65% std::_Rb_tree::_M_insert_node (inline) 124ms 0.11% 85.57% 654ms 0.6% MutableElement::GetNodeLocalIndex 650ms 0.6% 86.17% 650ms 0.6% Node::GetIndex 35ms 0.032% 86.20% 636ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.20% 636ms 0.58% boost::numeric::ublas::vector::vector (inline) 632ms 0.58% 86.78% 632ms 0.58% [libstdc++.so.6.0.33] 1ms 0.00092% 86.78% 626ms 0.58% vtkPolygon::New 1ms 0.00092% 86.78% 625ms 0.57% vtkPolygon::vtkPolygon 35ms 0.032% 86.82% 589ms 0.54% MutableElement::RegisterWithNodes (inline) 11ms 0.01% 86.83% 587ms 0.54% std::vector::_M_default_append (inline) 564ms 0.52% 87.34% 564ms 0.52% tcache_put (inline) 522ms 0.48% 87.82% 556ms 0.51% boost::detail::shared_count::shared_count (inline) 0 0% 87.82% 549ms 0.5% std::map::map (inline)