File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 55244ms, 87.86% of 62876ms total Dropped 983 nodes (cum <= 314.38ms) flat flat% sum% cum cum% 0 0% 0% 62597ms 99.56% __libc_start_call_main 0 0% 0% 62597ms 99.56% __libc_start_main_impl 0 0% 0% 62597ms 99.56% _start 0 0% 0% 62583ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62583ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62583ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62583ms 99.53% main 0 0% 0% 62547ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62547ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62547ms 99.48% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 62541ms 99.47% AbstractCellBasedSimulation::Solve 12ms 0.019% 0.019% 32623ms 51.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.022% 0.041% 30500ms 48.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 49ms 0.078% 0.12% 29903ms 47.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 150ms 0.24% 0.36% 22933ms 36.47% NagaiHondaForce::AddForceContribution 1ms 0.0016% 0.36% 22226ms 35.35% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.36% 13568ms 21.58% VertexBasedCellPopulation::Update 0 0% 0.36% 13491ms 21.46% MutableVertexMesh::ReMesh 6745ms 10.73% 11.09% 11709ms 18.62% Cylindrical2dVertexMesh::GetVectorFromAtoB 36ms 0.057% 11.14% 10296ms 16.38% Cell::ReadyToDivide 39ms 0.062% 11.21% 9711ms 15.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 69ms 0.11% 11.32% 9244ms 14.70% NagaiHondaForce::GetAdhesionParameter 33ms 0.052% 11.37% 8416ms 13.39% SimpleWntCellCycleModel::UpdateCellCyclePhase 238ms 0.38% 11.75% 8147ms 12.96% boost::numeric::ublas::c_vector::c_vector (partial-inline) 71ms 0.11% 11.86% 7243ms 11.52% CellPropertyCollection::GetPropertiesType (inline) 186ms 0.3% 12.16% 7232ms 11.50% boost::numeric::ublas::vector_assign (inline) 486ms 0.77% 12.93% 6701ms 10.66% std::__new_allocator::allocate (inline) 40ms 0.064% 12.99% 6694ms 10.65% VertexBasedCellPopulation::GetDampingConstant 66ms 0.1% 13.10% 6507ms 10.35% MutableVertexMesh::CheckForIntersections 0 0% 13.10% 6446ms 10.25% std::allocator_traits::allocate (inline) 0 0% 13.10% 6324ms 10.06% std::_Rb_tree::_M_create_node (inline) 620ms 0.99% 14.08% 6268ms 9.97% operator new 0 0% 14.08% 6094ms 9.69% std::_Rb_tree::_M_get_node (inline) 615ms 0.98% 15.06% 6087ms 9.68% std::_Rb_tree::_M_erase 1463ms 2.33% 17.39% 6072ms 9.66% __dynamic_cast 44ms 0.07% 17.46% 6062ms 9.64% AbstractCellProperty::IsSubType (inline) 28ms 0.045% 17.50% 6058ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 4ms 0.0064% 17.51% 6054ms 9.63% AbstractCellBasedSimulation::DoCellBirth 16ms 0.025% 17.53% 5999ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 17.53% 5929ms 9.43% std::_Rb_tree::_M_drop_node (inline) 273ms 0.43% 17.97% 5771ms 9.18% std::_Rb_tree::~_Rb_tree (inline) 2393ms 3.81% 21.77% 5541ms 8.81% __GI___libc_malloc 0 0% 21.77% 5536ms 8.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 21.77% 5507ms 8.76% std::set::~set (inline) 1658ms 2.64% 24.41% 5385ms 8.56% boost::numeric::ublas::indexing_vector_assign 86ms 0.14% 24.55% 5120ms 8.14% std::__new_allocator::deallocate (inline) 0 0% 24.55% 5119ms 8.14% std::allocator_traits::deallocate (inline) 0 0% 24.55% 5078ms 8.08% std::_Rb_tree::_M_put_node (inline) 57ms 0.091% 24.64% 4990ms 7.94% Cell::GetMutationState 185ms 0.29% 24.93% 4958ms 7.89% VertexMesh::GetNextEdgeGradientOfElementAtNode 965ms 1.53% 26.47% 4785ms 7.61% __GI___libc_free 513ms 0.82% 27.28% 4710ms 7.49% VertexMesh::ElementIncludesPoint 30ms 0.048% 27.33% 4616ms 7.34% VertexBasedCellPopulation::GetLocationOfCellCentre 6ms 0.0095% 27.34% 4563ms 7.26% MutableVertexMesh::RemoveDeletedNodesAndElements 282ms 0.45% 27.79% 4418ms 7.03% std::map::operator[] (partial-inline) 364ms 0.58% 28.37% 4387ms 6.98% VertexMesh::GetCentroidOfElement 882ms 1.40% 29.77% 4141ms 6.59% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 29.77% 4114ms 6.54% std::set::insert (inline) 115ms 0.18% 29.95% 3914ms 6.22% std::_Rb_tree::_Rb_tree (partial-inline) 3610ms 5.74% 35.70% 3803ms 6.05% _int_free 3714ms 5.91% 41.60% 3714ms 5.91% boost::numeric::ublas::c_vector::operator() 400ms 0.64% 42.24% 3670ms 5.84% std::_Rb_tree::_M_copy (inline) 3ms 0.0048% 42.24% 3620ms 5.76% std::set::set (inline) 573ms 0.91% 43.15% 3610ms 5.74% std::_Rb_tree::_M_insert_ (inline) 93ms 0.15% 43.30% 3526ms 5.61% SimpleWntCellCycleModel::GetWntLevel 58ms 0.092% 43.39% 3352ms 5.33% std::set_intersection (inline) 89ms 0.14% 43.54% 3342ms 5.32% WntConcentration::GetWntLevel 169ms 0.27% 43.81% 3294ms 5.24% std::__set_intersection 3254ms 5.18% 48.98% 3254ms 5.18% __strcmp_evex 15ms 0.024% 49.00% 3195ms 5.08% MutableVertexMesh::RemoveDeletedNodes 394ms 0.63% 49.63% 3152ms 5.01% std::_Rb_tree::_M_clone_node (inline) 1542ms 2.45% 52.08% 3140ms 4.99% std::_Rb_tree::_M_lower_bound (inline) 1972ms 3.14% 55.22% 3139ms 4.99% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.033% 55.25% 3085ms 4.91% EdgeHelper::RemoveDeletedEdges 903ms 1.44% 56.69% 3019ms 4.80% boost::numeric::ublas::c_vector::operator[] (inline) 21ms 0.033% 56.72% 2919ms 4.64% EdgeHelper::UpdateEdgesMapKey 81ms 0.13% 56.85% 2730ms 4.34% MutableElement::ResetIndex 0 0% 56.85% 2690ms 4.28% std::_Rb_tree::lower_bound (inline) 0 0% 56.85% 2690ms 4.28% std::map::lower_bound (inline) 68ms 0.11% 56.96% 2659ms 4.23% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.96% 2599ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 56.96% 2559ms 4.07% std::insert_iterator::operator= (inline) 25ms 0.04% 57.00% 2526ms 4.02% Cell::GetCellProliferativeType 2471ms 3.93% 60.93% 2471ms 3.93% boost::numeric::ublas::same_impl_ex 10ms 0.016% 60.95% 2367ms 3.76% std::_Rb_tree::_M_insert_unique_ (inline) 1861ms 2.96% 63.91% 2359ms 3.75% _int_malloc 113ms 0.18% 64.08% 2344ms 3.73% boost::detail::shared_count::~shared_count (inline) 0 0% 64.08% 2344ms 3.73% boost::shared_ptr::~shared_ptr (inline) 56ms 0.089% 64.17% 2244ms 3.57% Cell::SetCellProliferativeType 2200ms 3.50% 67.67% 2205ms 3.51% boost::detail::sp_counted_base::release 31ms 0.049% 67.72% 1976ms 3.14% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 64ms 0.1% 67.82% 1917ms 3.05% AbstractCellProperty::IsType (inline) 461ms 0.73% 68.56% 1754ms 2.79% AbstractElement::GetNodeLocation 0 0% 68.56% 1747ms 2.78% std::_Rb_tree::_M_insert_unique 0 0% 68.56% 1745ms 2.78% boost::numeric::ublas::c_vector::assign (inline) 35ms 0.056% 68.61% 1660ms 2.64% std::_Rb_tree::erase 0 0% 68.61% 1623ms 2.58% AbstractCellPopulation::WriteResultsToFiles 128ms 0.2% 68.82% 1574ms 2.50% VertexMesh::GetAreaGradientOfElementAtNode 263ms 0.42% 69.23% 1512ms 2.40% boost::numeric::ublas::vector_binary::size (inline) 11ms 0.017% 69.25% 1471ms 2.34% AbstractCellPopulation::Iterator::operator++ (inline) 118ms 0.19% 69.44% 1458ms 2.32% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0032% 69.44% 1439ms 2.29% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.44% 1439ms 2.29% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 19ms 0.03% 69.47% 1415ms 2.25% std::_Rb_tree::_M_emplace_hint_unique 269ms 0.43% 69.90% 1400ms 2.23% std::_Rb_tree_const_iterator::operator++ (inline) 26ms 0.041% 69.94% 1399ms 2.23% CellPropertyCollection::HasProperty 0 0% 69.94% 1355ms 2.16% Cell::HasCellProperty (inline) 0 0% 69.94% 1353ms 2.15% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0032% 69.95% 1344ms 2.14% VertexBasedCellPopulation::WriteCellVtkResultsToFile 287ms 0.46% 70.40% 1312ms 2.09% AbstractCellProperty::IsSame 15ms 0.024% 70.43% 1270ms 2.02% Cell::GetCellData 27ms 0.043% 70.47% 1251ms 1.99% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.47% 1224ms 1.95% VertexMeshWriter::WriteVtkUsingMesh 1200ms 1.91% 72.38% 1200ms 1.91% std::_Rb_tree::_S_right (inline) 0 0% 72.38% 1172ms 1.86% boost::numeric::ublas::c_vector::operator-= (inline) 80ms 0.13% 72.50% 1090ms 1.73% VertexMesh::GetVolumeOfElement 3ms 0.0048% 72.51% 1073ms 1.71% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 109ms 0.17% 72.68% 1041ms 1.66% CellPropertyCollection::AddProperty 135ms 0.21% 72.90% 1025ms 1.63% std::type_info::operator== (inline) 25ms 0.04% 72.94% 1024ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 1008ms 1.60% 74.54% 1008ms 1.60% std::_Rb_tree_increment 26ms 0.041% 74.58% 965ms 1.53% VertexMesh::GetSurfaceAreaOfElement 50ms 0.08% 74.66% 964ms 1.53% boost::numeric::ublas::vector_reference::operator() (inline) 205ms 0.33% 74.99% 944ms 1.50% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 60ms 0.095% 75.08% 923ms 1.47% std::_Rb_tree::_M_erase_aux (partial-inline) 865ms 1.38% 76.46% 865ms 1.38% [libchaste_cell_based.so] 0 0% 76.46% 852ms 1.36% std::__new_allocator::destroy (inline) 0 0% 76.46% 852ms 1.36% std::allocator_traits::destroy (inline) 19ms 0.03% 76.49% 851ms 1.35% Node::RemoveElement 0 0% 76.49% 851ms 1.35% boost::numeric::ublas::norm_2 (inline) 0 0% 76.49% 851ms 1.35% std::_Rb_tree::_M_destroy_node (inline) 349ms 0.56% 77.04% 847ms 1.35% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 3ms 0.0048% 77.05% 834ms 1.33% std::set::erase (inline) 1ms 0.0016% 77.05% 832ms 1.32% OffLatticeSimulation::ApplyBoundaries 518ms 0.82% 77.87% 825ms 1.31% std::_Rb_tree::equal_range (inline) 0 0% 77.87% 821ms 1.31% CellPropertyCollection::~CellPropertyCollection (inline) 797ms 1.27% 79.14% 797ms 1.27% [libchaste_mesh.so] 0 0% 79.14% 788ms 1.25% std::_Rb_tree::_Auto_node::_Auto_node (inline) 8ms 0.013% 79.15% 746ms 1.19% boost::numeric::ublas::detail::expression_type_check (inline) 60ms 0.095% 79.25% 731ms 1.16% std::less::operator() (inline) 79ms 0.13% 79.38% 721ms 1.15% boost::numeric::ublas::detail::equals 32ms 0.051% 79.43% 718ms 1.14% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 13ms 0.021% 79.45% 713ms 1.13% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 79.45% 698ms 1.11% boost::numeric::ublas::vector_binary::operator() (inline) 17ms 0.027% 79.47% 696ms 1.11% CellPropertyRegistry::Get 573ms 0.91% 80.39% 671ms 1.07% std::operator< (inline) 0 0% 80.39% 618ms 0.98% tcache_get (inline) 618ms 0.98% 81.37% 618ms 0.98% tcache_get_n (inline) 609ms 0.97% 82.34% 609ms 0.97% std::_Rb_tree_insert_and_rebalance 536ms 0.85% 83.19% 608ms 0.97% CellPropertyCollection::GetProperty 0 0% 83.19% 591ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.19% 590ms 0.94% std::_Rb_tree::clear (inline) 1ms 0.0016% 83.19% 588ms 0.94% VertexMeshWriter::MakeVtkMesh 0 0% 83.19% 588ms 0.94% boost::numeric::ublas::norm_inf (inline) 259ms 0.41% 83.60% 588ms 0.94% boost::numeric::ublas::vector_norm_inf::apply (inline) 582ms 0.93% 84.53% 582ms 0.93% [libstdc++.so.6.0.33] 0 0% 84.53% 582ms 0.93% std::map::clear (inline) 11ms 0.017% 84.55% 579ms 0.92% MutableElement::RegisterWithEdges (inline) 17ms 0.027% 84.57% 574ms 0.91% Edge::AddElement 0 0% 84.57% 572ms 0.91% boost::numeric::ublas::c_vector::assign_temporary (inline) 66ms 0.1% 84.68% 572ms 0.91% boost::numeric::ublas::c_vector::swap (inline) 295ms 0.47% 85.15% 506ms 0.8% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 85ms 0.14% 85.28% 506ms 0.8% std::swap_ranges (inline) 44ms 0.07% 85.35% 492ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 86ms 0.14% 85.49% 473ms 0.75% MutableElement::GetNodeLocalIndex 44ms 0.07% 85.56% 444ms 0.71% std::_Rb_tree::find (inline) 422ms 0.67% 86.23% 422ms 0.67% std::vector::size (inline) 0 0% 86.23% 421ms 0.67% std::iter_swap (inline) 421ms 0.67% 86.90% 421ms 0.67% std::swap (inline) 215ms 0.34% 87.24% 417ms 0.66% Edge::GetMapIndex 0 0% 87.24% 415ms 0.66% vtkPolygon::New 0 0% 87.24% 414ms 0.66% vtkPolygon::vtkPolygon 0 0% 87.24% 408ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.24% 388ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 13ms 0.021% 87.26% 388ms 0.62% std::_Rb_tree::_M_insert_node (inline) 1ms 0.0016% 87.26% 355ms 0.56% std::map::find (inline) 2ms 0.0032% 87.27% 353ms 0.56% std::_Vector_base::_M_allocate (inline) 14ms 0.022% 87.29% 342ms 0.54% MutableElement::RegisterWithNodes (inline) 1ms 0.0016% 87.29% 336ms 0.53% Cylindrical2dVertexMesh::GetMeshForVtk 335ms 0.53% 87.82% 335ms 0.53% Node::GetIndex 24ms 0.038% 87.86% 330ms 0.52% Node::AddElement 0 0% 87.86% 327ms 0.52% std::map::map (inline) 0 0% 87.86% 316ms 0.5% vtkCell::vtkCell