File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 73511ms, 87.08% of 84413ms total Dropped 1090 nodes (cum <= 422.06ms) flat flat% sum% cum cum% 0 0% 0% 84135ms 99.67% __libc_start_call_main 0 0% 0% 84135ms 99.67% __libc_start_main_impl 0 0% 0% 84135ms 99.67% _start 0 0% 0% 84117ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 84117ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 84117ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 84117ms 99.65% main 0 0% 0% 84076ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 84076ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 84076ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0012% 0.0012% 84070ms 99.59% AbstractCellBasedSimulation::Solve 14ms 0.017% 0.018% 43678ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 10ms 0.012% 0.03% 41098ms 48.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 127ms 0.15% 0.18% 39934ms 47.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 239ms 0.28% 0.46% 30503ms 36.14% NagaiHondaForce::AddForceContribution 0 0% 0.46% 29990ms 35.53% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0012% 0.46% 18383ms 21.78% VertexBasedCellPopulation::Update 0 0% 0.46% 18276ms 21.65% MutableVertexMesh::ReMesh 11472ms 13.59% 14.05% 17997ms 21.32% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.089% 14.14% 13900ms 16.47% Cell::ReadyToDivide 52ms 0.062% 14.21% 12780ms 15.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 265ms 0.31% 14.52% 10971ms 13.00% NagaiHondaForce::GetAdhesionParameter 121ms 0.14% 14.66% 10960ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 71ms 0.084% 14.75% 10931ms 12.95% CellPropertyCollection::GetPropertiesType (inline) 338ms 0.4% 15.15% 10593ms 12.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 208ms 0.25% 15.39% 9509ms 11.26% boost::numeric::ublas::vector_assign (inline) 2565ms 3.04% 18.43% 9454ms 11.20% __dynamic_cast 43ms 0.051% 18.48% 9377ms 11.11% AbstractCellProperty::IsSubType (inline) 101ms 0.12% 18.60% 9162ms 10.85% MutableVertexMesh::CheckForIntersections 64ms 0.076% 18.68% 8979ms 10.64% VertexBasedCellPopulation::GetDampingConstant 61ms 0.072% 18.75% 8421ms 9.98% AbstractTargetAreaModifier::UpdateTargetAreas 37ms 0.044% 18.79% 8355ms 9.90% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.032% 18.83% 8035ms 9.52% AbstractCellBasedSimulation::DoCellBirth 985ms 1.17% 19.99% 7516ms 8.90% std::__new_allocator::allocate (inline) 298ms 0.35% 20.35% 7290ms 8.64% VertexMesh::GetNextEdgeGradientOfElementAtNode 2206ms 2.61% 22.96% 7281ms 8.63% boost::numeric::ublas::indexing_vector_assign 0 0% 22.96% 7191ms 8.52% std::_Rb_tree::_M_create_node (inline) 0 0% 22.96% 7107ms 8.42% std::allocator_traits::allocate (inline) 55ms 0.065% 23.02% 6820ms 8.08% Cell::GetMutationState 23ms 0.027% 23.05% 6745ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 885ms 1.05% 24.10% 6704ms 7.94% std::_Rb_tree::_M_erase 671ms 0.79% 24.90% 6665ms 7.90% VertexMesh::ElementIncludesPoint 599ms 0.71% 25.61% 6634ms 7.86% operator new 0 0% 25.61% 6577ms 7.79% std::_Rb_tree::_M_get_node (inline) 0 0% 25.61% 6338ms 7.51% std::_Rb_tree::_Alloc_node::operator() (inline) 354ms 0.42% 26.02% 6306ms 7.47% VertexMesh::GetCentroidOfElement 210ms 0.25% 26.27% 6189ms 7.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.27% 6081ms 7.20% std::_Rb_tree::_M_drop_node (inline) 342ms 0.41% 26.68% 6050ms 7.17% std::map::operator[] (partial-inline) 174ms 0.21% 26.88% 5905ms 7.00% std::__new_allocator::deallocate (inline) 0 0% 26.88% 5889ms 6.98% std::allocator_traits::deallocate (inline) 2239ms 2.65% 29.54% 5874ms 6.96% __GI___libc_malloc 0 0% 29.54% 5870ms 6.95% std::set::~set (inline) 6ms 0.0071% 29.54% 5853ms 6.93% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.54% 5844ms 6.92% std::_Rb_tree::_M_put_node (inline) 1096ms 1.30% 30.84% 5661ms 6.71% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 5617ms 6.65% 37.50% 5617ms 6.65% __strcmp_evex 1901ms 2.25% 39.75% 5538ms 6.56% __GI___libc_free 117ms 0.14% 39.89% 5494ms 6.51% std::_Rb_tree::_Rb_tree (partial-inline) 593ms 0.7% 40.59% 5195ms 6.15% std::_Rb_tree::_M_copy (inline) 19ms 0.023% 40.61% 5086ms 6.03% std::set::set (inline) 93ms 0.11% 40.72% 4928ms 5.84% SimpleWntCellCycleModel::GetWntLevel 2033ms 2.41% 43.13% 4843ms 5.74% std::_Rb_tree::_M_lower_bound (inline) 129ms 0.15% 43.28% 4768ms 5.65% WntConcentration::GetWntLevel 4622ms 5.48% 48.76% 4622ms 5.48% boost::numeric::ublas::c_vector::operator() 2281ms 2.70% 51.46% 4422ms 5.24% __cxxabiv1::__si_class_type_info::__do_dyncast 624ms 0.74% 52.20% 4393ms 5.20% std::_Rb_tree::_M_clone_node (inline) 12ms 0.014% 52.21% 4062ms 4.81% MutableVertexMesh::RemoveDeletedNodes 1478ms 1.75% 53.97% 4037ms 4.78% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.97% 3991ms 4.73% std::set::insert (inline) 0 0% 53.97% 3971ms 4.70% std::_Rb_tree::lower_bound (inline) 0 0% 53.97% 3971ms 4.70% std::map::lower_bound (inline) 19ms 0.023% 53.99% 3935ms 4.66% EdgeHelper::RemoveDeletedEdges 36ms 0.043% 54.03% 3721ms 4.41% EdgeHelper::UpdateEdgesMapKey 3292ms 3.90% 57.93% 3622ms 4.29% _int_free 188ms 0.22% 58.15% 3594ms 4.26% MutableElement::ResetIndex 0 0% 58.15% 3566ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 95ms 0.11% 58.27% 3390ms 4.02% AbstractCellPopulation::GetCellUsingLocationIndex 390ms 0.46% 58.73% 3362ms 3.98% std::_Rb_tree::_M_insert_ (inline) 111ms 0.13% 58.86% 3256ms 3.86% std::set_intersection (inline) 38ms 0.045% 58.90% 3224ms 3.82% Cell::GetCellProliferativeType 210ms 0.25% 59.15% 3145ms 3.73% std::__set_intersection 35ms 0.041% 59.19% 3007ms 3.56% AbstractCellProperty::IsType (inline) 2970ms 3.52% 62.71% 2970ms 3.52% boost::numeric::ublas::same_impl_ex 10ms 0.012% 62.72% 2716ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 23ms 0.027% 62.75% 2550ms 3.02% Cell::SetCellProliferativeType 1656ms 1.96% 64.71% 2408ms 2.85% _int_malloc 0 0% 64.71% 2384ms 2.82% std::insert_iterator::operator= (inline) 665ms 0.79% 65.50% 2323ms 2.75% AbstractElement::GetNodeLocation 2281ms 2.70% 68.20% 2281ms 2.70% std::_Rb_tree::_S_right (inline) 604ms 0.72% 68.92% 2253ms 2.67% AbstractCellProperty::IsSame 56ms 0.066% 68.99% 2238ms 2.65% std::_Rb_tree::erase 27ms 0.032% 69.02% 2190ms 2.59% CellPropertyCollection::HasProperty 0 0% 69.02% 2129ms 2.52% Cell::HasCellProperty (inline) 168ms 0.2% 69.22% 2117ms 2.51% VertexMesh::GetAreaGradientOfElementAtNode 5ms 0.0059% 69.22% 2070ms 2.45% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 69.22% 2035ms 2.41% boost::numeric::ublas::c_vector::assign (inline) 466ms 0.55% 69.77% 1972ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.77% 1952ms 2.31% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.77% 1944ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 1ms 0.0012% 69.78% 1921ms 2.28% std::_Rb_tree::_M_insert_unique 19ms 0.023% 69.80% 1912ms 2.27% Cell::GetCellData 186ms 0.22% 70.02% 1857ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 61ms 0.072% 70.09% 1792ms 2.12% VertexMesh::GetVolumeOfElement 38ms 0.045% 70.14% 1750ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0024% 70.14% 1715ms 2.03% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.14% 1715ms 2.03% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.0071% 70.15% 1713ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.034% 70.18% 1710ms 2.03% std::_Rb_tree::_M_emplace_hint_unique 132ms 0.16% 70.34% 1702ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 370ms 0.44% 70.77% 1649ms 1.95% std::type_info::operator== (inline) 0 0% 70.77% 1602ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.77% 1594ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1499ms 1.78% 72.55% 1499ms 1.78% std::_Rb_tree_increment 0 0% 72.55% 1445ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 966ms 1.14% 73.69% 1433ms 1.70% std::_Rb_tree::equal_range (inline) 51ms 0.06% 73.76% 1412ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 15ms 0.018% 73.77% 1348ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 19ms 0.023% 73.80% 1214ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 22ms 0.026% 73.82% 1204ms 1.43% VertexMesh::GetSurfaceAreaOfElement 66ms 0.078% 73.90% 1196ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 44ms 0.052% 73.95% 1138ms 1.35% Node::RemoveElement 123ms 0.15% 74.10% 1107ms 1.31% CellPropertyCollection::AddProperty 6ms 0.0071% 74.10% 1095ms 1.30% std::set::erase (inline) 0 0% 74.10% 1095ms 1.30% tcache_get (inline) 1095ms 1.30% 75.40% 1095ms 1.30% tcache_get_n (inline) 0 0% 75.40% 1065ms 1.26% boost::numeric::ublas::norm_2 (inline) 436ms 0.52% 75.92% 1058ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 58ms 0.069% 75.99% 1052ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.99% 1041ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 57ms 0.068% 76.05% 1040ms 1.23% std::less::operator() (inline) 0 0% 76.05% 1017ms 1.20% OffLatticeSimulation::ApplyBoundaries 989ms 1.17% 77.23% 989ms 1.17% [libchaste_cell_based.so] 821ms 0.97% 78.20% 983ms 1.16% std::operator< (inline) 62ms 0.073% 78.27% 913ms 1.08% std::_Rb_tree::_M_erase_aux (partial-inline) 93ms 0.11% 78.38% 907ms 1.07% std::_Rb_tree::find (inline) 891ms 1.06% 79.44% 891ms 1.06% std::_Rb_tree_insert_and_rebalance 21ms 0.025% 79.46% 882ms 1.04% CellPropertyRegistry::Get 0 0% 79.46% 853ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 18ms 0.021% 79.48% 852ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.48% 833ms 0.99% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0071% 79.49% 833ms 0.99% boost::numeric::ublas::c_vector::swap (inline) 5ms 0.0059% 79.50% 828ms 0.98% boost::numeric::ublas::detail::expression_type_check (inline) 50ms 0.059% 79.56% 827ms 0.98% std::swap_ranges (inline) 6ms 0.0071% 79.56% 818ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 141ms 0.17% 79.73% 810ms 0.96% boost::numeric::ublas::detail::equals 110ms 0.13% 79.86% 793ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 79.86% 793ms 0.94% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.86% 777ms 0.92% std::iter_swap (inline) 777ms 0.92% 80.78% 777ms 0.92% std::swap (inline) 0 0% 80.78% 770ms 0.91% std::map::find (inline) 743ms 0.88% 81.66% 743ms 0.88% Node::rGetLocation 0 0% 81.66% 726ms 0.86% std::_Rb_tree::clear (inline) 0 0% 81.66% 716ms 0.85% std::map::clear (inline) 80ms 0.095% 81.76% 695ms 0.82% boost::numeric::ublas::c_vector::operator= (inline) 693ms 0.82% 82.58% 693ms 0.82% std::vector::size (inline) 0 0% 82.58% 689ms 0.82% VertexMeshWriter::MakeVtkMesh 200ms 0.24% 82.81% 675ms 0.8% std::__new_allocator::construct (inline) 0 0% 82.81% 675ms 0.8% std::allocator_traits::construct (inline) 639ms 0.76% 83.57% 659ms 0.78% boost::detail::sp_counted_base::release 0 0% 83.57% 650ms 0.77% boost::numeric::ublas::norm_inf (inline) 293ms 0.35% 83.92% 650ms 0.77% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 83.92% 614ms 0.73% std::_Rb_tree::_M_construct_node (inline) 18ms 0.021% 83.94% 598ms 0.71% Edge::AddElement 11ms 0.013% 83.95% 597ms 0.71% MutableElement::RegisterWithEdges (inline) 15ms 0.018% 83.97% 596ms 0.71% AbstractNumericalMethod::DetectStepSizeExceptions 139ms 0.16% 84.14% 592ms 0.7% boost::shared_ptr::shared_ptr (inline) 323ms 0.38% 84.52% 589ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 583ms 0.69% 85.21% 583ms 0.69% [libstdc++.so.6.0.33] 111ms 0.13% 85.34% 581ms 0.69% VertexBasedCellPopulation::CheckForStepSizeException 577ms 0.68% 86.02% 577ms 0.68% [libchaste_mesh.so] 0 0% 86.02% 557ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.02% 557ms 0.66% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.024% 86.05% 557ms 0.66% std::_Rb_tree::_M_insert_node (inline) 281ms 0.33% 86.38% 551ms 0.65% Edge::GetMapIndex 0 0% 86.38% 550ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.38% 527ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.38% 522ms 0.62% vtkPolygon::New 1ms 0.0012% 86.38% 522ms 0.62% vtkPolygon::vtkPolygon 96ms 0.11% 86.49% 499ms 0.59% MutableElement::GetNodeLocalIndex 437ms 0.52% 87.01% 453ms 0.54% boost::detail::shared_count::shared_count (inline) 19ms 0.023% 87.04% 451ms 0.53% MutableElement::RegisterWithNodes (inline) 3ms 0.0036% 87.04% 436ms 0.52% std::vector::_M_default_append (inline) 0 0% 87.04% 435ms 0.52% std::map::map (inline) 21ms 0.025% 87.06% 430ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.06% 430ms 0.51% boost::numeric::ublas::vector::vector (inline) 18ms 0.021% 87.08% 428ms 0.51% Node::AddElement