File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 75698ms, 87.87% of 86151ms total Dropped 1042 nodes (cum <= 430.75ms) flat flat% sum% cum cum% 0 0% 0% 85863ms 99.67% __libc_start_call_main 0 0% 0% 85863ms 99.67% __libc_start_main_impl 0 0% 0% 85863ms 99.67% _start 0 0% 0% 85845ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 85845ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 85845ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 85845ms 99.64% main 0 0% 0% 85809ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 85809ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 85809ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 85803ms 99.60% AbstractCellBasedSimulation::Solve 14ms 0.016% 0.016% 44318ms 51.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.0058% 0.022% 41678ms 48.38% ForwardEulerNumericalMethod::UpdateAllNodePositions 107ms 0.12% 0.15% 40828ms 47.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.15% 31045ms 36.04% AbstractCellBasedSimulation::UpdateCellPopulation 234ms 0.27% 0.42% 30957ms 35.93% NagaiHondaForce::AddForceContribution 3ms 0.0035% 0.42% 19005ms 22.06% VertexBasedCellPopulation::Update 1ms 0.0012% 0.42% 18887ms 21.92% MutableVertexMesh::ReMesh 11370ms 13.20% 13.62% 18056ms 20.96% Cylindrical2dVertexMesh::GetVectorFromAtoB 80ms 0.093% 13.71% 13988ms 16.24% Cell::ReadyToDivide 28ms 0.033% 13.75% 12830ms 14.89% AbstractPhaseBasedCellCycleModel::ReadyToDivide 253ms 0.29% 14.04% 11111ms 12.90% NagaiHondaForce::GetAdhesionParameter 141ms 0.16% 14.20% 11060ms 12.84% SimpleWntCellCycleModel::UpdateCellCyclePhase 70ms 0.081% 14.28% 10945ms 12.70% CellPropertyCollection::GetPropertiesType (inline) 401ms 0.47% 14.75% 10653ms 12.37% boost::numeric::ublas::c_vector::c_vector (partial-inline) 208ms 0.24% 14.99% 9509ms 11.04% boost::numeric::ublas::vector_assign (inline) 82ms 0.095% 15.09% 9402ms 10.91% VertexBasedCellPopulation::GetDampingConstant 2900ms 3.37% 18.45% 9346ms 10.85% __dynamic_cast 35ms 0.041% 18.49% 9227ms 10.71% AbstractCellProperty::IsSubType (inline) 101ms 0.12% 18.61% 9167ms 10.64% MutableVertexMesh::CheckForIntersections 76ms 0.088% 18.70% 8415ms 9.77% AbstractTargetAreaModifier::UpdateTargetAreas 28ms 0.033% 18.73% 8320ms 9.66% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 18ms 0.021% 18.75% 8215ms 9.54% AbstractCellBasedSimulation::DoCellBirth 1217ms 1.41% 20.16% 7952ms 9.23% std::__new_allocator::allocate (inline) 0 0% 20.16% 7619ms 8.84% std::_Rb_tree::_M_create_node (inline) 0 0% 20.16% 7563ms 8.78% std::allocator_traits::allocate (inline) 252ms 0.29% 20.46% 7304ms 8.48% VertexMesh::GetNextEdgeGradientOfElementAtNode 2207ms 2.56% 23.02% 7263ms 8.43% boost::numeric::ublas::indexing_vector_assign 29ms 0.034% 23.05% 7101ms 8.24% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 23.05% 7021ms 8.15% std::_Rb_tree::_M_get_node (inline) 1022ms 1.19% 24.24% 6958ms 8.08% std::_Rb_tree::_M_erase 93ms 0.11% 24.35% 6909ms 8.02% Cell::GetMutationState 551ms 0.64% 24.99% 6774ms 7.86% operator new 0 0% 24.99% 6734ms 7.82% std::_Rb_tree::_Alloc_node::operator() (inline) 636ms 0.74% 25.72% 6696ms 7.77% VertexMesh::ElementIncludesPoint 342ms 0.4% 26.12% 6648ms 7.72% VertexMesh::GetCentroidOfElement 341ms 0.4% 26.52% 6454ms 7.49% std::map::operator[] (partial-inline) 10ms 0.012% 26.53% 6286ms 7.30% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.53% 6210ms 7.21% std::_Rb_tree::_M_drop_node (inline) 135ms 0.16% 26.69% 6203ms 7.20% std::_Rb_tree::~_Rb_tree (inline) 2197ms 2.55% 29.24% 6065ms 7.04% __GI___libc_malloc 190ms 0.22% 29.46% 6007ms 6.97% std::__new_allocator::deallocate (inline) 0 0% 29.46% 5996ms 6.96% std::allocator_traits::deallocate (inline) 0 0% 29.46% 5953ms 6.91% std::_Rb_tree::_M_put_node (inline) 0 0% 29.46% 5857ms 6.80% std::set::~set (inline) 1140ms 1.32% 30.78% 5762ms 6.69% AbstractMesh::GetDistanceBetweenNodes 130ms 0.15% 30.93% 5723ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 1836ms 2.13% 33.06% 5534ms 6.42% __GI___libc_free 572ms 0.66% 33.73% 5387ms 6.25% std::_Rb_tree::_M_copy (inline) 23ms 0.027% 33.75% 5352ms 6.21% std::set::set (inline) 5281ms 6.13% 39.88% 5281ms 6.13% __strcmp_evex 2056ms 2.39% 42.27% 5253ms 6.10% std::_Rb_tree::_M_lower_bound (inline) 97ms 0.11% 42.38% 5002ms 5.81% SimpleWntCellCycleModel::GetWntLevel 130ms 0.15% 42.53% 4840ms 5.62% WntConcentration::GetWntLevel 4700ms 5.46% 47.99% 4700ms 5.46% boost::numeric::ublas::c_vector::operator() 639ms 0.74% 48.73% 4625ms 5.37% std::_Rb_tree::_M_clone_node (inline) 18ms 0.021% 48.75% 4457ms 5.17% MutableVertexMesh::RemoveDeletedNodes 0 0% 48.75% 4378ms 5.08% std::_Rb_tree::lower_bound (inline) 0 0% 48.75% 4378ms 5.08% std::map::lower_bound (inline) 21ms 0.024% 48.77% 4325ms 5.02% EdgeHelper::RemoveDeletedEdges 1510ms 1.75% 50.53% 4137ms 4.80% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 50.53% 4128ms 4.79% std::set::insert (inline) 19ms 0.022% 50.55% 4090ms 4.75% EdgeHelper::UpdateEdgesMapKey 2179ms 2.53% 53.08% 4047ms 4.70% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 53.08% 3812ms 4.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 181ms 0.21% 53.29% 3782ms 4.39% MutableElement::ResetIndex 106ms 0.12% 53.41% 3746ms 4.35% AbstractCellPopulation::GetCellUsingLocationIndex 3387ms 3.93% 57.34% 3686ms 4.28% _int_free 414ms 0.48% 57.82% 3518ms 4.08% std::_Rb_tree::_M_insert_ (inline) 113ms 0.13% 57.96% 3258ms 3.78% std::set_intersection (inline) 45ms 0.052% 58.01% 3220ms 3.74% AbstractCellProperty::IsType (inline) 158ms 0.18% 58.19% 3145ms 3.65% std::__set_intersection 24ms 0.028% 58.22% 3063ms 3.56% Cell::GetCellProliferativeType 9ms 0.01% 58.23% 2895ms 3.36% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2879ms 3.34% 61.57% 2879ms 3.34% boost::numeric::ublas::same_impl_ex 2683ms 3.11% 64.69% 2683ms 3.11% std::_Rb_tree::_S_right (inline) 1795ms 2.08% 66.77% 2591ms 3.01% _int_malloc 40ms 0.046% 66.82% 2510ms 2.91% Cell::SetCellProliferativeType 0 0% 66.82% 2495ms 2.90% std::insert_iterator::operator= (inline) 55ms 0.064% 66.88% 2466ms 2.86% std::_Rb_tree::erase 687ms 0.8% 67.68% 2400ms 2.79% AbstractElement::GetNodeLocation 639ms 0.74% 68.42% 2312ms 2.68% AbstractCellProperty::IsSame 7ms 0.0081% 68.43% 2301ms 2.67% CellPropertyCollection::HasProperty 0 0% 68.43% 2234ms 2.59% Cell::HasCellProperty (inline) 7ms 0.0081% 68.43% 2156ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 16ms 0.019% 68.45% 2026ms 2.35% Cell::GetCellData 1ms 0.0012% 68.45% 2000ms 2.32% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.45% 1996ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 169ms 0.2% 68.65% 1973ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0023% 68.65% 1972ms 2.29% std::_Rb_tree::_M_insert_unique 0 0% 68.65% 1969ms 2.29% boost::numeric::ublas::c_vector::operator-= (inline) 164ms 0.19% 68.84% 1954ms 2.27% std::_Rb_tree_const_iterator::operator++ (inline) 463ms 0.54% 69.38% 1913ms 2.22% boost::numeric::ublas::vector_binary::size (inline) 51ms 0.059% 69.44% 1773ms 2.06% VertexMesh::GetVolumeOfElement 23ms 0.027% 69.47% 1727ms 2.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0023% 69.47% 1713ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 165ms 0.19% 69.66% 1702ms 1.98% AbstractCellPopulation::Iterator::IsRealCell (inline) 31ms 0.036% 69.70% 1694ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0023% 69.70% 1680ms 1.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.70% 1680ms 1.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 409ms 0.47% 70.17% 1673ms 1.94% std::type_info::operator== (inline) 1656ms 1.92% 72.10% 1656ms 1.92% std::_Rb_tree_increment 0 0% 72.10% 1642ms 1.91% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.10% 1638ms 1.90% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1075ms 1.25% 73.34% 1620ms 1.88% std::_Rb_tree::equal_range (inline) 0 0% 73.34% 1477ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 67ms 0.078% 73.42% 1431ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 17ms 0.02% 73.44% 1276ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 34ms 0.039% 73.48% 1235ms 1.43% Node::RemoveElement 8ms 0.0093% 73.49% 1203ms 1.40% std::set::erase (inline) 129ms 0.15% 73.64% 1191ms 1.38% CellPropertyCollection::AddProperty 25ms 0.029% 73.67% 1185ms 1.38% VertexMesh::GetSurfaceAreaOfElement 27ms 0.031% 73.70% 1182ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.066% 73.77% 1124ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.77% 1119ms 1.30% tcache_get (inline) 1119ms 1.30% 75.06% 1119ms 1.30% tcache_get_n (inline) 0 0% 75.06% 1088ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0012% 75.07% 1079ms 1.25% OffLatticeSimulation::ApplyBoundaries 37ms 0.043% 75.11% 1075ms 1.25% std::less::operator() (inline) 66ms 0.077% 75.19% 1071ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.19% 1039ms 1.21% boost::numeric::ublas::norm_2 (inline) 880ms 1.02% 76.21% 1038ms 1.20% std::operator< (inline) 441ms 0.51% 76.72% 1026ms 1.19% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 982ms 1.14% 77.86% 982ms 1.14% [libchaste_cell_based.so] 13ms 0.015% 77.87% 923ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 59ms 0.068% 77.94% 911ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 18ms 0.021% 77.96% 892ms 1.04% CellPropertyRegistry::Get 1ms 0.0012% 77.96% 892ms 1.04% std::_Rb_tree::clear (inline) 4ms 0.0046% 77.97% 888ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 77.97% 885ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 71ms 0.082% 78.05% 881ms 1.02% std::_Rb_tree::find (inline) 0 0% 78.05% 878ms 1.02% std::map::clear (inline) 0 0% 78.05% 874ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.014% 78.07% 874ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 59ms 0.068% 78.13% 862ms 1.00% std::swap_ranges (inline) 843ms 0.98% 79.11% 843ms 0.98% std::_Rb_tree_insert_and_rebalance 0 0% 79.11% 803ms 0.93% std::iter_swap (inline) 803ms 0.93% 80.04% 803ms 0.93% std::swap (inline) 101ms 0.12% 80.16% 782ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.16% 782ms 0.91% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0093% 80.17% 776ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 63ms 0.073% 80.24% 770ms 0.89% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 80.24% 757ms 0.88% std::map::find (inline) 755ms 0.88% 81.12% 755ms 0.88% Node::rGetLocation 98ms 0.11% 81.23% 751ms 0.87% boost::numeric::ublas::detail::equals 1ms 0.0012% 81.24% 705ms 0.82% VertexMeshWriter::MakeVtkMesh 676ms 0.78% 82.02% 676ms 0.78% std::vector::size (inline) 640ms 0.74% 82.76% 659ms 0.76% boost::detail::sp_counted_base::release 182ms 0.21% 82.97% 657ms 0.76% std::__new_allocator::construct (inline) 0 0% 82.97% 657ms 0.76% std::allocator_traits::construct (inline) 312ms 0.36% 83.34% 653ms 0.76% Edge::GetMapIndex 0 0% 83.34% 642ms 0.75% boost::numeric::ublas::norm_inf (inline) 317ms 0.37% 83.70% 642ms 0.75% boost::numeric::ublas::vector_norm_inf::apply (inline) 153ms 0.18% 83.88% 614ms 0.71% boost::shared_ptr::shared_ptr (inline) 608ms 0.71% 84.59% 608ms 0.71% [libchaste_mesh.so] 111ms 0.13% 84.72% 602ms 0.7% MutableElement::GetNodeLocalIndex 0 0% 84.72% 598ms 0.69% std::_Rb_tree::_M_construct_node (inline) 15ms 0.017% 84.73% 593ms 0.69% MutableElement::RegisterWithEdges (inline) 0 0% 84.73% 590ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 15ms 0.017% 84.75% 585ms 0.68% Edge::AddElement 573ms 0.67% 85.42% 573ms 0.67% [libstdc++.so.6.0.33] 0 0% 85.42% 541ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.42% 541ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 12ms 0.014% 85.43% 541ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.43% 540ms 0.63% std::_Vector_base::_M_allocate (inline) 538ms 0.62% 86.05% 538ms 0.62% Node::GetIndex 301ms 0.35% 86.40% 533ms 0.62% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.40% 513ms 0.6% vtkPolygon::New 1ms 0.0012% 86.41% 511ms 0.59% vtkPolygon::vtkPolygon 4ms 0.0046% 86.41% 473ms 0.55% std::vector::_M_default_append (inline) 452ms 0.52% 86.93% 461ms 0.54% boost::detail::shared_count::shared_count (inline) 460ms 0.53% 87.47% 460ms 0.53% boost::shared_ptr::operator-> (inline) 30ms 0.035% 87.50% 445ms 0.52% MutableElement::RegisterWithNodes (inline) 313ms 0.36% 87.87% 440ms 0.51% malloc_consolidate