File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 67887ms, 88.95% of 76321ms total Dropped 1046 nodes (cum <= 381.61ms) flat flat% sum% cum cum% 0 0% 0% 76170ms 99.80% __libc_start_call_main 0 0% 0% 76170ms 99.80% __libc_start_main_impl 0 0% 0% 76170ms 99.80% _start 0 0% 0% 76154ms 99.78% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 76154ms 99.78% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 76154ms 99.78% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 76154ms 99.78% main 0 0% 0% 76120ms 99.74% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 76120ms 99.74% CxxTest::TestRunner::runTest (inline) 0 0% 0% 76119ms 99.74% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0039% 0.0039% 76115ms 99.73% AbstractCellBasedSimulation::Solve 7ms 0.0092% 0.013% 40099ms 52.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.012% 0.025% 37421ms 49.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 39ms 0.051% 0.076% 36729ms 48.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 250ms 0.33% 0.4% 28803ms 37.74% NagaiHondaForce::AddForceContribution 2ms 0.0026% 0.41% 26629ms 34.89% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.0079% 0.41% 16030ms 21.00% VertexBasedCellPopulation::Update 0 0% 0.41% 15929ms 20.87% MutableVertexMesh::ReMesh 6818ms 8.93% 9.35% 13343ms 17.48% Cylindrical2dVertexMesh::GetVectorFromAtoB 63ms 0.083% 9.43% 12419ms 16.27% Cell::ReadyToDivide 57ms 0.075% 9.50% 11799ms 15.46% NagaiHondaForce::GetAdhesionParameter 20ms 0.026% 9.53% 11595ms 15.19% AbstractPhaseBasedCellCycleModel::ReadyToDivide 47ms 0.062% 9.59% 9937ms 13.02% SimpleWntCellCycleModel::UpdateCellCyclePhase 301ms 0.39% 9.99% 9896ms 12.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 607ms 0.8% 10.78% 9871ms 12.93% std::__new_allocator::allocate (inline) 0 0% 10.78% 9452ms 12.38% std::allocator_traits::allocate (inline) 115ms 0.15% 10.93% 9226ms 12.09% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.93% 9219ms 12.08% std::_Rb_tree::_M_create_node (inline) 648ms 0.85% 11.78% 9153ms 11.99% operator new 0 0% 11.78% 8949ms 11.73% std::_Rb_tree::_M_get_node (inline) 179ms 0.23% 12.02% 8831ms 11.57% boost::numeric::ublas::vector_assign (inline) 2700ms 3.54% 15.55% 8249ms 10.81% __GI___libc_malloc 0 0% 15.55% 7984ms 10.46% std::_Rb_tree::_Alloc_node::operator() (inline) 80ms 0.1% 15.66% 7655ms 10.03% VertexBasedCellPopulation::GetDampingConstant 31ms 0.041% 15.70% 7650ms 10.02% AbstractTargetAreaModifier::UpdateTargetAreas 34ms 0.045% 15.74% 7587ms 9.94% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 53ms 0.069% 15.81% 7563ms 9.91% AbstractCellProperty::IsSubType (inline) 1898ms 2.49% 18.30% 7513ms 9.84% __dynamic_cast 99ms 0.13% 18.43% 7386ms 9.68% MutableVertexMesh::CheckForIntersections 2ms 0.0026% 18.43% 7348ms 9.63% AbstractCellBasedSimulation::DoCellBirth 710ms 0.93% 19.36% 6677ms 8.75% std::_Rb_tree::_M_erase 0 0% 19.36% 6587ms 8.63% std::_Rb_tree::_M_drop_node (inline) 1931ms 2.53% 21.89% 6467ms 8.47% boost::numeric::ublas::indexing_vector_assign 292ms 0.38% 22.28% 6303ms 8.26% std::_Rb_tree::~_Rb_tree (inline) 377ms 0.49% 22.77% 6074ms 7.96% std::map::operator[] (partial-inline) 0 0% 22.77% 5996ms 7.86% std::set::~set (inline) 76ms 0.1% 22.87% 5821ms 7.63% std::__new_allocator::deallocate (inline) 0 0% 22.87% 5809ms 7.61% std::allocator_traits::deallocate (inline) 0 0% 22.87% 5773ms 7.56% std::_Rb_tree::_M_put_node (inline) 283ms 0.37% 23.24% 5731ms 7.51% VertexMesh::GetNextEdgeGradientOfElementAtNode 44ms 0.058% 23.30% 5716ms 7.49% Cell::GetMutationState 35ms 0.046% 23.34% 5687ms 7.45% VertexBasedCellPopulation::GetLocationOfCellCentre 1545ms 2.02% 25.37% 5632ms 7.38% __GI___libc_free 7ms 0.0092% 25.38% 5624ms 7.37% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 25.38% 5581ms 7.31% std::set::insert (inline) 367ms 0.48% 25.86% 5492ms 7.20% VertexMesh::ElementIncludesPoint 429ms 0.56% 26.42% 5488ms 7.19% VertexMesh::GetCentroidOfElement 98ms 0.13% 26.55% 5331ms 6.98% std::_Rb_tree::_Rb_tree (partial-inline) 666ms 0.87% 27.42% 5096ms 6.68% std::_Rb_tree::_M_insert_ (inline) 503ms 0.66% 28.08% 5060ms 6.63% std::_Rb_tree::_M_copy (inline) 17ms 0.022% 28.10% 4949ms 6.48% std::set::set (inline) 4738ms 6.21% 34.31% 4738ms 6.21% boost::numeric::ublas::c_vector::operator() 45ms 0.059% 34.37% 4533ms 5.94% std::set_intersection (inline) 188ms 0.25% 34.62% 4488ms 5.88% std::__set_intersection 4462ms 5.85% 40.46% 4462ms 5.85% __strcmp_evex 579ms 0.76% 41.22% 4436ms 5.81% std::_Rb_tree::_M_clone_node (inline) 117ms 0.15% 41.37% 4311ms 5.65% SimpleWntCellCycleModel::GetWntLevel 627ms 0.82% 42.20% 4262ms 5.58% AbstractMesh::GetDistanceBetweenNodes 1612ms 2.11% 44.31% 4143ms 5.43% std::_Rb_tree::_M_lower_bound (inline) 100ms 0.13% 44.44% 4119ms 5.40% WntConcentration::GetWntLevel 3667ms 4.80% 49.24% 4046ms 5.30% _int_free 17ms 0.022% 49.27% 4045ms 5.30% MutableVertexMesh::RemoveDeletedNodes 3371ms 4.42% 53.68% 3991ms 5.23% _int_malloc 427ms 0.56% 54.24% 3946ms 5.17% boost::numeric::ublas::c_vector::operator[] (inline) 33ms 0.043% 54.29% 3941ms 5.16% EdgeHelper::RemoveDeletedEdges 9ms 0.012% 54.30% 3790ms 4.97% EdgeHelper::UpdateEdgesMapKey 1777ms 2.33% 56.63% 3606ms 4.72% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.63% 3595ms 4.71% std::insert_iterator::operator= (inline) 0 0% 56.63% 3559ms 4.66% std::_Rb_tree::lower_bound (inline) 0 0% 56.63% 3559ms 4.66% std::map::lower_bound (inline) 88ms 0.12% 56.74% 3389ms 4.44% MutableElement::ResetIndex 0 0% 56.74% 3352ms 4.39% std::_Rb_tree::_M_insert_unique_ (inline) 3304ms 4.33% 61.07% 3304ms 4.33% boost::numeric::ublas::same_impl_ex 0 0% 61.07% 3242ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 45ms 0.059% 61.13% 3237ms 4.24% AbstractCellPopulation::GetCellUsingLocationIndex 22ms 0.029% 61.16% 3087ms 4.04% Cell::GetCellProliferativeType 2549ms 3.34% 64.50% 2549ms 3.34% [libchaste_cell_based.so] 124ms 0.16% 64.66% 2516ms 3.30% AbstractCellProperty::IsType (inline) 32ms 0.042% 64.70% 2464ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 66ms 0.086% 64.79% 2396ms 3.14% boost::detail::shared_count::~shared_count (inline) 0 0% 64.79% 2396ms 3.14% boost::shared_ptr::~shared_ptr (inline) 613ms 0.8% 65.59% 2318ms 3.04% AbstractElement::GetNodeLocation 75ms 0.098% 65.69% 2302ms 3.02% Cell::SetCellProliferativeType 2274ms 2.98% 68.67% 2279ms 2.99% boost::detail::sp_counted_base::release 2ms 0.0026% 68.67% 2229ms 2.92% std::_Rb_tree::_M_insert_unique 162ms 0.21% 68.88% 2165ms 2.84% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.0066% 68.89% 2157ms 2.83% AbstractCellPopulation::Iterator::operator++ (inline) 2105ms 2.76% 71.65% 2105ms 2.76% std::_Rb_tree::_S_right (inline) 34ms 0.045% 71.69% 2095ms 2.74% std::_Rb_tree::_M_emplace_hint_unique 57ms 0.075% 71.77% 1971ms 2.58% std::_Rb_tree::erase 0 0% 71.77% 1957ms 2.56% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.0092% 71.78% 1931ms 2.53% Cell::GetCellData 64ms 0.084% 71.86% 1850ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 45ms 0.059% 71.92% 1785ms 2.34% CellPropertyCollection::HasProperty 188ms 0.25% 72.17% 1725ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 72.17% 1724ms 2.26% Cell::HasCellProperty (inline) 0 0% 72.17% 1714ms 2.25% AbstractCellPopulation::WriteResultsToFiles 236ms 0.31% 72.48% 1708ms 2.24% std::_Rb_tree_const_iterator::operator++ (inline) 1693ms 2.22% 74.69% 1693ms 2.22% [libchaste_mesh.so] 36ms 0.047% 74.74% 1623ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.017% 74.76% 1594ms 2.09% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 260ms 0.34% 75.10% 1556ms 2.04% AbstractCellProperty::IsSame 0 0% 75.10% 1551ms 2.03% boost::numeric::ublas::c_vector::operator-= (inline) 291ms 0.38% 75.48% 1428ms 1.87% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.48% 1400ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0013% 75.48% 1389ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 71ms 0.093% 75.57% 1331ms 1.74% VertexMesh::GetVolumeOfElement 86ms 0.11% 75.69% 1296ms 1.70% std::type_info::operator== (inline) 1ms 0.0013% 75.69% 1272ms 1.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.69% 1272ms 1.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.69% 1271ms 1.67% tcache_get (inline) 1271ms 1.67% 77.35% 1271ms 1.67% tcache_get_n (inline) 0 0% 77.35% 1255ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 0 0% 77.35% 1235ms 1.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 80ms 0.1% 77.46% 1199ms 1.57% CellPropertyCollection::AddProperty 51ms 0.067% 77.53% 1171ms 1.53% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0013% 77.53% 1129ms 1.48% OffLatticeSimulation::ApplyBoundaries 46ms 0.06% 77.59% 1117ms 1.46% VertexMesh::GetSurfaceAreaOfElement 60ms 0.079% 77.67% 1067ms 1.40% MutableVertexMesh::CheckForSwapsFromShortEdges 664ms 0.87% 78.54% 1059ms 1.39% std::_Rb_tree::equal_range (inline) 0 0% 78.54% 1014ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 38ms 0.05% 78.59% 1006ms 1.32% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 986ms 1.29% 79.88% 986ms 1.29% std::_Rb_tree_increment 55ms 0.072% 79.95% 981ms 1.29% std::_Rb_tree::_M_erase_aux (partial-inline) 18ms 0.024% 79.97% 932ms 1.22% Node::RemoveElement 1ms 0.0013% 79.97% 914ms 1.20% std::set::erase (inline) 10ms 0.013% 79.99% 860ms 1.13% MutableElement::RegisterWithEdges (inline) 33ms 0.043% 80.03% 851ms 1.12% Edge::AddElement 55ms 0.072% 80.10% 849ms 1.11% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 80.10% 818ms 1.07% std::__new_allocator::destroy (inline) 0 0% 80.10% 818ms 1.07% std::allocator_traits::destroy (inline) 0 0% 80.10% 814ms 1.07% std::_Rb_tree::_M_destroy_node (inline) 41ms 0.054% 80.16% 812ms 1.06% CellPropertyRegistry::Get 17ms 0.022% 80.18% 800ms 1.05% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.18% 799ms 1.05% CellPropertyCollection::~CellPropertyCollection (inline) 770ms 1.01% 81.19% 770ms 1.01% [libstdc++.so.6.0.33] 159ms 0.21% 81.40% 758ms 0.99% boost::numeric::ublas::detail::equals 6ms 0.0079% 81.40% 757ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 745ms 0.98% 82.38% 745ms 0.98% std::_Rb_tree_insert_and_rebalance 0 0% 82.38% 737ms 0.97% boost::numeric::ublas::norm_2 (inline) 259ms 0.34% 82.72% 716ms 0.94% boost::numeric::ublas::vector_norm_2::apply 0 0% 82.72% 685ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0026% 82.72% 685ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 87ms 0.11% 82.84% 683ms 0.89% std::swap_ranges (inline) 682ms 0.89% 83.73% 682ms 0.89% Node::rGetLocation 1ms 0.0013% 83.73% 669ms 0.88% std::_Rb_tree::clear (inline) 0 0% 83.73% 664ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 83.73% 659ms 0.86% std::map::clear (inline) 53ms 0.069% 83.80% 638ms 0.84% std::less::operator() (inline) 74ms 0.097% 83.90% 620ms 0.81% std::_Rb_tree::find (inline) 0 0% 83.90% 596ms 0.78% std::iter_swap (inline) 596ms 0.78% 84.68% 596ms 0.78% std::swap (inline) 437ms 0.57% 85.25% 585ms 0.77% std::operator< (inline) 454ms 0.59% 85.85% 582ms 0.76% CellPropertyCollection::GetProperty 28ms 0.037% 85.88% 574ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 291ms 0.38% 86.26% 574ms 0.75% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.26% 564ms 0.74% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.03% 86.29% 564ms 0.74% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.29% 545ms 0.71% boost::numeric::ublas::norm_inf (inline) 203ms 0.27% 86.56% 545ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 59ms 0.077% 86.64% 506ms 0.66% MutableElement::GetNodeLocalIndex 1ms 0.0013% 86.64% 504ms 0.66% std::map::find (inline) 2ms 0.0026% 86.64% 501ms 0.66% std::_Vector_base::_M_allocate (inline) 488ms 0.64% 87.28% 488ms 0.64% std::vector::size (inline) 1ms 0.0013% 87.28% 475ms 0.62% vtkPolygon::New 0 0% 87.28% 474ms 0.62% vtkPolygon::vtkPolygon 0 0% 87.28% 459ms 0.6% std::map::map (inline) 11ms 0.014% 87.30% 426ms 0.56% MutableElement::RegisterWithNodes (inline) 2ms 0.0026% 87.30% 421ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.30% 421ms 0.55% boost::numeric::ublas::vector::vector (inline) 10ms 0.013% 87.31% 417ms 0.55% std::vector::_M_default_append (inline) 414ms 0.54% 87.85% 414ms 0.54% Node::GetIndex 410ms 0.54% 88.39% 410ms 0.54% tcache_put (inline) 36ms 0.047% 88.44% 405ms 0.53% Node::AddElement 390ms 0.51% 88.95% 390ms 0.51% boost::numeric::ublas::scalar_minus::apply (inline)