File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97821ms, 88.52% of 110509ms total Dropped 1124 nodes (cum <= 552.54ms) flat flat% sum% cum cum% 0 0% 0% 110049ms 99.58% __libc_start_call_main 0 0% 0% 110049ms 99.58% __libc_start_main_impl 0 0% 0% 110049ms 99.58% _start 0 0% 0% 110030ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110030ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110030ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110030ms 99.57% main 0 0% 0% 109993ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109993ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109993ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109985ms 99.53% AbstractCellBasedSimulation::Solve 16ms 0.014% 0.016% 56675ms 51.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.029% 53290ms 48.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 130ms 0.12% 0.15% 52256ms 47.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 447ms 0.4% 0.55% 40375ms 36.54% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.55% 40299ms 36.47% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.56% 25182ms 22.79% VertexBasedCellPopulation::Update 0 0% 0.56% 25044ms 22.66% MutableVertexMesh::ReMesh 14445ms 13.07% 13.63% 22819ms 20.65% Cylindrical2dVertexMesh::GetVectorFromAtoB 112ms 0.1% 13.73% 17530ms 15.86% Cell::ReadyToDivide 99ms 0.09% 13.82% 16302ms 14.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 333ms 0.3% 14.12% 15021ms 13.59% NagaiHondaForce::GetAdhesionParameter 416ms 0.38% 14.50% 14192ms 12.84% boost::numeric::ublas::c_vector::c_vector (partial-inline) 137ms 0.12% 14.62% 13890ms 12.57% SimpleWntCellCycleModel::UpdateCellCyclePhase 142ms 0.13% 14.75% 13676ms 12.38% CellPropertyCollection::GetPropertiesType (inline) 413ms 0.37% 15.12% 12665ms 11.46% boost::numeric::ublas::vector_assign (inline) 143ms 0.13% 15.25% 12188ms 11.03% MutableVertexMesh::CheckForIntersections 71ms 0.064% 15.32% 11351ms 10.27% VertexBasedCellPopulation::GetDampingConstant 3343ms 3.03% 18.34% 11189ms 10.12% __dynamic_cast 76ms 0.069% 18.41% 11058ms 10.01% AbstractCellProperty::IsSubType (inline) 89ms 0.081% 18.49% 10505ms 9.51% AbstractTargetAreaModifier::UpdateTargetAreas 59ms 0.053% 18.54% 10395ms 9.41% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1447ms 1.31% 19.85% 10359ms 9.37% std::__new_allocator::allocate (inline) 27ms 0.024% 19.88% 10333ms 9.35% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.88% 9792ms 8.86% std::allocator_traits::allocate (inline) 0 0% 19.88% 9713ms 8.79% std::_Rb_tree::_M_create_node (inline) 1541ms 1.39% 21.27% 9479ms 8.58% std::_Rb_tree::_M_erase 2684ms 2.43% 23.70% 9425ms 8.53% boost::numeric::ublas::indexing_vector_assign 0 0% 23.70% 9025ms 8.17% std::_Rb_tree::_M_get_node (inline) 377ms 0.34% 24.04% 9024ms 8.17% VertexMesh::GetNextEdgeGradientOfElementAtNode 802ms 0.73% 24.77% 9024ms 8.17% operator new 780ms 0.71% 25.47% 9022ms 8.16% VertexMesh::ElementIncludesPoint 42ms 0.038% 25.51% 8864ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 80ms 0.072% 25.58% 8662ms 7.84% Cell::GetMutationState 218ms 0.2% 25.78% 8517ms 7.71% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.78% 8505ms 7.70% std::_Rb_tree::_Alloc_node::operator() (inline) 492ms 0.45% 26.23% 8364ms 7.57% VertexMesh::GetCentroidOfElement 17ms 0.015% 26.24% 8277ms 7.49% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.24% 8275ms 7.49% std::_Rb_tree::_M_drop_node (inline) 270ms 0.24% 26.49% 8085ms 7.32% std::__new_allocator::deallocate (inline) 0 0% 26.49% 8048ms 7.28% std::allocator_traits::deallocate (inline) 3029ms 2.74% 29.23% 8023ms 7.26% __GI___libc_malloc 0 0% 29.23% 8018ms 7.26% std::set::~set (inline) 0 0% 29.23% 7985ms 7.23% std::_Rb_tree::_M_put_node (inline) 3048ms 2.76% 31.98% 7844ms 7.10% __GI___libc_free 484ms 0.44% 32.42% 7682ms 6.95% std::map::operator[] (partial-inline) 1379ms 1.25% 33.67% 7196ms 6.51% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 123ms 0.11% 33.78% 6946ms 6.29% std::_Rb_tree::_Rb_tree (partial-inline) 612ms 0.55% 34.34% 6615ms 5.99% std::_Rb_tree::_M_copy (inline) 16ms 0.014% 34.35% 6416ms 5.81% std::set::set (inline) 118ms 0.11% 34.46% 6395ms 5.79% SimpleWntCellCycleModel::GetWntLevel 6366ms 5.76% 40.22% 6366ms 5.76% boost::numeric::ublas::c_vector::operator() 133ms 0.12% 40.34% 6166ms 5.58% WntConcentration::GetWntLevel 2538ms 2.30% 42.63% 6162ms 5.58% std::_Rb_tree::_M_lower_bound (inline) 6154ms 5.57% 48.20% 6154ms 5.57% __strcmp_avx2 28ms 0.025% 48.23% 5763ms 5.21% MutableVertexMesh::RemoveDeletedNodes 799ms 0.72% 48.95% 5726ms 5.18% std::_Rb_tree::_M_clone_node (inline) 47ms 0.043% 48.99% 5586ms 5.05% EdgeHelper::RemoveDeletedEdges 0 0% 48.99% 5567ms 5.04% std::set::insert (inline) 2716ms 2.46% 51.45% 5510ms 4.99% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.022% 51.47% 5286ms 4.78% EdgeHelper::UpdateEdgesMapKey 281ms 0.25% 51.73% 5184ms 4.69% MutableElement::ResetIndex 1470ms 1.33% 53.06% 4956ms 4.48% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.06% 4927ms 4.46% std::_Rb_tree::lower_bound (inline) 0 0% 53.06% 4927ms 4.46% std::map::lower_bound (inline) 4435ms 4.01% 57.07% 4791ms 4.34% _int_free 2ms 0.0018% 57.07% 4768ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 543ms 0.49% 57.56% 4692ms 4.25% std::_Rb_tree::_M_insert_ (inline) 57ms 0.052% 57.62% 4684ms 4.24% std::set_intersection (inline) 261ms 0.24% 57.85% 4627ms 4.19% std::__set_intersection 119ms 0.11% 57.96% 4181ms 3.78% AbstractCellPopulation::GetCellUsingLocationIndex 42ms 0.038% 58.00% 3937ms 3.56% Cell::GetCellProliferativeType 3846ms 3.48% 61.48% 3846ms 3.48% boost::numeric::ublas::same_impl_ex 64ms 0.058% 61.54% 3631ms 3.29% AbstractCellProperty::IsType (inline) 1ms 0.0009% 61.54% 3613ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 61.54% 3472ms 3.14% std::insert_iterator::operator= (inline) 37ms 0.033% 61.57% 3401ms 3.08% std::_Rb_tree::erase 2328ms 2.11% 63.68% 3333ms 3.02% _int_malloc 793ms 0.72% 64.39% 3223ms 2.92% AbstractElement::GetNodeLocation 57ms 0.052% 64.45% 3169ms 2.87% Cell::SetCellProliferativeType 3096ms 2.80% 67.25% 3096ms 2.80% std::_Rb_tree::_S_right (inline) 5ms 0.0045% 67.25% 3066ms 2.77% std::_Rb_tree::_M_insert_unique_ (inline) 468ms 0.42% 67.68% 2929ms 2.65% std::_Rb_tree_const_iterator::operator++ (inline) 598ms 0.54% 68.22% 2669ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 775ms 0.7% 68.92% 2625ms 2.38% AbstractCellProperty::IsSame 41ms 0.037% 68.96% 2501ms 2.26% CellPropertyCollection::HasProperty 2ms 0.0018% 68.96% 2501ms 2.26% std::_Rb_tree::_M_insert_unique (inline) 0 0% 68.96% 2487ms 2.25% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.96% 2444ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.96% 2434ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 33ms 0.03% 68.99% 2429ms 2.20% Cell::GetCellData 5ms 0.0045% 68.99% 2408ms 2.18% AbstractCellPopulation::Iterator::operator++ (inline) 237ms 0.21% 69.21% 2403ms 2.17% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.21% 2401ms 2.17% Cell::HasCellProperty (inline) 239ms 0.22% 69.42% 2376ms 2.15% AbstractCellPopulation::Iterator::IsRealCell 1595ms 1.44% 70.87% 2362ms 2.14% std::_Rb_tree::equal_range (inline) 109ms 0.099% 70.96% 2294ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2281ms 2.06% 73.03% 2281ms 2.06% std::_Rb_tree_increment 43ms 0.039% 73.07% 2230ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 82ms 0.074% 73.14% 2195ms 1.99% VertexMesh::GetVolumeOfElement 0 0% 73.14% 2052ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.14% 2040ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 17ms 0.015% 73.16% 1868ms 1.69% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 445ms 0.4% 73.56% 1850ms 1.67% std::type_info::operator== (inline) 60ms 0.054% 73.61% 1836ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.61% 1830ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0009% 73.61% 1815ms 1.64% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.61% 1815ms 1.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 45ms 0.041% 73.66% 1707ms 1.54% Node::RemoveElement 12ms 0.011% 73.67% 1671ms 1.51% std::set::erase (inline) 30ms 0.027% 73.69% 1639ms 1.48% VertexMesh::GetSurfaceAreaOfElement 30ms 0.027% 73.72% 1632ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 83ms 0.075% 73.80% 1616ms 1.46% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 129ms 0.12% 73.91% 1529ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 172ms 0.16% 74.07% 1508ms 1.36% CellPropertyCollection::AddProperty 0 0% 74.07% 1463ms 1.32% tcache_get (inline) 1463ms 1.32% 75.39% 1463ms 1.32% tcache_get_n (inline) 0 0% 75.39% 1462ms 1.32% boost::numeric::ublas::vector_binary::operator() (inline) 1401ms 1.27% 76.66% 1401ms 1.27% Node::rGetLocation 0 0% 76.66% 1360ms 1.23% OffLatticeSimulation::ApplyBoundaries 79ms 0.071% 76.73% 1256ms 1.14% std::less::operator() (inline) 94ms 0.085% 76.82% 1222ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 104ms 0.094% 76.91% 1216ms 1.10% std::_Rb_tree::find (inline) 0 0% 76.91% 1208ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.91% 1182ms 1.07% std::_Rb_tree::clear (inline) 967ms 0.88% 77.79% 1177ms 1.07% std::operator< (inline) 0 0% 77.79% 1170ms 1.06% std::map::clear (inline) 1166ms 1.06% 78.84% 1166ms 1.06% std::_Rb_tree_insert_and_rebalance 22ms 0.02% 78.86% 1143ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.86% 1137ms 1.03% boost::numeric::ublas::norm_2 (inline) 550ms 0.5% 79.36% 1128ms 1.02% boost::numeric::ublas::vector_norm_2::apply 20ms 0.018% 79.38% 1106ms 1.00% CellPropertyRegistry::Get 6ms 0.0054% 79.38% 1100ms 1% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1071ms 0.97% 80.35% 1071ms 0.97% [libchaste_cell_based.so] 0 0% 80.35% 1011ms 0.91% std::map::find (inline) 981ms 0.89% 81.24% 981ms 0.89% std::vector::size (inline) 155ms 0.14% 81.38% 978ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.38% 978ms 0.88% boost::shared_ptr::~shared_ptr (inline) 425ms 0.38% 81.76% 974ms 0.88% Edge::GetMapIndex 938ms 0.85% 82.61% 938ms 0.85% [libchaste_mesh.so] 24ms 0.022% 82.63% 892ms 0.81% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.63% 891ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 82.64% 891ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 60ms 0.054% 82.69% 888ms 0.8% std::swap_ranges (inline) 93ms 0.084% 82.78% 881ms 0.8% MutableElement::GetNodeLocalIndex 0 0% 82.78% 870ms 0.79% VertexMeshWriter::MakeVtkMesh 142ms 0.13% 82.90% 858ms 0.78% boost::numeric::ublas::detail::equals 829ms 0.75% 83.65% 829ms 0.75% std::swap (inline) 0 0% 83.65% 828ms 0.75% std::iter_swap (inline) 802ms 0.73% 84.38% 802ms 0.73% Node::GetIndex 460ms 0.42% 84.80% 802ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 795ms 0.72% 85.52% 800ms 0.72% boost::detail::sp_counted_base::release 20ms 0.018% 85.53% 785ms 0.71% MutableElement::RegisterWithEdges (inline) 124ms 0.11% 85.65% 785ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 175ms 0.16% 85.80% 782ms 0.71% boost::shared_ptr::shared_ptr (inline) 32ms 0.029% 85.83% 776ms 0.7% Edge::AddElement 2ms 0.0018% 85.83% 765ms 0.69% std::_Vector_base::_M_allocate (inline) 108ms 0.098% 85.93% 750ms 0.68% std::__new_allocator::construct (inline) 0 0% 85.93% 750ms 0.68% std::allocator_traits::construct (inline) 0 0% 85.93% 717ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.93% 688ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.93% 678ms 0.61% boost::numeric::ublas::norm_inf (inline) 333ms 0.3% 86.23% 678ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.23% 668ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.25% 668ms 0.6% std::_Rb_tree::_M_insert_node (inline) 635ms 0.57% 86.83% 635ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 86.83% 621ms 0.56% vtkPolygon::New 0 0% 86.83% 621ms 0.56% vtkPolygon::vtkPolygon 16ms 0.014% 86.84% 616ms 0.56% std::vector::_M_default_append (inline) 608ms 0.55% 87.39% 608ms 0.55% operator delete 607ms 0.55% 87.94% 607ms 0.55% [libstdc++.so.6.0.33] 588ms 0.53% 88.47% 607ms 0.55% boost::detail::shared_count::shared_count (inline) 18ms 0.016% 88.49% 585ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.49% 585ms 0.53% boost::numeric::ublas::vector::vector (inline) 32ms 0.029% 88.52% 580ms 0.52% MutableElement::RegisterWithNodes (inline) 0 0% 88.52% 554ms 0.5% std::map::map (inline)