File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 101634ms, 87.75% of 115820ms total Dropped 1084 nodes (cum <= 579.10ms) flat flat% sum% cum cum% 0 0% 0% 115472ms 99.70% __libc_start_call_main 0 0% 0% 115472ms 99.70% __libc_start_main_impl 0 0% 0% 115472ms 99.70% _start 0 0% 0% 115450ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 115450ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 115450ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 115450ms 99.68% main 0 0% 0% 115406ms 99.64% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 115406ms 99.64% CxxTest::TestRunner::runTest (inline) 0 0% 0% 115406ms 99.64% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 7ms 0.006% 0.006% 115399ms 99.64% AbstractCellBasedSimulation::Solve 22ms 0.019% 0.025% 61782ms 53.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.013% 0.038% 58315ms 50.35% ForwardEulerNumericalMethod::UpdateAllNodePositions 145ms 0.13% 0.16% 57269ms 49.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.3% 0.46% 43650ms 37.69% NagaiHondaForce::AddForceContribution 0 0% 0.46% 39738ms 34.31% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0017% 0.46% 24014ms 20.73% VertexBasedCellPopulation::Update 1ms 0.00086% 0.46% 23900ms 20.64% MutableVertexMesh::ReMesh 14752ms 12.74% 13.20% 23810ms 20.56% Cylindrical2dVertexMesh::GetVectorFromAtoB 91ms 0.079% 13.28% 18886ms 16.31% Cell::ReadyToDivide 54ms 0.047% 13.33% 17607ms 15.20% AbstractPhaseBasedCellCycleModel::ReadyToDivide 359ms 0.31% 13.64% 16742ms 14.46% NagaiHondaForce::GetAdhesionParameter 518ms 0.45% 14.08% 15280ms 13.19% boost::numeric::ublas::c_vector::c_vector (partial-inline) 181ms 0.16% 14.24% 15248ms 13.17% SimpleWntCellCycleModel::UpdateCellCyclePhase 111ms 0.096% 14.34% 14664ms 12.66% CellPropertyCollection::GetPropertiesType (inline) 315ms 0.27% 14.61% 13603ms 11.74% boost::numeric::ublas::vector_assign (inline) 98ms 0.085% 14.69% 13046ms 11.26% VertexBasedCellPopulation::GetDampingConstant 3999ms 3.45% 18.14% 12500ms 10.79% __dynamic_cast 51ms 0.044% 18.19% 12345ms 10.66% AbstractCellProperty::IsSubType (inline) 1059ms 0.91% 19.10% 12105ms 10.45% std::__new_allocator::allocate (inline) 142ms 0.12% 19.23% 11902ms 10.28% MutableVertexMesh::CheckForIntersections 0 0% 19.23% 11576ms 9.99% std::_Rb_tree::_M_create_node (inline) 0 0% 19.23% 11432ms 9.87% std::allocator_traits::allocate (inline) 94ms 0.081% 19.31% 11393ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 44ms 0.038% 19.34% 11261ms 9.72% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 898ms 0.78% 20.12% 11036ms 9.53% operator new 26ms 0.022% 20.14% 10819ms 9.34% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.14% 10716ms 9.25% std::_Rb_tree::_M_get_node (inline) 0 0% 20.14% 10450ms 9.02% std::_Rb_tree::_Alloc_node::operator() (inline) 81ms 0.07% 20.21% 10043ms 8.67% Cell::GetMutationState 4801ms 4.15% 24.36% 9876ms 8.53% __GI___libc_malloc 2965ms 2.56% 26.92% 9854ms 8.51% boost::numeric::ublas::indexing_vector_assign 38ms 0.033% 26.95% 9661ms 8.34% VertexBasedCellPopulation::GetLocationOfCellCentre 1303ms 1.13% 28.08% 9375ms 8.09% std::_Rb_tree::~_Rb_tree (inline) 338ms 0.29% 28.37% 9301ms 8.03% VertexMesh::GetNextEdgeGradientOfElementAtNode 1436ms 1.24% 29.61% 9151ms 7.90% std::_Rb_tree::_M_erase 473ms 0.41% 30.02% 9139ms 7.89% VertexMesh::GetCentroidOfElement 210ms 0.18% 30.20% 9139ms 7.89% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 30.20% 8924ms 7.71% std::set::~set (inline) 875ms 0.76% 30.95% 8701ms 7.51% VertexMesh::ElementIncludesPoint 12ms 0.01% 30.96% 8600ms 7.43% std::set::set (inline) 1115ms 0.96% 31.93% 8546ms 7.38% std::_Rb_tree::_M_copy (inline) 0 0% 31.93% 8222ms 7.10% std::_Rb_tree::_M_drop_node (inline) 169ms 0.15% 32.07% 7939ms 6.85% std::__new_allocator::deallocate (inline) 0 0% 32.07% 7926ms 6.84% std::allocator_traits::deallocate (inline) 3109ms 2.68% 34.76% 7921ms 6.84% __GI___libc_free 0 0% 34.76% 7858ms 6.78% std::_Rb_tree::_M_put_node (inline) 14ms 0.012% 34.77% 7769ms 6.71% MutableVertexMesh::RemoveDeletedNodesAndElements 530ms 0.46% 35.23% 7749ms 6.69% std::map::operator[] (partial-inline) 1372ms 1.18% 36.41% 7432ms 6.42% AbstractMesh::GetDistanceBetweenNodes 771ms 0.67% 37.08% 7204ms 6.22% std::_Rb_tree::_M_clone_node (inline) 152ms 0.13% 37.21% 7063ms 6.10% SimpleWntCellCycleModel::GetWntLevel 160ms 0.14% 37.35% 6815ms 5.88% WntConcentration::GetWntLevel 6414ms 5.54% 42.88% 6414ms 5.54% __strcmp_avx2 6364ms 5.49% 48.38% 6364ms 5.49% boost::numeric::ublas::c_vector::operator() 2435ms 2.10% 50.48% 6114ms 5.28% std::_Rb_tree::_M_lower_bound (inline) 0 0% 50.48% 6101ms 5.27% std::set::insert (inline) 3233ms 2.79% 53.27% 5995ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 498ms 0.43% 53.70% 5441ms 4.70% std::_Rb_tree::_M_insert_ (inline) 15ms 0.013% 53.71% 5345ms 4.61% MutableVertexMesh::RemoveDeletedNodes 1972ms 1.70% 55.42% 5279ms 4.56% boost::numeric::ublas::c_vector::operator[] (inline) 29ms 0.025% 55.44% 5164ms 4.46% EdgeHelper::RemoveDeletedEdges 0 0% 55.44% 5012ms 4.33% std::_Rb_tree::lower_bound (inline) 0 0% 55.44% 5012ms 4.33% std::map::lower_bound (inline) 127ms 0.11% 55.55% 4946ms 4.27% AbstractCellPopulation::GetCellUsingLocationIndex 106ms 0.092% 55.64% 4924ms 4.25% std::set_intersection (inline) 0 0% 55.64% 4890ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 38ms 0.033% 55.68% 4872ms 4.21% EdgeHelper::UpdateEdgesMapKey 217ms 0.19% 55.86% 4818ms 4.16% std::__set_intersection 4262ms 3.68% 59.54% 4788ms 4.13% _int_free 194ms 0.17% 59.71% 4784ms 4.13% MutableElement::ResetIndex 66ms 0.057% 59.77% 4257ms 3.68% Cell::GetCellProliferativeType 0 0% 59.77% 4041ms 3.49% std::insert_iterator::operator= (inline) 3825ms 3.30% 63.07% 3825ms 3.30% boost::numeric::ublas::same_impl_ex 10ms 0.0086% 63.08% 3732ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 53ms 0.046% 63.12% 3633ms 3.14% AbstractCellProperty::IsType (inline) 7ms 0.006% 63.13% 3483ms 3.01% std::_Rb_tree::_M_insert_unique_ (inline) 83ms 0.072% 63.20% 3358ms 2.90% Cell::SetCellProliferativeType 2262ms 1.95% 65.16% 3274ms 2.83% _int_malloc 3096ms 2.67% 67.83% 3096ms 2.67% std::_Rb_tree::_S_right (inline) 56ms 0.048% 67.88% 3066ms 2.65% std::_Rb_tree::erase 0 0% 67.88% 2916ms 2.52% boost::numeric::ublas::c_vector::operator-= (inline) 833ms 0.72% 68.60% 2883ms 2.49% AbstractElement::GetNodeLocation 613ms 0.53% 69.13% 2821ms 2.44% boost::numeric::ublas::vector_binary::size (inline) 36ms 0.031% 69.16% 2710ms 2.34% CellPropertyCollection::HasProperty 0 0% 69.16% 2637ms 2.28% Cell::HasCellProperty (inline) 226ms 0.2% 69.35% 2637ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0017% 69.35% 2618ms 2.26% std::_Rb_tree::_M_insert_unique 0 0% 69.35% 2578ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 602ms 0.52% 69.87% 2552ms 2.20% AbstractCellProperty::IsSame 16ms 0.014% 69.89% 2495ms 2.15% Cell::GetCellData 0 0% 69.89% 2446ms 2.11% AbstractCellPopulation::WriteResultsToFiles 205ms 0.18% 70.06% 2410ms 2.08% std::_Rb_tree_const_iterator::operator++ (inline) 70ms 0.06% 70.12% 2321ms 2.00% VertexMesh::GetVolumeOfElement 60ms 0.052% 70.18% 2290ms 1.98% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0026% 70.18% 2237ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 156ms 0.13% 70.31% 2212ms 1.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 33ms 0.028% 70.34% 2160ms 1.86% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.34% 1999ms 1.73% VertexBasedCellPopulation::WriteVtkResultsToFile 1325ms 1.14% 71.49% 1999ms 1.73% std::_Rb_tree::equal_range (inline) 1992ms 1.72% 73.21% 1992ms 1.72% std::_Rb_tree_increment 0 0% 73.21% 1986ms 1.71% VertexBasedCellPopulation::WriteCellVtkResultsToFile 437ms 0.38% 73.58% 1950ms 1.68% std::type_info::operator== (inline) 3ms 0.0026% 73.59% 1889ms 1.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.59% 1889ms 1.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 59ms 0.051% 73.64% 1808ms 1.56% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.64% 1786ms 1.54% VertexMeshWriter::WriteVtkUsingMesh 27ms 0.023% 73.66% 1730ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 231ms 0.2% 73.86% 1688ms 1.46% CellPropertyCollection::AddProperty 73ms 0.063% 73.92% 1676ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 29ms 0.025% 73.95% 1625ms 1.40% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.95% 1617ms 1.40% tcache_get (inline) 1617ms 1.40% 75.34% 1617ms 1.40% tcache_get_n (inline) 48ms 0.041% 75.39% 1583ms 1.37% Node::RemoveElement 38ms 0.033% 75.42% 1569ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 1565ms 1.35% 76.77% 1565ms 1.35% [libchaste_cell_based.so] 85ms 0.073% 76.84% 1548ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 11ms 0.0095% 76.85% 1539ms 1.33% std::set::erase (inline) 0 0% 76.85% 1509ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 1509ms 1.30% 78.15% 1509ms 1.30% std::_Rb_tree_insert_and_rebalance 0 0% 78.15% 1434ms 1.24% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 78.15% 1382ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 78.15% 1308ms 1.13% boost::numeric::ublas::norm_2 (inline) 604ms 0.52% 78.68% 1296ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 51ms 0.044% 78.72% 1294ms 1.12% std::less::operator() (inline) 1014ms 0.88% 79.60% 1243ms 1.07% std::operator< (inline) 20ms 0.017% 79.61% 1175ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 37ms 0.032% 79.65% 1168ms 1.01% CellPropertyRegistry::Get 83ms 0.072% 79.72% 1164ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.72% 1160ms 1.00% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0078% 79.72% 1160ms 1.00% boost::numeric::ublas::c_vector::swap (inline) 82ms 0.071% 79.80% 1151ms 0.99% std::swap_ranges (inline) 0 0% 79.80% 1126ms 0.97% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0017% 79.80% 1118ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 151ms 0.13% 79.93% 1106ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 79.93% 1106ms 0.95% boost::shared_ptr::~shared_ptr (inline) 79ms 0.068% 80.00% 1098ms 0.95% std::_Rb_tree::find (inline) 1ms 0.00086% 80.00% 1083ms 0.94% std::_Rb_tree::clear (inline) 1070ms 0.92% 80.92% 1070ms 0.92% std::swap (inline) 0 0% 80.92% 1069ms 0.92% std::iter_swap (inline) 0 0% 80.92% 1064ms 0.92% std::map::clear (inline) 0 0% 80.92% 990ms 0.85% std::map::find (inline) 102ms 0.088% 81.01% 932ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 924ms 0.8% 81.81% 924ms 0.8% Node::rGetLocation 896ms 0.77% 82.58% 916ms 0.79% boost::detail::sp_counted_base::release 293ms 0.25% 82.83% 909ms 0.78% std::__new_allocator::construct (inline) 0 0% 82.83% 909ms 0.78% std::allocator_traits::construct (inline) 22ms 0.019% 82.85% 899ms 0.78% boost::numeric::ublas::detail::expression_type_check (inline) 1ms 0.00086% 82.85% 871ms 0.75% VertexMeshWriter::MakeVtkMesh 0 0% 82.85% 860ms 0.74% std::_Rb_tree::_M_construct_node (inline) 858ms 0.74% 83.59% 858ms 0.74% std::vector::size (inline) 219ms 0.19% 83.78% 853ms 0.74% boost::numeric::ublas::detail::equals 169ms 0.15% 83.93% 842ms 0.73% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.93% 842ms 0.73% boost::numeric::ublas::vector::vector (inline) 818ms 0.71% 84.63% 818ms 0.71% [libchaste_mesh.so] 21ms 0.018% 84.65% 793ms 0.68% MutableElement::RegisterWithEdges (inline) 277ms 0.24% 84.89% 790ms 0.68% boost::shared_ptr::shared_ptr (inline) 410ms 0.35% 85.25% 784ms 0.68% Edge::GetMapIndex 26ms 0.022% 85.27% 778ms 0.67% Edge::AddElement 754ms 0.65% 85.92% 754ms 0.65% [libstdc++.so.6.0.33] 162ms 0.14% 86.06% 750ms 0.65% MutableElement::GetNodeLocalIndex 0 0% 86.06% 712ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.06% 692ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.06% 681ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.017% 86.08% 681ms 0.59% std::_Rb_tree::_M_insert_node (inline) 648ms 0.56% 86.64% 648ms 0.56% Node::GetIndex 643ms 0.56% 87.19% 643ms 0.56% tcache_put (inline) 0 0% 87.19% 623ms 0.54% vtkPolygon::New 2ms 0.0017% 87.19% 622ms 0.54% vtkPolygon::vtkPolygon 4ms 0.0035% 87.20% 619ms 0.53% std::vector::_M_default_append (inline) 272ms 0.23% 87.43% 611ms 0.53% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 44ms 0.038% 87.47% 597ms 0.52% MutableElement::RegisterWithNodes (inline) 0 0% 87.47% 581ms 0.5% boost::numeric::ublas::norm_inf (inline) 327ms 0.28% 87.75% 581ms 0.5% boost::numeric::ublas::vector_norm_inf::apply (inline)