File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94340ms, 88.14% of 107036ms total Dropped 1117 nodes (cum <= 535.18ms) flat flat% sum% cum cum% 0 0% 0% 106550ms 99.55% __libc_start_call_main 0 0% 0% 106550ms 99.55% __libc_start_main_impl 0 0% 0% 106550ms 99.55% _start 0 0% 0% 106531ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106531ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106531ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106531ms 99.53% main 0 0% 0% 106497ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106497ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106497ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 106488ms 99.49% AbstractCellBasedSimulation::Solve 15ms 0.014% 0.016% 55341ms 51.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.021% 0.036% 52124ms 48.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 105ms 0.098% 0.13% 51050ms 47.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 382ms 0.36% 0.49% 39826ms 37.21% NagaiHondaForce::AddForceContribution 0 0% 0.49% 38460ms 35.93% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.5% 23824ms 22.26% VertexBasedCellPopulation::Update 0 0% 0.5% 23684ms 22.13% MutableVertexMesh::ReMesh 14368ms 13.42% 13.92% 22996ms 21.48% Cylindrical2dVertexMesh::GetVectorFromAtoB 106ms 0.099% 14.02% 17267ms 16.13% Cell::ReadyToDivide 57ms 0.053% 14.07% 16080ms 15.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 353ms 0.33% 14.40% 14882ms 13.90% NagaiHondaForce::GetAdhesionParameter 414ms 0.39% 14.79% 14733ms 13.76% boost::numeric::ublas::c_vector::c_vector (partial-inline) 142ms 0.13% 14.92% 13847ms 12.94% SimpleWntCellCycleModel::UpdateCellCyclePhase 348ms 0.33% 15.25% 13136ms 12.27% boost::numeric::ublas::vector_assign (inline) 133ms 0.12% 15.37% 13023ms 12.17% CellPropertyCollection::GetPropertiesType (inline) 122ms 0.11% 15.48% 12086ms 11.29% MutableVertexMesh::CheckForIntersections 2985ms 2.79% 18.27% 10905ms 10.19% __dynamic_cast 73ms 0.068% 18.34% 10782ms 10.07% AbstractCellProperty::IsSubType (inline) 81ms 0.076% 18.42% 10739ms 10.03% VertexBasedCellPopulation::GetDampingConstant 80ms 0.075% 18.49% 10306ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 65ms 0.061% 18.55% 10204ms 9.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.57% 10103ms 9.44% AbstractCellBasedSimulation::DoCellBirth 1176ms 1.10% 19.67% 9792ms 9.15% std::__new_allocator::allocate (inline) 2722ms 2.54% 22.21% 9664ms 9.03% boost::numeric::ublas::indexing_vector_assign 1325ms 1.24% 23.45% 9357ms 8.74% std::_Rb_tree::_M_erase 0 0% 23.45% 9209ms 8.60% std::allocator_traits::allocate (inline) 0 0% 23.45% 9160ms 8.56% std::_Rb_tree::_M_create_node (inline) 783ms 0.73% 24.18% 8979ms 8.39% VertexMesh::ElementIncludesPoint 394ms 0.37% 24.55% 8895ms 8.31% VertexMesh::GetNextEdgeGradientOfElementAtNode 785ms 0.73% 25.29% 8696ms 8.12% operator new 22ms 0.021% 25.31% 8623ms 8.06% VertexBasedCellPopulation::GetLocationOfCellCentre 239ms 0.22% 25.53% 8583ms 8.02% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.53% 8528ms 7.97% std::_Rb_tree::_M_get_node (inline) 0 0% 25.53% 8492ms 7.93% std::_Rb_tree::_M_drop_node (inline) 81ms 0.076% 25.61% 8357ms 7.81% Cell::GetMutationState 235ms 0.22% 25.82% 8273ms 7.73% std::__new_allocator::deallocate (inline) 512ms 0.48% 26.30% 8264ms 7.72% VertexMesh::GetCentroidOfElement 0 0% 26.30% 8239ms 7.70% std::allocator_traits::deallocate (inline) 3266ms 3.05% 29.35% 8197ms 7.66% __GI___libc_free 0 0% 29.35% 8181ms 7.64% std::_Rb_tree::_M_put_node (inline) 0 0% 29.35% 8112ms 7.58% std::set::~set (inline) 0 0% 29.35% 8014ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 3060ms 2.86% 32.21% 7714ms 7.21% __GI___libc_malloc 12ms 0.011% 32.22% 7393ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 1310ms 1.22% 33.45% 7088ms 6.62% AbstractMesh::GetDistanceBetweenNodes 470ms 0.44% 33.89% 6819ms 6.37% std::map::operator[] (partial-inline) 138ms 0.13% 34.02% 6561ms 6.13% std::_Rb_tree::_Rb_tree (partial-inline) 6332ms 5.92% 39.93% 6332ms 5.92% boost::numeric::ublas::c_vector::operator() 140ms 0.13% 40.06% 6298ms 5.88% SimpleWntCellCycleModel::GetWntLevel 6255ms 5.84% 45.91% 6255ms 5.84% __strcmp_avx2 640ms 0.6% 46.50% 6179ms 5.77% std::_Rb_tree::_M_copy (inline) 9ms 0.0084% 46.51% 6118ms 5.72% std::set::set (inline) 149ms 0.14% 46.65% 6047ms 5.65% WntConcentration::GetWntLevel 2697ms 2.52% 49.17% 5621ms 5.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 49.17% 5355ms 5.00% std::set::insert (inline) 669ms 0.63% 49.80% 5245ms 4.90% std::_Rb_tree::_M_clone_node (inline) 2255ms 2.11% 51.90% 5220ms 4.88% std::_Rb_tree::_M_lower_bound (inline) 31ms 0.029% 51.93% 5143ms 4.80% MutableVertexMesh::RemoveDeletedNodes 42ms 0.039% 51.97% 4968ms 4.64% EdgeHelper::RemoveDeletedEdges 4570ms 4.27% 56.24% 4922ms 4.60% _int_free 1452ms 1.36% 57.60% 4868ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 68ms 0.064% 57.66% 4700ms 4.39% std::set_intersection (inline) 26ms 0.024% 57.69% 4637ms 4.33% EdgeHelper::UpdateEdgesMapKey 276ms 0.26% 57.94% 4632ms 4.33% std::__set_intersection 212ms 0.2% 58.14% 4569ms 4.27% MutableElement::ResetIndex 1ms 0.00093% 58.14% 4527ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 532ms 0.5% 58.64% 4484ms 4.19% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.64% 4202ms 3.93% std::_Rb_tree::lower_bound (inline) 0 0% 58.64% 4202ms 3.93% std::map::lower_bound (inline) 4059ms 3.79% 62.43% 4059ms 3.79% boost::numeric::ublas::same_impl_ex 31ms 0.029% 62.46% 3945ms 3.69% Cell::GetCellProliferativeType 101ms 0.094% 62.56% 3689ms 3.45% AbstractCellPopulation::GetCellUsingLocationIndex 84ms 0.078% 62.63% 3633ms 3.39% AbstractCellProperty::IsType (inline) 12ms 0.011% 62.65% 3458ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.65% 3288ms 3.07% std::insert_iterator::operator= (inline) 56ms 0.052% 62.70% 3251ms 3.04% Cell::SetCellProliferativeType 2197ms 2.05% 64.75% 3043ms 2.84% _int_malloc 716ms 0.67% 65.42% 2969ms 2.77% AbstractElement::GetNodeLocation 6ms 0.0056% 65.42% 2930ms 2.74% std::_Rb_tree::_M_insert_unique_ (inline) 633ms 0.59% 66.02% 2915ms 2.72% boost::numeric::ublas::vector_binary::size (inline) 46ms 0.043% 66.06% 2849ms 2.66% std::_Rb_tree::erase 484ms 0.45% 66.51% 2739ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 261ms 0.24% 66.76% 2543ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 691ms 0.65% 67.40% 2526ms 2.36% AbstractCellProperty::IsSame 0 0% 67.40% 2469ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 40ms 0.037% 67.44% 2465ms 2.30% CellPropertyCollection::HasProperty 2428ms 2.27% 69.71% 2428ms 2.27% std::_Rb_tree::_S_right (inline) 3ms 0.0028% 69.71% 2425ms 2.27% std::_Rb_tree::_M_insert_unique 0 0% 69.71% 2366ms 2.21% Cell::HasCellProperty (inline) 0 0% 69.71% 2355ms 2.20% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.71% 2330ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 123ms 0.11% 69.82% 2284ms 2.13% VertexMesh::GetVolumeOfElement 21ms 0.02% 69.84% 2194ms 2.05% Cell::GetCellData 94ms 0.088% 69.93% 2153ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 25ms 0.023% 69.95% 2103ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0028% 69.96% 2098ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 2097ms 1.96% 71.92% 2097ms 1.96% std::_Rb_tree_increment 205ms 0.19% 72.11% 2067ms 1.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.11% 1958ms 1.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.11% 1958ms 1.83% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.11% 1947ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00093% 72.11% 1934ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 461ms 0.43% 72.54% 1835ms 1.71% std::type_info::operator== (inline) 79ms 0.074% 72.61% 1812ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 1235ms 1.15% 73.77% 1810ms 1.69% std::_Rb_tree::equal_range (inline) 0 0% 73.77% 1741ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 15ms 0.014% 73.78% 1584ms 1.48% VertexMesh::GetSurfaceAreaOfElement 44ms 0.041% 73.82% 1563ms 1.46% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 133ms 0.12% 73.95% 1558ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 46ms 0.043% 73.99% 1492ms 1.39% Node::RemoveElement 26ms 0.024% 74.01% 1461ms 1.36% std::set::erase (inline) 0 0% 74.01% 1425ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.01% 1425ms 1.33% tcache_get (inline) 1425ms 1.33% 75.35% 1425ms 1.33% tcache_get_n (inline) 140ms 0.13% 75.48% 1415ms 1.32% CellPropertyCollection::AddProperty 39ms 0.036% 75.51% 1381ms 1.29% AbstractCellPopulation::GetLocationIndexUsingCell 94ms 0.088% 75.60% 1361ms 1.27% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1ms 0.00093% 75.60% 1271ms 1.19% OffLatticeSimulation::ApplyBoundaries 108ms 0.1% 75.70% 1205ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.70% 1180ms 1.10% boost::numeric::ublas::norm_2 (inline) 71ms 0.066% 75.77% 1171ms 1.09% std::less::operator() (inline) 519ms 0.48% 76.25% 1167ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1158ms 1.08% 77.34% 1158ms 1.08% [libchaste_cell_based.so] 0 0% 77.34% 1146ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 875ms 0.82% 78.15% 1100ms 1.03% std::operator< (inline) 1083ms 1.01% 79.16% 1083ms 1.01% std::_Rb_tree_insert_and_rebalance 1066ms 1% 80.16% 1066ms 1% Node::rGetLocation 24ms 0.022% 80.18% 1063ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 18ms 0.017% 80.20% 1047ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 33ms 0.031% 80.23% 1046ms 0.98% CellPropertyRegistry::Get 185ms 0.17% 80.40% 1033ms 0.97% boost::numeric::ublas::detail::equals 99ms 0.092% 80.50% 1026ms 0.96% std::_Rb_tree::find (inline) 0 0% 80.50% 1019ms 0.95% std::_Rb_tree::clear (inline) 14ms 0.013% 80.51% 1015ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.51% 1004ms 0.94% std::map::clear (inline) 156ms 0.15% 80.66% 989ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.66% 989ms 0.92% boost::shared_ptr::~shared_ptr (inline) 979ms 0.91% 81.57% 979ms 0.91% [libchaste_mesh.so] 925ms 0.86% 82.43% 925ms 0.86% std::vector::size (inline) 0 0% 82.43% 882ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.44% 882ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.08% 82.52% 878ms 0.82% std::swap_ranges (inline) 128ms 0.12% 82.64% 870ms 0.81% MutableElement::GetNodeLocalIndex 179ms 0.17% 82.80% 843ms 0.79% boost::shared_ptr::shared_ptr (inline) 0 0% 82.80% 841ms 0.79% std::map::find (inline) 363ms 0.34% 83.14% 836ms 0.78% Edge::GetMapIndex 1ms 0.00093% 83.14% 834ms 0.78% VertexMeshWriter::MakeVtkMesh 811ms 0.76% 83.90% 817ms 0.76% boost::detail::sp_counted_base::release 0 0% 83.90% 811ms 0.76% CellPropertyCollection::~CellPropertyCollection (inline) 28ms 0.026% 83.93% 795ms 0.74% MutableElement::RegisterWithEdges (inline) 0 0% 83.93% 792ms 0.74% std::iter_swap (inline) 792ms 0.74% 84.67% 792ms 0.74% std::swap (inline) 32ms 0.03% 84.70% 788ms 0.74% Edge::AddElement 0 0% 84.70% 778ms 0.73% boost::numeric::ublas::norm_inf (inline) 416ms 0.39% 85.09% 778ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 489ms 0.46% 85.54% 763ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 120ms 0.11% 85.66% 745ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 718ms 0.67% 86.33% 718ms 0.67% Node::GetIndex 83ms 0.078% 86.40% 689ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.40% 689ms 0.64% std::allocator_traits::construct (inline) 1ms 0.00093% 86.41% 679ms 0.63% std::_Vector_base::_M_allocate (inline) 632ms 0.59% 87.00% 664ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 87.00% 647ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 87.02% 647ms 0.6% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.02% 632ms 0.59% std::_Rb_tree::_M_construct_node (inline) 15ms 0.014% 87.03% 598ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.03% 598ms 0.56% boost::numeric::ublas::vector::vector (inline) 0 0% 87.03% 595ms 0.56% vtkPolygon::New 0 0% 87.03% 595ms 0.56% vtkPolygon::vtkPolygon 50ms 0.047% 87.08% 576ms 0.54% MutableElement::RegisterWithNodes (inline) 573ms 0.54% 87.62% 573ms 0.54% [libstdc++.so.6.0.33] 0 0% 87.62% 562ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 5ms 0.0047% 87.62% 555ms 0.52% std::vector::_M_default_append (inline) 554ms 0.52% 88.14% 554ms 0.52% operator delete