File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 105560ms, 88.21% of 119669ms total Dropped 1113 nodes (cum <= 598.35ms) flat flat% sum% cum cum% 0 0% 0% 119370ms 99.75% __libc_start_call_main 0 0% 0% 119370ms 99.75% __libc_start_main_impl 0 0% 0% 119370ms 99.75% _start 0 0% 0% 119351ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 119351ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 119351ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 119351ms 99.73% main 0 0% 0% 119321ms 99.71% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 119321ms 99.71% CxxTest::TestRunner::runTest (inline) 0 0% 0% 119321ms 99.71% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0042% 0.0042% 119313ms 99.70% AbstractCellBasedSimulation::Solve 19ms 0.016% 0.02% 62901ms 52.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 27ms 0.023% 0.043% 58755ms 49.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 147ms 0.12% 0.17% 56579ms 47.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 548ms 0.46% 0.62% 44683ms 37.34% NagaiHondaForce::AddForceContribution 2ms 0.0017% 0.63% 41253ms 34.47% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0017% 0.63% 23908ms 19.98% VertexBasedCellPopulation::Update 2ms 0.0017% 0.63% 23762ms 19.86% MutableVertexMesh::ReMesh 125ms 0.1% 0.73% 21065ms 17.60% Cell::ReadyToDivide 9946ms 8.31% 9.04% 20084ms 16.78% Cylindrical2dVertexMesh::GetVectorFromAtoB 42ms 0.035% 9.08% 19727ms 16.48% AbstractPhaseBasedCellCycleModel::ReadyToDivide 444ms 0.37% 9.45% 17853ms 14.92% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.094% 9.54% 17169ms 14.35% NagaiHondaForce::GetAdhesionParameter 207ms 0.17% 9.72% 16677ms 13.94% SimpleWntCellCycleModel::UpdateCellCyclePhase 514ms 0.43% 10.15% 15874ms 13.26% boost::numeric::ublas::vector_assign (inline) 1375ms 1.15% 11.30% 15010ms 12.54% std::__new_allocator::allocate (inline) 63ms 0.053% 11.35% 14558ms 12.17% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.35% 14394ms 12.03% std::allocator_traits::allocate (inline) 0 0% 11.35% 14011ms 11.71% std::_Rb_tree::_M_create_node (inline) 940ms 0.79% 12.13% 13635ms 11.39% operator new 0 0% 12.13% 13517ms 11.30% std::_Rb_tree::_M_get_node (inline) 56ms 0.047% 12.18% 12487ms 10.43% AbstractTargetAreaModifier::UpdateTargetAreas 13ms 0.011% 12.19% 12436ms 10.39% AbstractCellBasedSimulation::DoCellBirth 32ms 0.027% 12.22% 12398ms 10.36% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 12.22% 12204ms 10.20% std::_Rb_tree::_Alloc_node::operator() (inline) 4403ms 3.68% 15.90% 12106ms 10.12% __GI___libc_malloc 119ms 0.099% 16.00% 11966ms 10.00% AbstractCellProperty::IsSubType (inline) 3723ms 3.11% 19.11% 11867ms 9.92% __dynamic_cast 2946ms 2.46% 21.57% 11791ms 9.85% boost::numeric::ublas::indexing_vector_assign 108ms 0.09% 21.66% 11377ms 9.51% VertexBasedCellPopulation::GetDampingConstant 163ms 0.14% 21.80% 10696ms 8.94% MutableVertexMesh::CheckForIntersections 1253ms 1.05% 22.84% 9738ms 8.14% std::_Rb_tree::_M_erase 0 0% 22.84% 9698ms 8.10% std::_Rb_tree::_M_drop_node (inline) 541ms 0.45% 23.30% 9241ms 7.72% VertexMesh::GetNextEdgeGradientOfElementAtNode 66ms 0.055% 23.35% 9165ms 7.66% VertexBasedCellPopulation::GetLocationOfCellCentre 24ms 0.02% 23.37% 8970ms 7.50% MutableVertexMesh::RemoveDeletedNodesAndElements 96ms 0.08% 23.45% 8965ms 7.49% std::_Rb_tree::_Rb_tree (partial-inline) 361ms 0.3% 23.75% 8929ms 7.46% std::_Rb_tree::~_Rb_tree (inline) 217ms 0.18% 23.93% 8882ms 7.42% std::__new_allocator::deallocate (inline) 0 0% 23.93% 8877ms 7.42% std::allocator_traits::deallocate (inline) 826ms 0.69% 24.62% 8844ms 7.39% VertexMesh::GetCentroidOfElement 76ms 0.064% 24.69% 8770ms 7.33% Cell::GetMutationState 0 0% 24.69% 8769ms 7.33% std::_Rb_tree::_M_put_node (inline) 2185ms 1.83% 26.51% 8722ms 7.29% __GI___libc_free 762ms 0.64% 27.15% 8680ms 7.25% std::_Rb_tree::_M_copy (inline) 0 0% 27.15% 8488ms 7.09% std::set::~set (inline) 619ms 0.52% 27.67% 8142ms 6.80% std::map::operator[] (partial-inline) 0 0% 27.67% 8030ms 6.71% std::set::insert (inline) 16ms 0.013% 27.68% 8026ms 6.71% std::set::set (inline) 610ms 0.51% 28.19% 7828ms 6.54% VertexMesh::ElementIncludesPoint 1089ms 0.91% 29.10% 7615ms 6.36% std::_Rb_tree::_M_clone_node (inline) 7547ms 6.31% 35.41% 7547ms 6.31% boost::numeric::ublas::c_vector::operator() 266ms 0.22% 35.63% 7115ms 5.95% SimpleWntCellCycleModel::GetWntLevel 872ms 0.73% 36.36% 7087ms 5.92% std::_Rb_tree::_M_insert_ (inline) 165ms 0.14% 36.50% 6726ms 5.62% WntConcentration::GetWntLevel 5567ms 4.65% 41.15% 6254ms 5.23% _int_free 83ms 0.069% 41.22% 6144ms 5.13% std::set_intersection (inline) 6116ms 5.11% 46.33% 6116ms 5.11% __strcmp_evex 939ms 0.78% 47.11% 6099ms 5.10% AbstractMesh::GetDistanceBetweenNodes 191ms 0.16% 47.27% 6061ms 5.06% std::__set_intersection 25ms 0.021% 47.29% 5709ms 4.77% MutableVertexMesh::RemoveDeletedNodes 4293ms 3.59% 50.88% 5625ms 4.70% _int_malloc 201ms 0.17% 51.05% 5622ms 4.70% MutableElement::ResetIndex 89ms 0.074% 51.12% 5538ms 4.63% EdgeHelper::RemoveDeletedEdges 2124ms 1.77% 52.90% 5528ms 4.62% std::_Rb_tree::_M_lower_bound (inline) 2650ms 2.21% 55.11% 5524ms 4.62% __cxxabiv1::__si_class_type_info::__do_dyncast 951ms 0.79% 55.91% 5341ms 4.46% boost::numeric::ublas::c_vector::operator[] (inline) 24ms 0.02% 55.93% 5226ms 4.37% EdgeHelper::UpdateEdgesMapKey 5071ms 4.24% 60.17% 5071ms 4.24% boost::numeric::ublas::same_impl_ex 56ms 0.047% 60.21% 5052ms 4.22% Cell::GetCellProliferativeType 1ms 0.00084% 60.21% 4884ms 4.08% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 60.21% 4881ms 4.08% std::insert_iterator::operator= (inline) 102ms 0.085% 60.30% 4744ms 3.96% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 60.30% 4663ms 3.90% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 60.30% 4629ms 3.87% std::_Rb_tree::lower_bound (inline) 0 0% 60.30% 4629ms 3.87% std::map::lower_bound (inline) 165ms 0.14% 60.44% 4187ms 3.50% AbstractCellProperty::IsType (inline) 75ms 0.063% 60.50% 3864ms 3.23% Cell::SetCellProliferativeType 882ms 0.74% 61.24% 3829ms 3.20% AbstractElement::GetNodeLocation 41ms 0.034% 61.27% 3618ms 3.02% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 52ms 0.043% 61.31% 3516ms 2.94% std::_Rb_tree::erase 0 0% 61.31% 3445ms 2.88% boost::numeric::ublas::c_vector::assign (inline) 3441ms 2.88% 64.19% 3441ms 2.88% [libchaste_cell_based.so] 827ms 0.69% 64.88% 3379ms 2.82% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.00084% 64.88% 3367ms 2.81% std::_Rb_tree::_M_insert_unique 339ms 0.28% 65.16% 3014ms 2.52% boost::detail::shared_count::~shared_count (inline) 0 0% 65.16% 3014ms 2.52% boost::shared_ptr::~shared_ptr (inline) 64ms 0.053% 65.22% 2980ms 2.49% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2886ms 2.41% 67.63% 2886ms 2.41% std::_Rb_tree::_S_right (inline) 18ms 0.015% 67.64% 2870ms 2.40% Cell::GetCellData 396ms 0.33% 67.97% 2846ms 2.38% std::_Rb_tree_const_iterator::operator++ (inline) 40ms 0.033% 68.01% 2838ms 2.37% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.0058% 68.01% 2765ms 2.31% AbstractCellPopulation::Iterator::operator++ (inline) 217ms 0.18% 68.20% 2755ms 2.30% AbstractCellPopulation::Iterator::IsRealCell 45ms 0.038% 68.23% 2719ms 2.27% CellPropertyCollection::HasProperty 721ms 0.6% 68.84% 2717ms 2.27% AbstractCellProperty::IsSame 327ms 0.27% 69.11% 2657ms 2.22% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.11% 2645ms 2.21% Cell::HasCellProperty (inline) 0 0% 69.11% 2620ms 2.19% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.11% 2615ms 2.19% AbstractCellPopulation::WriteResultsToFiles 2580ms 2.16% 71.26% 2597ms 2.17% boost::detail::sp_counted_base::release 2499ms 2.09% 73.35% 2499ms 2.09% [libchaste_mesh.so] 140ms 0.12% 73.47% 2263ms 1.89% VertexMesh::GetVolumeOfElement 0 0% 73.47% 2145ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0017% 73.47% 2132ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 39ms 0.033% 73.50% 2091ms 1.75% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 536ms 0.45% 73.95% 1996ms 1.67% std::type_info::operator== (inline) 0 0% 73.95% 1962ms 1.64% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 73.95% 1952ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 1183ms 0.99% 74.94% 1933ms 1.62% std::_Rb_tree::equal_range (inline) 141ms 0.12% 75.06% 1903ms 1.59% CellPropertyCollection::AddProperty 151ms 0.13% 75.18% 1903ms 1.59% boost::numeric::ublas::vector_reference::operator() (inline) 11ms 0.0092% 75.19% 1847ms 1.54% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.19% 1847ms 1.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 268ms 0.22% 75.42% 1829ms 1.53% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.42% 1807ms 1.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 76ms 0.064% 75.48% 1790ms 1.50% std::_Rb_tree::_M_erase_aux (partial-inline) 1759ms 1.47% 76.95% 1759ms 1.47% std::_Rb_tree_increment 1ms 0.00084% 76.95% 1750ms 1.46% tcache_get (inline) 1749ms 1.46% 78.41% 1749ms 1.46% tcache_get_n (inline) 89ms 0.074% 78.49% 1642ms 1.37% MutableVertexMesh::CheckForSwapsFromShortEdges 84ms 0.07% 78.56% 1567ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 5ms 0.0042% 78.56% 1531ms 1.28% OffLatticeSimulation::ApplyBoundaries 69ms 0.058% 78.62% 1503ms 1.26% VertexMesh::GetSurfaceAreaOfElement 33ms 0.028% 78.65% 1460ms 1.22% Node::RemoveElement 10ms 0.0084% 78.66% 1427ms 1.19% std::set::erase (inline) 1396ms 1.17% 79.82% 1396ms 1.17% [libstdc++.so.6.0.33] 43ms 0.036% 79.86% 1353ms 1.13% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 74ms 0.062% 79.92% 1306ms 1.09% CellPropertyRegistry::Get 15ms 0.013% 79.93% 1232ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1205ms 1.01% 80.94% 1205ms 1.01% Node::rGetLocation 1ms 0.00084% 80.94% 1179ms 0.99% std::_Rb_tree::clear (inline) 0 0% 80.94% 1152ms 0.96% std::map::clear (inline) 19ms 0.016% 80.96% 1133ms 0.95% MutableElement::RegisterWithEdges (inline) 39ms 0.033% 80.99% 1127ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 34ms 0.028% 81.02% 1126ms 0.94% Edge::AddElement 0 0% 81.02% 1092ms 0.91% CellPropertyCollection::~CellPropertyCollection (inline) 229ms 0.19% 81.21% 1063ms 0.89% boost::numeric::ublas::detail::equals 0 0% 81.21% 1057ms 0.88% boost::numeric::ublas::norm_2 (inline) 448ms 0.37% 81.58% 1032ms 0.86% boost::numeric::ublas::vector_norm_2::apply 1005ms 0.84% 82.42% 1005ms 0.84% std::_Rb_tree_insert_and_rebalance 1ms 0.00084% 82.42% 999ms 0.83% VertexMeshWriter::MakeVtkMesh 0 0% 82.42% 997ms 0.83% std::map::map (inline) 605ms 0.51% 82.93% 983ms 0.82% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 123ms 0.1% 83.03% 975ms 0.81% std::_Rb_tree::find (inline) 0 0% 83.03% 936ms 0.78% std::__new_allocator::destroy (inline) 0 0% 83.03% 936ms 0.78% std::allocator_traits::destroy (inline) 0 0% 83.03% 932ms 0.78% std::_Rb_tree::_M_destroy_node (inline) 52ms 0.043% 83.08% 883ms 0.74% std::less::operator() (inline) 0 0% 83.08% 878ms 0.73% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.00084% 83.08% 878ms 0.73% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.075% 83.15% 877ms 0.73% std::swap_ranges (inline) 2ms 0.0017% 83.15% 872ms 0.73% std::_Vector_base::_M_allocate (inline) 75ms 0.063% 83.22% 868ms 0.73% AbstractNumericalMethod::DetectStepSizeExceptions 611ms 0.51% 83.73% 831ms 0.69% std::operator< (inline) 1ms 0.00084% 83.73% 818ms 0.68% std::map::find (inline) 99ms 0.083% 83.81% 812ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 623ms 0.52% 84.33% 807ms 0.67% CellPropertyCollection::GetProperty 106ms 0.089% 84.42% 793ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 84.42% 792ms 0.66% boost::numeric::ublas::norm_inf (inline) 398ms 0.33% 84.75% 792ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 110ms 0.092% 84.84% 788ms 0.66% MutableElement::GetNodeLocalIndex 788ms 0.66% 85.50% 788ms 0.66% std::swap (inline) 0 0% 85.50% 787ms 0.66% std::iter_swap (inline) 756ms 0.63% 86.13% 756ms 0.63% tcache_put (inline) 68ms 0.057% 86.19% 751ms 0.63% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 86.19% 701ms 0.59% vtkPolygon::New 3ms 0.0025% 86.19% 700ms 0.58% vtkPolygon::vtkPolygon 694ms 0.58% 86.77% 694ms 0.58% std::vector::size (inline) 7ms 0.0058% 86.78% 693ms 0.58% std::vector::_M_default_append (inline) 682ms 0.57% 87.35% 682ms 0.57% Node::GetIndex 570ms 0.48% 87.83% 676ms 0.56% malloc_consolidate 22ms 0.018% 87.84% 673ms 0.56% MutableElement::RegisterWithNodes (inline) 47ms 0.039% 87.88% 663ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.88% 663ms 0.55% boost::numeric::ublas::vector::vector (inline) 0 0% 87.88% 650ms 0.54% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.014% 87.90% 650ms 0.54% std::_Rb_tree::_M_insert_node (inline) 349ms 0.29% 88.19% 648ms 0.54% Edge::GetMapIndex 1ms 0.00084% 88.19% 632ms 0.53% VertexElementMap::VertexElementMap 0 0% 88.19% 631ms 0.53% std::vector::resize (inline) 24ms 0.02% 88.21% 629ms 0.53% Node::AddElement