File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95172ms, 87.63% of 108605ms total Dropped 1098 nodes (cum <= 543.02ms) flat flat% sum% cum cum% 0 0% 0% 108226ms 99.65% __libc_start_call_main 0 0% 0% 108226ms 99.65% __libc_start_main_impl 0 0% 0% 108226ms 99.65% _start 0 0% 0% 108205ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108205ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108205ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108205ms 99.63% main 0 0% 0% 108163ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108163ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108163ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 108155ms 99.59% AbstractCellBasedSimulation::Solve 25ms 0.023% 0.025% 56206ms 51.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.041% 52770ms 48.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 127ms 0.12% 0.16% 51630ms 47.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 292ms 0.27% 0.43% 40075ms 36.90% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.43% 38922ms 35.84% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.43% 23982ms 22.08% VertexBasedCellPopulation::Update 2ms 0.0018% 0.43% 23832ms 21.94% MutableVertexMesh::ReMesh 14817ms 13.64% 14.07% 23557ms 21.69% Cylindrical2dVertexMesh::GetVectorFromAtoB 95ms 0.087% 14.16% 17598ms 16.20% Cell::ReadyToDivide 67ms 0.062% 14.22% 16349ms 15.05% AbstractPhaseBasedCellCycleModel::ReadyToDivide 304ms 0.28% 14.50% 14239ms 13.11% NagaiHondaForce::GetAdhesionParameter 438ms 0.4% 14.91% 14192ms 13.07% boost::numeric::ublas::c_vector::c_vector (partial-inline) 148ms 0.14% 15.04% 14098ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 98ms 0.09% 15.13% 13286ms 12.23% CellPropertyCollection::GetPropertiesType (inline) 369ms 0.34% 15.47% 12758ms 11.75% boost::numeric::ublas::vector_assign (inline) 145ms 0.13% 15.61% 11884ms 10.94% MutableVertexMesh::CheckForIntersections 3229ms 2.97% 18.58% 11442ms 10.54% __dynamic_cast 80ms 0.074% 18.65% 11345ms 10.45% AbstractCellProperty::IsSubType (inline) 76ms 0.07% 18.72% 10974ms 10.10% VertexBasedCellPopulation::GetDampingConstant 67ms 0.062% 18.78% 10536ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 45ms 0.041% 18.83% 10451ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 39ms 0.036% 18.86% 10272ms 9.46% AbstractCellBasedSimulation::DoCellBirth 2853ms 2.63% 21.49% 9749ms 8.98% boost::numeric::ublas::indexing_vector_assign 1310ms 1.21% 22.70% 9743ms 8.97% std::__new_allocator::allocate (inline) 317ms 0.29% 22.99% 9532ms 8.78% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.99% 9265ms 8.53% std::_Rb_tree::_M_create_node (inline) 0 0% 22.99% 9207ms 8.48% std::allocator_traits::allocate (inline) 1225ms 1.13% 24.11% 9021ms 8.31% std::_Rb_tree::_M_erase 37ms 0.034% 24.15% 8731ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 834ms 0.77% 24.92% 8685ms 8.00% VertexMesh::ElementIncludesPoint 0 0% 24.92% 8501ms 7.83% std::_Rb_tree::_M_get_node (inline) 745ms 0.69% 25.60% 8475ms 7.80% operator new 447ms 0.41% 26.01% 8415ms 7.75% VertexMesh::GetCentroidOfElement 91ms 0.084% 26.10% 8349ms 7.69% Cell::GetMutationState 0 0% 26.10% 8242ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 278ms 0.26% 26.35% 8197ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.35% 8184ms 7.54% std::_Rb_tree::_M_drop_node (inline) 225ms 0.21% 26.56% 7931ms 7.30% std::__new_allocator::deallocate (inline) 0 0% 26.56% 7923ms 7.30% std::allocator_traits::deallocate (inline) 0 0% 26.56% 7854ms 7.23% std::_Rb_tree::_M_put_node (inline) 0 0% 26.56% 7773ms 7.16% std::set::~set (inline) 8ms 0.0074% 26.57% 7742ms 7.13% MutableVertexMesh::RemoveDeletedNodesAndElements 1495ms 1.38% 27.95% 7570ms 6.97% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 3016ms 2.78% 30.72% 7482ms 6.89% __GI___libc_malloc 2701ms 2.49% 33.21% 7478ms 6.89% __GI___libc_free 497ms 0.46% 33.67% 7283ms 6.71% std::map::operator[] (partial-inline) 153ms 0.14% 33.81% 7091ms 6.53% std::_Rb_tree::_Rb_tree (partial-inline) 6846ms 6.30% 40.11% 6846ms 6.30% __strcmp_avx2 709ms 0.65% 40.76% 6657ms 6.13% std::_Rb_tree::_M_copy (inline) 29ms 0.027% 40.79% 6565ms 6.04% std::set::set (inline) 6290ms 5.79% 46.58% 6290ms 5.79% boost::numeric::ublas::c_vector::operator() 101ms 0.093% 46.68% 6236ms 5.74% SimpleWntCellCycleModel::GetWntLevel 153ms 0.14% 46.82% 6097ms 5.61% WntConcentration::GetWntLevel 2482ms 2.29% 49.10% 5711ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 780ms 0.72% 49.82% 5677ms 5.23% std::_Rb_tree::_M_clone_node (inline) 2859ms 2.63% 52.45% 5602ms 5.16% __cxxabiv1::__si_class_type_info::__do_dyncast 1999ms 1.84% 54.29% 5428ms 5.00% boost::numeric::ublas::c_vector::operator[] (inline) 21ms 0.019% 54.31% 5245ms 4.83% MutableVertexMesh::RemoveDeletedNodes 0 0% 54.31% 5177ms 4.77% std::set::insert (inline) 44ms 0.041% 54.35% 5065ms 4.66% EdgeHelper::RemoveDeletedEdges 160ms 0.15% 54.50% 4768ms 4.39% MutableElement::ResetIndex 4281ms 3.94% 58.44% 4767ms 4.39% _int_free 23ms 0.021% 58.46% 4719ms 4.35% EdgeHelper::UpdateEdgesMapKey 0 0% 58.46% 4702ms 4.33% std::_Rb_tree::lower_bound (inline) 0 0% 58.46% 4702ms 4.33% std::map::lower_bound (inline) 1ms 0.00092% 58.46% 4649ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 487ms 0.45% 58.91% 4348ms 4.00% std::_Rb_tree::_M_insert_ (inline) 172ms 0.16% 59.07% 4217ms 3.88% AbstractCellPopulation::GetCellUsingLocationIndex 129ms 0.12% 59.19% 4176ms 3.85% std::set_intersection (inline) 69ms 0.064% 59.25% 4051ms 3.73% AbstractCellProperty::IsType (inline) 191ms 0.18% 59.43% 4047ms 3.73% std::__set_intersection 3954ms 3.64% 63.07% 3954ms 3.64% boost::numeric::ublas::same_impl_ex 40ms 0.037% 63.11% 3795ms 3.49% Cell::GetCellProliferativeType 11ms 0.01% 63.12% 3542ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 63.12% 3175ms 2.92% std::insert_iterator::operator= (inline) 946ms 0.87% 63.99% 3133ms 2.88% AbstractElement::GetNodeLocation 54ms 0.05% 64.04% 3049ms 2.81% Cell::SetCellProliferativeType 60ms 0.055% 64.09% 3014ms 2.78% std::_Rb_tree::erase 22ms 0.02% 64.11% 2944ms 2.71% CellPropertyCollection::HasProperty 1972ms 1.82% 65.93% 2941ms 2.71% _int_malloc 738ms 0.68% 66.61% 2927ms 2.70% AbstractCellProperty::IsSame 0 0% 66.61% 2859ms 2.63% Cell::HasCellProperty (inline) 11ms 0.01% 66.62% 2757ms 2.54% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 66.62% 2742ms 2.52% boost::numeric::ublas::c_vector::operator-= (inline) 223ms 0.21% 66.82% 2701ms 2.49% VertexMesh::GetAreaGradientOfElementAtNode 2686ms 2.47% 69.30% 2686ms 2.47% std::_Rb_tree::_S_right (inline) 0 0% 69.30% 2583ms 2.38% boost::numeric::ublas::c_vector::assign (inline) 598ms 0.55% 69.85% 2551ms 2.35% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.85% 2449ms 2.25% AbstractCellPopulation::WriteResultsToFiles 32ms 0.029% 69.88% 2439ms 2.25% Cell::GetCellData 3ms 0.0028% 69.88% 2420ms 2.23% std::_Rb_tree::_M_insert_unique 233ms 0.21% 70.09% 2412ms 2.22% std::_Rb_tree_const_iterator::operator++ (inline) 88ms 0.081% 70.18% 2354ms 2.17% VertexMesh::GetVolumeOfElement 207ms 0.19% 70.37% 2228ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 8ms 0.0074% 70.37% 2224ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 461ms 0.42% 70.80% 2189ms 2.02% std::type_info::operator== (inline) 52ms 0.048% 70.85% 2172ms 2.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.00092% 70.85% 2060ms 1.90% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.85% 2060ms 1.90% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 42ms 0.039% 70.89% 2035ms 1.87% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.89% 1994ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 70.89% 1982ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1320ms 1.22% 72.10% 1955ms 1.80% std::_Rb_tree::equal_range (inline) 1954ms 1.80% 73.90% 1954ms 1.80% std::_Rb_tree_increment 66ms 0.061% 73.96% 1866ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.96% 1785ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 29ms 0.027% 73.99% 1752ms 1.61% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 38ms 0.035% 74.02% 1584ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 56ms 0.052% 74.07% 1563ms 1.44% Node::RemoveElement 48ms 0.044% 74.12% 1549ms 1.43% VertexMesh::GetSurfaceAreaOfElement 88ms 0.081% 74.20% 1526ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 10ms 0.0092% 74.21% 1511ms 1.39% std::set::erase (inline) 1ms 0.00092% 74.21% 1427ms 1.31% OffLatticeSimulation::ApplyBoundaries 52ms 0.048% 74.26% 1384ms 1.27% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.26% 1367ms 1.26% boost::numeric::ublas::norm_2 (inline) 0 0% 74.26% 1362ms 1.25% boost::numeric::ublas::vector_binary::operator() (inline) 621ms 0.57% 74.83% 1358ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.00092% 74.83% 1351ms 1.24% tcache_get (inline) 1350ms 1.24% 76.07% 1350ms 1.24% tcache_get_n (inline) 124ms 0.11% 76.19% 1290ms 1.19% CellPropertyCollection::AddProperty 1256ms 1.16% 77.34% 1256ms 1.16% [libchaste_cell_based.so] 64ms 0.059% 77.40% 1250ms 1.15% std::less::operator() (inline) 20ms 0.018% 77.42% 1226ms 1.13% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 77.42% 1219ms 1.12% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 77.43% 1219ms 1.12% boost::numeric::ublas::c_vector::swap 93ms 0.086% 77.51% 1215ms 1.12% std::swap_ranges (inline) 104ms 0.096% 77.61% 1205ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 963ms 0.89% 78.49% 1186ms 1.09% std::operator< (inline) 1123ms 1.03% 79.53% 1123ms 1.03% std::swap (inline) 0 0% 79.53% 1122ms 1.03% std::iter_swap (inline) 23ms 0.021% 79.55% 1120ms 1.03% CellPropertyRegistry::Get 0 0% 79.55% 1108ms 1.02% std::_Rb_tree::clear (inline) 0 0% 79.55% 1094ms 1.01% std::map::clear (inline) 6ms 0.0055% 79.55% 1074ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1072ms 0.99% 80.54% 1072ms 0.99% std::_Rb_tree_insert_and_rebalance 97ms 0.089% 80.63% 1044ms 0.96% std::_Rb_tree::find (inline) 0 0% 80.63% 1023ms 0.94% std::_Rb_tree::_Auto_node::_Auto_node (inline) 116ms 0.11% 80.74% 994ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.74% 994ms 0.92% boost::shared_ptr::~shared_ptr (inline) 968ms 0.89% 81.63% 968ms 0.89% Node::rGetLocation 6ms 0.0055% 81.63% 952ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 188ms 0.17% 81.81% 931ms 0.86% boost::numeric::ublas::detail::equals 1ms 0.00092% 81.81% 879ms 0.81% std::map::find (inline) 1ms 0.00092% 81.81% 847ms 0.78% VertexMeshWriter::MakeVtkMesh 826ms 0.76% 82.57% 846ms 0.78% boost::detail::sp_counted_base::release 826ms 0.76% 83.33% 826ms 0.76% std::vector::size (inline) 276ms 0.25% 83.58% 824ms 0.76% std::__new_allocator::construct (inline) 0 0% 83.58% 824ms 0.76% std::allocator_traits::construct (inline) 103ms 0.095% 83.68% 817ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 810ms 0.75% 84.43% 810ms 0.75% [libchaste_mesh.so] 21ms 0.019% 84.44% 803ms 0.74% MutableElement::RegisterWithEdges (inline) 28ms 0.026% 84.47% 795ms 0.73% Edge::AddElement 0 0% 84.47% 764ms 0.7% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.47% 744ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 402ms 0.37% 84.84% 719ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 710ms 0.65% 85.49% 710ms 0.65% [libstdc++.so.6.0.33] 373ms 0.34% 85.84% 708ms 0.65% Edge::GetMapIndex 0 0% 85.84% 707ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0018% 85.84% 703ms 0.65% std::_Vector_base::_M_allocate (inline) 0 0% 85.84% 693ms 0.64% boost::numeric::ublas::norm_inf (inline) 370ms 0.34% 86.18% 693ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 134ms 0.12% 86.30% 677ms 0.62% MutableElement::GetNodeLocalIndex 47ms 0.043% 86.35% 652ms 0.6% MutableElement::RegisterWithNodes (inline) 0 0% 86.35% 651ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.017% 86.36% 651ms 0.6% std::_Rb_tree::_M_insert_node (inline) 159ms 0.15% 86.51% 650ms 0.6% boost::shared_ptr::shared_ptr (inline) 31ms 0.029% 86.54% 607ms 0.56% Node::AddElement 8ms 0.0074% 86.55% 604ms 0.56% std::vector::_M_default_append (inline) 599ms 0.55% 87.10% 599ms 0.55% Node::GetIndex 0 0% 87.10% 591ms 0.54% vtkPolygon::New 1ms 0.00092% 87.10% 590ms 0.54% vtkPolygon::vtkPolygon 35ms 0.032% 87.13% 571ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.13% 571ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 87.13% 559ms 0.51% std::map::map (inline) 544ms 0.5% 87.63% 544ms 0.5% tcache_put (inline)