File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95364ms, 88.35% of 107943ms total Dropped 1063 nodes (cum <= 539.72ms) flat flat% sum% cum cum% 0 0% 0% 107472ms 99.56% __libc_start_call_main 0 0% 0% 107472ms 99.56% __libc_start_main_impl 0 0% 0% 107472ms 99.56% _start 0 0% 0% 107453ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107453ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107453ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107453ms 99.55% main 0 0% 0% 107419ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107419ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107419ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107412ms 99.51% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.013% 55848ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.024% 52600ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.14% 51590ms 47.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 334ms 0.31% 0.45% 40201ms 37.24% NagaiHondaForce::AddForceContribution 0 0% 0.45% 38936ms 36.07% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.45% 24129ms 22.35% VertexBasedCellPopulation::Update 3ms 0.0028% 0.46% 24005ms 22.24% MutableVertexMesh::ReMesh 14396ms 13.34% 13.79% 22918ms 21.23% Cylindrical2dVertexMesh::GetVectorFromAtoB 95ms 0.088% 13.88% 17153ms 15.89% Cell::ReadyToDivide 71ms 0.066% 13.95% 15943ms 14.77% AbstractPhaseBasedCellCycleModel::ReadyToDivide 335ms 0.31% 14.26% 14811ms 13.72% NagaiHondaForce::GetAdhesionParameter 402ms 0.37% 14.63% 14740ms 13.66% boost::numeric::ublas::c_vector::c_vector (partial-inline) 121ms 0.11% 14.74% 13669ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 388ms 0.36% 15.10% 13188ms 12.22% boost::numeric::ublas::vector_assign (inline) 123ms 0.11% 15.22% 13130ms 12.16% CellPropertyCollection::GetPropertiesType (inline) 148ms 0.14% 15.35% 12001ms 11.12% MutableVertexMesh::CheckForIntersections 76ms 0.07% 15.42% 10918ms 10.11% VertexBasedCellPopulation::GetDampingConstant 3107ms 2.88% 18.30% 10833ms 10.04% __dynamic_cast 80ms 0.074% 18.38% 10738ms 9.95% AbstractCellProperty::IsSubType (inline) 65ms 0.06% 18.44% 10225ms 9.47% AbstractTargetAreaModifier::UpdateTargetAreas 23ms 0.021% 18.46% 10161ms 9.41% AbstractCellBasedSimulation::DoCellBirth 53ms 0.049% 18.51% 10130ms 9.38% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1269ms 1.18% 19.68% 9915ms 9.19% std::__new_allocator::allocate (inline) 2783ms 2.58% 22.26% 9789ms 9.07% boost::numeric::ublas::indexing_vector_assign 0 0% 22.26% 9347ms 8.66% std::allocator_traits::allocate (inline) 0 0% 22.26% 9316ms 8.63% std::_Rb_tree::_M_create_node (inline) 1366ms 1.27% 23.53% 9253ms 8.57% std::_Rb_tree::_M_erase 342ms 0.32% 23.84% 9031ms 8.37% VertexMesh::GetNextEdgeGradientOfElementAtNode 774ms 0.72% 24.56% 8876ms 8.22% VertexMesh::ElementIncludesPoint 25ms 0.023% 24.58% 8800ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 787ms 0.73% 25.31% 8718ms 8.08% operator new 0 0% 25.31% 8666ms 8.03% std::_Rb_tree::_M_get_node (inline) 219ms 0.2% 25.51% 8448ms 7.83% std::_Rb_tree::~_Rb_tree (inline) 474ms 0.44% 25.95% 8342ms 7.73% VertexMesh::GetCentroidOfElement 82ms 0.076% 26.03% 8294ms 7.68% Cell::GetMutationState 0 0% 26.03% 8181ms 7.58% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.03% 8181ms 7.58% std::_Rb_tree::_M_drop_node (inline) 255ms 0.24% 26.27% 7955ms 7.37% std::__new_allocator::deallocate (inline) 0 0% 26.27% 7952ms 7.37% std::set::~set (inline) 0 0% 26.27% 7926ms 7.34% std::allocator_traits::deallocate (inline) 0 0% 26.27% 7875ms 7.30% std::_Rb_tree::_M_put_node (inline) 3056ms 2.83% 29.10% 7783ms 7.21% __GI___libc_free 3095ms 2.87% 31.96% 7733ms 7.16% __GI___libc_malloc 26ms 0.024% 31.99% 7459ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 482ms 0.45% 32.43% 7452ms 6.90% std::map::operator[] (partial-inline) 1392ms 1.29% 33.72% 7227ms 6.70% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 134ms 0.12% 33.85% 6745ms 6.25% std::_Rb_tree::_Rb_tree (partial-inline) 688ms 0.64% 34.49% 6374ms 5.90% std::_Rb_tree::_M_copy (inline) 6343ms 5.88% 40.36% 6343ms 5.88% boost::numeric::ublas::c_vector::operator() 102ms 0.094% 40.46% 6332ms 5.87% SimpleWntCellCycleModel::GetWntLevel 15ms 0.014% 40.47% 6307ms 5.84% std::set::set (inline) 6127ms 5.68% 46.15% 6127ms 5.68% __strcmp_avx2 116ms 0.11% 46.25% 6119ms 5.67% WntConcentration::GetWntLevel 2416ms 2.24% 48.49% 5959ms 5.52% std::_Rb_tree::_M_lower_bound (inline) 0 0% 48.49% 5486ms 5.08% std::set::insert (inline) 44ms 0.041% 48.53% 5428ms 5.03% MutableVertexMesh::RemoveDeletedNodes 2660ms 2.46% 51.00% 5417ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 744ms 0.69% 51.69% 5399ms 5.00% std::_Rb_tree::_M_clone_node (inline) 39ms 0.036% 51.72% 5264ms 4.88% EdgeHelper::RemoveDeletedEdges 37ms 0.034% 51.76% 4975ms 4.61% EdgeHelper::UpdateEdgesMapKey 1455ms 1.35% 53.10% 4774ms 4.42% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.10% 4763ms 4.41% std::_Rb_tree::lower_bound (inline) 0 0% 53.10% 4763ms 4.41% std::map::lower_bound (inline) 4429ms 4.10% 57.21% 4716ms 4.37% _int_free 2ms 0.0019% 57.21% 4639ms 4.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 515ms 0.48% 57.69% 4587ms 4.25% std::_Rb_tree::_M_insert_ (inline) 209ms 0.19% 57.88% 4584ms 4.25% MutableElement::ResetIndex 46ms 0.043% 57.92% 4557ms 4.22% std::set_intersection (inline) 283ms 0.26% 58.19% 4511ms 4.18% std::__set_intersection 4031ms 3.73% 61.92% 4031ms 3.73% boost::numeric::ublas::same_impl_ex 109ms 0.1% 62.02% 4008ms 3.71% AbstractCellPopulation::GetCellUsingLocationIndex 40ms 0.037% 62.06% 3845ms 3.56% Cell::GetCellProliferativeType 73ms 0.068% 62.13% 3705ms 3.43% AbstractCellProperty::IsType (inline) 7ms 0.0065% 62.13% 3542ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.13% 3298ms 3.06% std::insert_iterator::operator= (inline) 787ms 0.73% 62.86% 3232ms 2.99% AbstractElement::GetNodeLocation 57ms 0.053% 62.91% 3056ms 2.83% Cell::SetCellProliferativeType 2183ms 2.02% 64.94% 3041ms 2.82% _int_malloc 2957ms 2.74% 67.68% 2957ms 2.74% std::_Rb_tree::_S_right (inline) 8ms 0.0074% 67.68% 2930ms 2.71% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.035% 67.72% 2858ms 2.65% std::_Rb_tree::erase 0 0% 67.72% 2853ms 2.64% boost::numeric::ublas::c_vector::operator-= (inline) 608ms 0.56% 68.28% 2835ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 441ms 0.41% 68.69% 2659ms 2.46% std::_Rb_tree_const_iterator::operator++ (inline) 695ms 0.64% 69.33% 2571ms 2.38% AbstractCellProperty::IsSame 0 0% 69.33% 2556ms 2.37% std::_Rb_tree::_M_insert_unique 44ms 0.041% 69.37% 2521ms 2.34% CellPropertyCollection::HasProperty 0 0% 69.37% 2462ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 218ms 0.2% 69.58% 2439ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.58% 2425ms 2.25% Cell::HasCellProperty (inline) 0 0% 69.58% 2375ms 2.20% AbstractCellPopulation::WriteResultsToFiles 26ms 0.024% 69.60% 2364ms 2.19% Cell::GetCellData 1ms 0.00093% 69.60% 2304ms 2.13% AbstractCellPopulation::Iterator::operator++ (inline) 216ms 0.2% 69.80% 2279ms 2.11% AbstractCellPopulation::Iterator::IsRealCell (inline) 82ms 0.076% 69.88% 2211ms 2.05% VertexMesh::GetVolumeOfElement 110ms 0.1% 69.98% 2185ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 39ms 0.036% 70.02% 2167ms 2.01% std::_Rb_tree::_M_emplace_hint_unique 2027ms 1.88% 71.89% 2027ms 1.88% std::_Rb_tree_increment 0 0% 71.89% 1948ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 1313ms 1.22% 73.11% 1946ms 1.80% std::_Rb_tree::equal_range (inline) 1ms 0.00093% 73.11% 1937ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 73.11% 1933ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.11% 1933ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 90ms 0.083% 73.19% 1908ms 1.77% MutableVertexMesh::CheckForSwapsFromShortEdges 434ms 0.4% 73.60% 1876ms 1.74% std::type_info::operator== (inline) 25ms 0.023% 73.62% 1772ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.62% 1732ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 133ms 0.12% 73.74% 1632ms 1.51% boost::numeric::ublas::vector_reference::operator() (inline) 27ms 0.025% 73.77% 1613ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 23ms 0.021% 73.79% 1598ms 1.48% VertexMesh::GetSurfaceAreaOfElement 55ms 0.051% 73.84% 1580ms 1.46% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 180ms 0.17% 74.01% 1533ms 1.42% CellPropertyCollection::AddProperty 0 0% 74.01% 1520ms 1.41% boost::numeric::ublas::vector_binary::operator() (inline) 37ms 0.034% 74.04% 1516ms 1.40% Node::RemoveElement 10ms 0.0093% 74.05% 1486ms 1.38% std::set::erase (inline) 0 0% 74.05% 1442ms 1.34% tcache_get (inline) 1442ms 1.34% 75.39% 1442ms 1.34% tcache_get_n (inline) 3ms 0.0028% 75.39% 1311ms 1.21% OffLatticeSimulation::ApplyBoundaries 0 0% 75.39% 1303ms 1.21% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 75.39% 1303ms 1.21% boost::numeric::ublas::c_vector::swap (inline) 350ms 0.32% 75.71% 1303ms 1.21% std::swap_ranges (inline) 0 0% 75.71% 1215ms 1.13% boost::numeric::ublas::norm_2 (inline) 540ms 0.5% 76.21% 1213ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 72ms 0.067% 76.28% 1209ms 1.12% std::less::operator() (inline) 1161ms 1.08% 77.36% 1161ms 1.08% [libchaste_cell_based.so] 1158ms 1.07% 78.43% 1158ms 1.07% Node::rGetLocation 83ms 0.077% 78.51% 1147ms 1.06% std::_Rb_tree::find (inline) 1140ms 1.06% 79.56% 1140ms 1.06% std::_Rb_tree_insert_and_rebalance 934ms 0.87% 80.43% 1137ms 1.05% std::operator< (inline) 0 0% 80.43% 1135ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 22ms 0.02% 80.45% 1110ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 31ms 0.029% 80.48% 1094ms 1.01% CellPropertyRegistry::Get 67ms 0.062% 80.54% 1058ms 0.98% std::_Rb_tree::_M_erase_aux (partial-inline) 5ms 0.0046% 80.54% 1049ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.54% 1028ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.54% 1012ms 0.94% std::map::clear (inline) 127ms 0.12% 80.66% 992ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.66% 992ms 0.92% boost::shared_ptr::~shared_ptr (inline) 978ms 0.91% 81.57% 978ms 0.91% std::vector::size (inline) 963ms 0.89% 82.46% 963ms 0.89% [libchaste_mesh.so] 24ms 0.022% 82.48% 963ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.48% 961ms 0.89% std::map::find (inline) 954ms 0.88% 83.36% 954ms 0.88% std::swap (inline) 0 0% 83.36% 953ms 0.88% std::iter_swap (inline) 396ms 0.37% 83.73% 945ms 0.88% Edge::GetMapIndex 123ms 0.11% 83.85% 931ms 0.86% boost::numeric::ublas::c_vector::operator= (inline) 154ms 0.14% 83.99% 930ms 0.86% boost::numeric::ublas::detail::equals 1ms 0.00093% 83.99% 863ms 0.8% VertexMeshWriter::MakeVtkMesh 830ms 0.77% 84.76% 841ms 0.78% boost::detail::sp_counted_base::release 130ms 0.12% 84.88% 789ms 0.73% boost::shared_ptr::shared_ptr (inline) 473ms 0.44% 85.32% 773ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 19ms 0.018% 85.33% 756ms 0.7% MutableElement::RegisterWithEdges (inline) 756ms 0.7% 86.03% 756ms 0.7% Node::GetIndex 24ms 0.022% 86.06% 751ms 0.7% Edge::AddElement 95ms 0.088% 86.14% 747ms 0.69% MutableElement::GetNodeLocalIndex 0 0% 86.14% 733ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.14% 718ms 0.67% boost::numeric::ublas::norm_inf (inline) 345ms 0.32% 86.46% 718ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 104ms 0.096% 86.56% 704ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.56% 704ms 0.65% std::allocator_traits::construct (inline) 0 0% 86.56% 691ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 86.58% 691ms 0.64% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0019% 86.59% 677ms 0.63% std::_Vector_base::_M_allocate (inline) 631ms 0.58% 87.17% 659ms 0.61% boost::detail::shared_count::shared_count (inline) 0 0% 87.17% 650ms 0.6% std::_Rb_tree::_M_construct_node (inline) 30ms 0.028% 87.20% 628ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 87.20% 608ms 0.56% vtkPolygon::New 0 0% 87.20% 607ms 0.56% vtkPolygon::vtkPolygon 601ms 0.56% 87.76% 601ms 0.56% operator delete 40ms 0.037% 87.79% 594ms 0.55% Node::AddElement 23ms 0.021% 87.81% 591ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.81% 591ms 0.55% boost::numeric::ublas::vector::vector (inline) 7ms 0.0065% 87.82% 576ms 0.53% std::vector::_M_default_append (inline) 0 0% 87.82% 573ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 568ms 0.53% 88.35% 568ms 0.53% [libstdc++.so.6.0.33]