File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 93801ms, 87.47% of 107237ms total Dropped 1081 nodes (cum <= 536.18ms) flat flat% sum% cum cum% 0 0% 0% 106880ms 99.67% __libc_start_call_main 0 0% 0% 106880ms 99.67% __libc_start_main_impl 0 0% 0% 106880ms 99.67% _start 0 0% 0% 106859ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106859ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106859ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106859ms 99.65% main 0 0% 0% 106818ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106818ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106818ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0047% 0.0047% 106811ms 99.60% AbstractCellBasedSimulation::Solve 22ms 0.021% 0.025% 55807ms 52.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.016% 0.041% 52550ms 49.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 152ms 0.14% 0.18% 51440ms 47.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 342ms 0.32% 0.5% 39959ms 37.26% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.5% 38213ms 35.63% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.5% 23469ms 21.89% VertexBasedCellPopulation::Update 2ms 0.0019% 0.51% 23344ms 21.77% MutableVertexMesh::ReMesh 14661ms 13.67% 14.18% 23317ms 21.74% Cylindrical2dVertexMesh::GetVectorFromAtoB 98ms 0.091% 14.27% 17507ms 16.33% Cell::ReadyToDivide 88ms 0.082% 14.35% 16221ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 313ms 0.29% 14.64% 14442ms 13.47% NagaiHondaForce::GetAdhesionParameter 163ms 0.15% 14.79% 13910ms 12.97% SimpleWntCellCycleModel::UpdateCellCyclePhase 472ms 0.44% 15.23% 13895ms 12.96% boost::numeric::ublas::c_vector::c_vector (partial-inline) 82ms 0.076% 15.31% 13221ms 12.33% CellPropertyCollection::GetPropertiesType (inline) 292ms 0.27% 15.58% 12383ms 11.55% boost::numeric::ublas::vector_assign (inline) 152ms 0.14% 15.72% 11859ms 11.06% MutableVertexMesh::CheckForIntersections 3315ms 3.09% 18.82% 11164ms 10.41% __dynamic_cast 65ms 0.061% 18.88% 11046ms 10.30% AbstractCellProperty::IsSubType (inline) 74ms 0.069% 18.95% 10906ms 10.17% VertexBasedCellPopulation::GetDampingConstant 76ms 0.071% 19.02% 10333ms 9.64% AbstractTargetAreaModifier::UpdateTargetAreas 39ms 0.036% 19.05% 10238ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 26ms 0.024% 19.08% 10203ms 9.51% AbstractCellBasedSimulation::DoCellBirth 1182ms 1.10% 20.18% 9640ms 8.99% std::__new_allocator::allocate (inline) 379ms 0.35% 20.53% 9523ms 8.88% VertexMesh::GetNextEdgeGradientOfElementAtNode 2828ms 2.64% 23.17% 9490ms 8.85% boost::numeric::ublas::indexing_vector_assign 1241ms 1.16% 24.33% 9188ms 8.57% std::_Rb_tree::_M_erase 0 0% 24.33% 9167ms 8.55% std::_Rb_tree::_M_create_node (inline) 0 0% 24.33% 9112ms 8.50% std::allocator_traits::allocate (inline) 856ms 0.8% 25.13% 8715ms 8.13% VertexMesh::ElementIncludesPoint 38ms 0.035% 25.16% 8708ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 742ms 0.69% 25.85% 8463ms 7.89% operator new 0 0% 25.85% 8432ms 7.86% std::_Rb_tree::_M_get_node (inline) 111ms 0.1% 25.96% 8406ms 7.84% Cell::GetMutationState 227ms 0.21% 26.17% 8312ms 7.75% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.17% 8269ms 7.71% std::_Rb_tree::_M_drop_node (inline) 496ms 0.46% 26.63% 8263ms 7.71% VertexMesh::GetCentroidOfElement 0 0% 26.63% 8115ms 7.57% std::_Rb_tree::_Alloc_node::operator() (inline) 237ms 0.22% 26.85% 7997ms 7.46% std::__new_allocator::deallocate (inline) 0 0% 26.85% 7993ms 7.45% std::allocator_traits::deallocate (inline) 0 0% 26.85% 7936ms 7.40% std::_Rb_tree::_M_put_node (inline) 0 0% 26.85% 7851ms 7.32% std::set::~set (inline) 1460ms 1.36% 28.21% 7543ms 7.03% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2904ms 2.71% 30.92% 7526ms 7.02% __GI___libc_malloc 2386ms 2.22% 33.15% 7509ms 7.00% __GI___libc_free 15ms 0.014% 33.16% 7343ms 6.85% MutableVertexMesh::RemoveDeletedNodesAndElements 486ms 0.45% 33.61% 7095ms 6.62% std::map::operator[] (partial-inline) 180ms 0.17% 33.78% 7052ms 6.58% std::_Rb_tree::_Rb_tree (partial-inline) 723ms 0.67% 34.46% 6629ms 6.18% std::_Rb_tree::_M_copy (inline) 32ms 0.03% 34.49% 6610ms 6.16% std::set::set (inline) 116ms 0.11% 34.59% 6302ms 5.88% SimpleWntCellCycleModel::GetWntLevel 6268ms 5.84% 40.44% 6268ms 5.84% boost::numeric::ublas::c_vector::operator() 6215ms 5.80% 46.23% 6215ms 5.80% __strcmp_avx2 194ms 0.18% 46.41% 6109ms 5.70% WntConcentration::GetWntLevel 791ms 0.74% 47.15% 5644ms 5.26% std::_Rb_tree::_M_clone_node (inline) 2411ms 2.25% 49.40% 5474ms 5.10% std::_Rb_tree::_M_lower_bound (inline) 2825ms 2.63% 52.04% 5423ms 5.06% __cxxabiv1::__si_class_type_info::__do_dyncast 1935ms 1.80% 53.84% 5359ms 5.00% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.84% 5151ms 4.80% std::set::insert (inline) 20ms 0.019% 53.86% 5127ms 4.78% MutableVertexMesh::RemoveDeletedNodes 4669ms 4.35% 58.21% 5103ms 4.76% _int_free 27ms 0.025% 58.24% 4943ms 4.61% EdgeHelper::RemoveDeletedEdges 23ms 0.021% 58.26% 4659ms 4.34% EdgeHelper::UpdateEdgesMapKey 2ms 0.0019% 58.26% 4533ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.26% 4505ms 4.20% std::_Rb_tree::lower_bound (inline) 0 0% 58.26% 4505ms 4.20% std::map::lower_bound (inline) 191ms 0.18% 58.44% 4497ms 4.19% MutableElement::ResetIndex 550ms 0.51% 58.95% 4343ms 4.05% std::_Rb_tree::_M_insert_ (inline) 125ms 0.12% 59.07% 4212ms 3.93% std::set_intersection (inline) 125ms 0.12% 59.18% 4123ms 3.84% AbstractCellPopulation::GetCellUsingLocationIndex 246ms 0.23% 59.41% 4087ms 3.81% std::__set_intersection 33ms 0.031% 59.44% 3853ms 3.59% Cell::GetCellProliferativeType 3816ms 3.56% 63.00% 3816ms 3.56% boost::numeric::ublas::same_impl_ex 57ms 0.053% 63.06% 3742ms 3.49% AbstractCellProperty::IsType (inline) 11ms 0.01% 63.07% 3496ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2183ms 2.04% 65.10% 3105ms 2.90% _int_malloc 54ms 0.05% 65.15% 3094ms 2.89% Cell::SetCellProliferativeType 0 0% 65.15% 3072ms 2.86% std::insert_iterator::operator= (inline) 848ms 0.79% 65.94% 2977ms 2.78% AbstractElement::GetNodeLocation 70ms 0.065% 66.01% 2827ms 2.64% std::_Rb_tree::erase 7ms 0.0065% 66.02% 2681ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 273ms 0.25% 66.27% 2680ms 2.50% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 66.27% 2673ms 2.49% boost::numeric::ublas::c_vector::operator-= (inline) 701ms 0.65% 66.92% 2628ms 2.45% AbstractCellProperty::IsSame 647ms 0.6% 67.53% 2612ms 2.44% boost::numeric::ublas::vector_binary::size (inline) 32ms 0.03% 67.56% 2586ms 2.41% CellPropertyCollection::HasProperty 288ms 0.27% 67.83% 2558ms 2.39% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 67.83% 2541ms 2.37% boost::numeric::ublas::c_vector::assign (inline) 0 0% 67.83% 2495ms 2.33% Cell::HasCellProperty (inline) 2486ms 2.32% 70.14% 2486ms 2.32% std::_Rb_tree::_S_right (inline) 2ms 0.0019% 70.15% 2470ms 2.30% std::_Rb_tree::_M_insert_unique (inline) 0 0% 70.15% 2413ms 2.25% AbstractCellPopulation::WriteResultsToFiles 24ms 0.022% 70.17% 2349ms 2.19% Cell::GetCellData 101ms 0.094% 70.26% 2311ms 2.16% VertexMesh::GetVolumeOfElement 52ms 0.048% 70.31% 2206ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0019% 70.31% 2092ms 1.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.31% 2092ms 1.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 30ms 0.028% 70.34% 2063ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 1998ms 1.86% 72.20% 1998ms 1.86% std::_Rb_tree_increment 160ms 0.15% 72.35% 1984ms 1.85% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.0037% 72.36% 1983ms 1.85% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 72.36% 1973ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.36% 1957ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 454ms 0.42% 72.78% 1927ms 1.80% std::type_info::operator== (inline) 68ms 0.063% 72.84% 1815ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 1180ms 1.10% 73.94% 1787ms 1.67% std::_Rb_tree::equal_range (inline) 0 0% 73.94% 1767ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.031% 73.97% 1604ms 1.50% VertexMesh::GetSurfaceAreaOfElement 34ms 0.032% 74.01% 1507ms 1.41% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 142ms 0.13% 74.14% 1437ms 1.34% CellPropertyCollection::AddProperty 52ms 0.048% 74.19% 1408ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 43ms 0.04% 74.23% 1398ms 1.30% Node::RemoveElement 33ms 0.031% 74.26% 1364ms 1.27% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.0093% 74.27% 1360ms 1.27% std::set::erase (inline) 0 0% 74.27% 1355ms 1.26% boost::numeric::ublas::norm_2 (inline) 606ms 0.57% 74.83% 1344ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 74.83% 1343ms 1.25% boost::numeric::ublas::vector_binary::operator() (inline) 1338ms 1.25% 76.08% 1338ms 1.25% [libchaste_cell_based.so] 0 0% 76.08% 1332ms 1.24% tcache_get (inline) 1332ms 1.24% 77.32% 1332ms 1.24% tcache_get_n (inline) 59ms 0.055% 77.38% 1315ms 1.23% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 2ms 0.0019% 77.38% 1293ms 1.21% OffLatticeSimulation::ApplyBoundaries 53ms 0.049% 77.43% 1181ms 1.10% std::less::operator() (inline) 86ms 0.08% 77.51% 1175ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 930ms 0.87% 78.38% 1128ms 1.05% std::operator< (inline) 38ms 0.035% 78.41% 1125ms 1.05% CellPropertyRegistry::Get 0 0% 78.41% 1118ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 19ms 0.018% 78.43% 1118ms 1.04% boost::numeric::ublas::c_vector::swap (inline) 0 0% 78.43% 1109ms 1.03% std::_Rb_tree::clear (inline) 82ms 0.076% 78.51% 1099ms 1.02% std::swap_ranges (inline) 1091ms 1.02% 79.52% 1091ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 79.52% 1091ms 1.02% std::map::clear (inline) 18ms 0.017% 79.54% 1090ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.54% 1052ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 120ms 0.11% 79.65% 1026ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.65% 1026ms 0.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.65% 1017ms 0.95% std::iter_swap (inline) 1017ms 0.95% 80.60% 1017ms 0.95% std::swap (inline) 12ms 0.011% 80.61% 1003ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 2ms 0.0019% 80.61% 1000ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 106ms 0.099% 80.71% 990ms 0.92% std::_Rb_tree::find (inline) 170ms 0.16% 80.87% 972ms 0.91% boost::numeric::ublas::detail::equals 948ms 0.88% 81.75% 948ms 0.88% Node::rGetLocation 837ms 0.78% 82.53% 863ms 0.8% boost::detail::sp_counted_base::release 841ms 0.78% 83.32% 841ms 0.78% [libchaste_mesh.so] 0 0% 83.32% 837ms 0.78% std::map::find (inline) 1ms 0.00093% 83.32% 834ms 0.78% VertexMeshWriter::MakeVtkMesh 232ms 0.22% 83.54% 792ms 0.74% std::__new_allocator::construct (inline) 0 0% 83.54% 792ms 0.74% std::allocator_traits::construct (inline) 104ms 0.097% 83.63% 791ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 19ms 0.018% 83.65% 768ms 0.72% MutableElement::RegisterWithEdges (inline) 189ms 0.18% 83.83% 766ms 0.71% boost::shared_ptr::shared_ptr (inline) 21ms 0.02% 83.85% 759ms 0.71% Edge::AddElement 0 0% 83.85% 746ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.85% 739ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 83.85% 737ms 0.69% boost::numeric::ublas::norm_inf (inline) 388ms 0.36% 84.21% 737ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 84.21% 735ms 0.69% std::_Rb_tree::_M_construct_node (inline) 396ms 0.37% 84.58% 732ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 703ms 0.66% 85.23% 703ms 0.66% std::vector::size (inline) 379ms 0.35% 85.59% 688ms 0.64% Edge::GetMapIndex 2ms 0.0019% 85.59% 678ms 0.63% std::_Vector_base::_M_allocate (inline) 662ms 0.62% 86.21% 662ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.21% 655ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.22% 655ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.22% 609ms 0.57% vtkPolygon::New 2ms 0.0019% 86.23% 608ms 0.57% vtkPolygon::vtkPolygon 31ms 0.029% 86.25% 595ms 0.55% MutableElement::RegisterWithNodes (inline) 584ms 0.54% 86.80% 584ms 0.54% Node::GetIndex 551ms 0.51% 87.31% 577ms 0.54% boost::detail::shared_count::shared_count (inline) 111ms 0.1% 87.42% 570ms 0.53% MutableElement::GetNodeLocalIndex 24ms 0.022% 87.44% 562ms 0.52% Node::AddElement 10ms 0.0093% 87.45% 558ms 0.52% std::vector::_M_default_append (inline) 24ms 0.022% 87.47% 552ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.47% 552ms 0.51% boost::numeric::ublas::vector::vector (inline)