File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 105457ms, 89.82% of 117408ms total Dropped 1056 nodes (cum <= 587.04ms) flat flat% sum% cum cum% 0 0% 0% 116937ms 99.60% __libc_start_call_main 0 0% 0% 116937ms 99.60% __libc_start_main_impl 0 0% 0% 116937ms 99.60% _start 0 0% 0% 116918ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 116918ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 116918ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 116918ms 99.58% main 0 0% 0% 116885ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 116885ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 116885ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00085% 0.00085% 116877ms 99.55% AbstractCellBasedSimulation::Solve 14ms 0.012% 0.013% 65127ms 55.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.019% 0.032% 61895ms 52.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 127ms 0.11% 0.14% 60509ms 51.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 336ms 0.29% 0.43% 48981ms 41.72% NagaiHondaForce::AddForceContribution 0 0% 0.43% 38831ms 33.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.43% 24035ms 20.47% VertexBasedCellPopulation::Update 2ms 0.0017% 0.43% 23908ms 20.36% MutableVertexMesh::ReMesh 694ms 0.59% 1.02% 23605ms 20.11% NagaiHondaForce::GetAdhesionParameter 14225ms 12.12% 13.13% 22699ms 19.33% Cylindrical2dVertexMesh::GetVectorFromAtoB 73ms 0.062% 13.20% 17663ms 15.04% Cell::ReadyToDivide 41ms 0.035% 13.23% 16542ms 14.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1428ms 1.22% 14.45% 16214ms 13.81% std::__new_allocator::allocate (inline) 0 0% 14.45% 15587ms 13.28% std::_Rb_tree::_M_create_node (inline) 0 0% 14.45% 15506ms 13.21% std::allocator_traits::allocate (inline) 0 0% 14.45% 14851ms 12.65% std::_Rb_tree::_M_get_node (inline) 1373ms 1.17% 15.62% 14825ms 12.63% operator new 551ms 0.47% 16.09% 14531ms 12.38% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 16.09% 14391ms 12.26% std::_Rb_tree::_Alloc_node::operator() (inline) 105ms 0.089% 16.18% 14100ms 12.01% SimpleWntCellCycleModel::UpdateCellCyclePhase 124ms 0.11% 16.28% 13701ms 11.67% CellPropertyCollection::GetPropertiesType (inline) 6390ms 5.44% 21.72% 13219ms 11.26% __GI___libc_malloc 354ms 0.3% 22.03% 12775ms 10.88% boost::numeric::ublas::vector_assign (inline) 1260ms 1.07% 23.10% 12067ms 10.28% std::_Rb_tree::_M_erase 130ms 0.11% 23.21% 12041ms 10.26% MutableVertexMesh::CheckForIntersections 134ms 0.11% 23.32% 11389ms 9.70% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 23.32% 11292ms 9.62% std::_Rb_tree::_M_drop_node (inline) 211ms 0.18% 23.50% 11275ms 9.60% std::_Rb_tree::~_Rb_tree (inline) 3033ms 2.58% 26.09% 11242ms 9.58% __dynamic_cast 96ms 0.082% 26.17% 11150ms 9.50% AbstractCellProperty::IsSubType (inline) 926ms 0.79% 26.96% 11046ms 9.41% std::_Rb_tree::_M_copy (inline) 66ms 0.056% 27.01% 11020ms 9.39% VertexBasedCellPopulation::GetDampingConstant 209ms 0.18% 27.19% 11014ms 9.38% std::__new_allocator::deallocate (inline) 0 0% 27.19% 10988ms 9.36% std::allocator_traits::deallocate (inline) 16ms 0.014% 27.21% 10979ms 9.35% std::set::set (inline) 0 0% 27.21% 10919ms 9.30% std::_Rb_tree::_M_put_node (inline) 2669ms 2.27% 29.48% 10788ms 9.19% __GI___libc_free 0 0% 29.48% 10754ms 9.16% std::set::~set (inline) 64ms 0.055% 29.53% 10539ms 8.98% AbstractTargetAreaModifier::UpdateTargetAreas 72ms 0.061% 29.59% 10451ms 8.90% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 20ms 0.017% 29.61% 10196ms 8.68% AbstractCellBasedSimulation::DoCellBirth 751ms 0.64% 30.25% 9924ms 8.45% std::_Rb_tree::_M_clone_node (inline) 2805ms 2.39% 32.64% 9532ms 8.12% boost::numeric::ublas::indexing_vector_assign 326ms 0.28% 32.92% 9102ms 7.75% VertexMesh::GetNextEdgeGradientOfElementAtNode 775ms 0.66% 33.58% 8934ms 7.61% VertexMesh::ElementIncludesPoint 100ms 0.085% 33.66% 8747ms 7.45% Cell::GetMutationState 26ms 0.022% 33.69% 8487ms 7.23% VertexBasedCellPopulation::GetLocationOfCellCentre 6687ms 5.70% 39.38% 8112ms 6.91% _int_free 514ms 0.44% 39.82% 8076ms 6.88% VertexMesh::GetCentroidOfElement 21ms 0.018% 39.84% 7440ms 6.34% MutableVertexMesh::RemoveDeletedNodesAndElements 482ms 0.41% 40.25% 7242ms 6.17% std::map::operator[] (partial-inline) 1455ms 1.24% 41.49% 7203ms 6.14% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 41.49% 7103ms 6.05% std::set::insert (inline) 6644ms 5.66% 47.14% 6644ms 5.66% __strcmp_avx2 550ms 0.47% 47.61% 6307ms 5.37% std::_Rb_tree::_M_insert_ (inline) 102ms 0.087% 47.70% 6128ms 5.22% SimpleWntCellCycleModel::GetWntLevel 6086ms 5.18% 52.88% 6086ms 5.18% boost::numeric::ublas::c_vector::operator() 140ms 0.12% 53.00% 5912ms 5.04% WntConcentration::GetWntLevel 42ms 0.036% 53.04% 5771ms 4.92% std::set_intersection (inline) 220ms 0.19% 53.23% 5729ms 4.88% std::__set_intersection 2628ms 2.24% 55.46% 5705ms 4.86% __cxxabiv1::__si_class_type_info::__do_dyncast 2400ms 2.04% 57.51% 5586ms 4.76% std::_Rb_tree::_M_lower_bound (inline) 41ms 0.035% 57.54% 5327ms 4.54% MutableVertexMesh::RemoveDeletedNodes 39ms 0.033% 57.58% 5182ms 4.41% EdgeHelper::RemoveDeletedEdges 42ms 0.036% 57.61% 4932ms 4.20% EdgeHelper::UpdateEdgesMapKey 0 0% 57.61% 4871ms 4.15% std::insert_iterator::operator= (inline) 1502ms 1.28% 58.89% 4816ms 4.10% boost::numeric::ublas::c_vector::operator[] (inline) 193ms 0.16% 59.06% 4590ms 3.91% MutableElement::ResetIndex 0 0% 59.06% 4588ms 3.91% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 59.06% 4527ms 3.86% std::_Rb_tree::lower_bound (inline) 0 0% 59.06% 4527ms 3.86% std::map::lower_bound (inline) 4ms 0.0034% 59.06% 4502ms 3.83% std::_Rb_tree::_M_insert_unique_ (inline) 4263ms 3.63% 62.69% 4263ms 3.63% boost::numeric::ublas::same_impl_ex 40ms 0.034% 62.72% 4026ms 3.43% Cell::GetCellProliferativeType 3000ms 2.56% 65.28% 3970ms 3.38% _int_malloc 97ms 0.083% 65.36% 3955ms 3.37% AbstractCellProperty::IsType (inline) 122ms 0.1% 65.47% 3949ms 3.36% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.0085% 65.48% 3481ms 2.96% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 48ms 0.041% 65.52% 3195ms 2.72% Cell::SetCellProliferativeType 761ms 0.65% 66.16% 3040ms 2.59% AbstractElement::GetNodeLocation 39ms 0.033% 66.20% 2965ms 2.53% std::_Rb_tree::erase 592ms 0.5% 66.70% 2913ms 2.48% boost::numeric::ublas::vector_binary::size (inline) 800ms 0.68% 67.38% 2801ms 2.39% AbstractCellProperty::IsSame 0 0% 67.38% 2665ms 2.27% tcache_get (inline) 2665ms 2.27% 69.65% 2665ms 2.27% tcache_get_n (inline) 1ms 0.00085% 69.65% 2601ms 2.22% std::_Rb_tree::_M_insert_unique 2590ms 2.21% 71.86% 2590ms 2.21% std::_Rb_tree::_S_right (inline) 48ms 0.041% 71.90% 2543ms 2.17% CellPropertyCollection::HasProperty 381ms 0.32% 72.23% 2490ms 2.12% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.23% 2445ms 2.08% Cell::HasCellProperty (inline) 0 0% 72.23% 2386ms 2.03% boost::numeric::ublas::c_vector::assign (inline) 114ms 0.097% 72.32% 2380ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 217ms 0.18% 72.51% 2378ms 2.03% VertexMesh::GetAreaGradientOfElementAtNode 85ms 0.072% 72.58% 2365ms 2.01% VertexMesh::GetVolumeOfElement 0 0% 72.58% 2357ms 2.01% AbstractCellPopulation::WriteResultsToFiles 0 0% 72.58% 2351ms 2.00% boost::numeric::ublas::c_vector::operator-= (inline) 25ms 0.021% 72.60% 2320ms 1.98% Cell::GetCellData 2ms 0.0017% 72.60% 2208ms 1.88% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.16% 72.77% 2206ms 1.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 37ms 0.032% 72.80% 2183ms 1.86% std::_Rb_tree::_M_emplace_hint_unique 479ms 0.41% 73.21% 2001ms 1.70% std::type_info::operator== (inline) 1365ms 1.16% 74.37% 1990ms 1.69% std::_Rb_tree::equal_range (inline) 2ms 0.0017% 74.37% 1948ms 1.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.37% 1948ms 1.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.37% 1932ms 1.65% VertexBasedCellPopulation::WriteVtkResultsToFile 1928ms 1.64% 76.01% 1928ms 1.64% std::_Rb_tree_increment 3ms 0.0026% 76.01% 1921ms 1.64% VertexBasedCellPopulation::WriteCellVtkResultsToFile 81ms 0.069% 76.08% 1876ms 1.60% MutableVertexMesh::CheckForSwapsFromShortEdges 47ms 0.04% 76.12% 1737ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 76.12% 1720ms 1.46% VertexMeshWriter::WriteVtkUsingMesh 1687ms 1.44% 77.56% 1687ms 1.44% tcache_put (inline) 35ms 0.03% 77.59% 1674ms 1.43% VertexMesh::GetSurfaceAreaOfElement 150ms 0.13% 77.72% 1634ms 1.39% CellPropertyCollection::AddProperty 73ms 0.062% 77.78% 1575ms 1.34% boost::numeric::ublas::vector_reference::operator() (inline) 41ms 0.035% 77.81% 1555ms 1.32% Node::RemoveElement 17ms 0.014% 77.83% 1526ms 1.30% std::set::erase (inline) 32ms 0.027% 77.86% 1524ms 1.30% AbstractCellPopulation::GetLocationIndexUsingCell 88ms 0.075% 77.93% 1490ms 1.27% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 77.93% 1336ms 1.14% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0017% 77.93% 1286ms 1.10% OffLatticeSimulation::ApplyBoundaries 0 0% 77.93% 1237ms 1.05% boost::numeric::ublas::norm_2 (inline) 570ms 0.49% 78.42% 1228ms 1.05% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 32ms 0.027% 78.45% 1201ms 1.02% CellPropertyRegistry::Get 1197ms 1.02% 79.47% 1197ms 1.02% [libchaste_cell_based.so] 0 0% 79.47% 1196ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 80ms 0.068% 79.53% 1193ms 1.02% std::less::operator() (inline) 96ms 0.082% 79.62% 1169ms 1% std::_Rb_tree::_M_erase_aux (partial-inline) 24ms 0.02% 79.64% 1126ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1123ms 0.96% 80.59% 1123ms 0.96% std::_Rb_tree_insert_and_rebalance 1117ms 0.95% 81.54% 1117ms 0.95% Node::GetIndex 149ms 0.13% 81.67% 1115ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 81.67% 1115ms 0.95% boost::shared_ptr::~shared_ptr (inline) 929ms 0.79% 82.46% 1113ms 0.95% std::operator< (inline) 1091ms 0.93% 83.39% 1091ms 0.93% Node::rGetLocation 10ms 0.0085% 83.40% 1063ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 93ms 0.079% 83.48% 1022ms 0.87% std::_Rb_tree::find (inline) 1ms 0.00085% 83.48% 1007ms 0.86% std::_Rb_tree::clear (inline) 994ms 0.85% 84.33% 994ms 0.85% std::vector::size (inline) 0 0% 84.33% 985ms 0.84% std::map::clear (inline) 934ms 0.8% 85.12% 937ms 0.8% boost::detail::sp_counted_base::release 18ms 0.015% 85.14% 933ms 0.79% boost::numeric::ublas::detail::expression_type_check (inline) 383ms 0.33% 85.46% 929ms 0.79% Edge::GetMapIndex 0 0% 85.46% 925ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0043% 85.47% 925ms 0.79% boost::numeric::ublas::c_vector::swap (inline) 92ms 0.078% 85.55% 920ms 0.78% std::swap_ranges (inline) 148ms 0.13% 85.67% 902ms 0.77% boost::numeric::ublas::detail::equals 898ms 0.76% 86.44% 898ms 0.76% [libchaste_mesh.so] 101ms 0.086% 86.52% 892ms 0.76% MutableElement::GetNodeLocalIndex 0 0% 86.52% 845ms 0.72% std::map::find (inline) 829ms 0.71% 87.23% 829ms 0.71% std::swap (inline) 0 0% 87.23% 828ms 0.71% std::iter_swap (inline) 0 0% 87.23% 826ms 0.7% VertexMeshWriter::MakeVtkMesh 119ms 0.1% 87.33% 792ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 225ms 0.19% 87.52% 786ms 0.67% std::__new_allocator::construct (inline) 0 0% 87.52% 786ms 0.67% std::allocator_traits::construct (inline) 0 0% 87.52% 777ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 174ms 0.15% 87.67% 766ms 0.65% boost::shared_ptr::shared_ptr (inline) 45ms 0.038% 87.71% 753ms 0.64% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.71% 753ms 0.64% boost::numeric::ublas::vector::vector (inline) 0 0% 87.71% 736ms 0.63% std::_Rb_tree::_M_construct_node (inline) 274ms 0.23% 87.94% 717ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 87.94% 711ms 0.61% boost::numeric::ublas::norm_inf (inline) 321ms 0.27% 88.22% 711ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 19ms 0.016% 88.23% 691ms 0.59% MutableElement::RegisterWithEdges (inline) 19ms 0.016% 88.25% 688ms 0.59% Edge::AddElement 0 0% 88.25% 652ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.02% 88.27% 652ms 0.56% std::_Rb_tree::_M_insert_node (inline) 0 0% 88.27% 651ms 0.55% std::_Vector_base::_M_allocate (inline) 616ms 0.52% 88.79% 616ms 0.52% [libstdc++.so.6.0.33] 613ms 0.52% 89.32% 613ms 0.52% operator delete 0 0% 89.32% 610ms 0.52% vtkPolygon::New 0 0% 89.32% 609ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.00085% 89.32% 609ms 0.52% vtkPolygon::vtkPolygon 30ms 0.026% 89.34% 605ms 0.52% MutableElement::RegisterWithNodes (inline) 563ms 0.48% 89.82% 592ms 0.5% boost::detail::shared_count::shared_count (inline)