File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96925ms, 88.61% of 109388ms total Dropped 1084 nodes (cum <= 546.94ms) flat flat% sum% cum cum% 0 0% 0% 108952ms 99.60% __libc_start_call_main 0 0% 0% 108952ms 99.60% __libc_start_main_impl 0 0% 0% 108952ms 99.60% _start 0 0% 0% 108933ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108933ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108933ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108933ms 99.58% main 0 0% 0% 108895ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108895ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108895ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108887ms 99.54% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.019% 56319ms 51.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.033% 53053ms 48.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.16% 52031ms 47.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 377ms 0.34% 0.5% 39600ms 36.20% NagaiHondaForce::AddForceContribution 0 0% 0.5% 39590ms 36.19% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.5% 24445ms 22.35% VertexBasedCellPopulation::Update 1ms 0.00091% 0.51% 24313ms 22.23% MutableVertexMesh::ReMesh 14575ms 13.32% 13.83% 22912ms 20.95% Cylindrical2dVertexMesh::GetVectorFromAtoB 64ms 0.059% 13.89% 17586ms 16.08% Cell::ReadyToDivide 98ms 0.09% 13.98% 16331ms 14.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 372ms 0.34% 14.32% 14513ms 13.27% NagaiHondaForce::GetAdhesionParameter 117ms 0.11% 14.42% 14280ms 13.05% CellPropertyCollection::GetPropertiesType (inline) 411ms 0.38% 14.80% 14128ms 12.92% boost::numeric::ublas::c_vector::c_vector (partial-inline) 122ms 0.11% 14.91% 13932ms 12.74% SimpleWntCellCycleModel::UpdateCellCyclePhase 437ms 0.4% 15.31% 12605ms 11.52% boost::numeric::ublas::vector_assign (inline) 121ms 0.11% 15.42% 12043ms 11.01% MutableVertexMesh::CheckForIntersections 96ms 0.088% 15.51% 11965ms 10.94% VertexBasedCellPopulation::GetDampingConstant 3641ms 3.33% 18.84% 11910ms 10.89% __dynamic_cast 73ms 0.067% 18.91% 11796ms 10.78% AbstractCellProperty::IsSubType (inline) 81ms 0.074% 18.98% 10555ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.037% 19.02% 10446ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 19.04% 10410ms 9.52% AbstractCellBasedSimulation::DoCellBirth 1470ms 1.34% 20.38% 10299ms 9.42% std::__new_allocator::allocate (inline) 0 0% 20.38% 9739ms 8.90% std::allocator_traits::allocate (inline) 0 0% 20.38% 9681ms 8.85% std::_Rb_tree::_M_create_node (inline) 2613ms 2.39% 22.77% 9389ms 8.58% boost::numeric::ublas::indexing_vector_assign 1348ms 1.23% 24.00% 9115ms 8.33% std::_Rb_tree::_M_erase 79ms 0.072% 24.08% 9107ms 8.33% Cell::GetMutationState 0 0% 24.08% 9086ms 8.31% std::_Rb_tree::_M_get_node (inline) 789ms 0.72% 24.80% 8953ms 8.18% operator new 801ms 0.73% 25.53% 8942ms 8.17% VertexMesh::ElementIncludesPoint 25ms 0.023% 25.55% 8778ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 343ms 0.31% 25.87% 8744ms 7.99% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.87% 8464ms 7.74% std::_Rb_tree::_Alloc_node::operator() (inline) 210ms 0.19% 26.06% 8253ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 420ms 0.38% 26.44% 8183ms 7.48% VertexMesh::GetCentroidOfElement 0 0% 26.44% 8113ms 7.42% std::_Rb_tree::_M_drop_node (inline) 3058ms 2.80% 29.24% 8001ms 7.31% __GI___libc_malloc 470ms 0.43% 29.67% 7884ms 7.21% std::map::operator[] (partial-inline) 232ms 0.21% 29.88% 7853ms 7.18% std::__new_allocator::deallocate (inline) 0 0% 29.88% 7823ms 7.15% std::allocator_traits::deallocate (inline) 0 0% 29.88% 7781ms 7.11% std::_Rb_tree::_M_put_node (inline) 30ms 0.027% 29.91% 7756ms 7.09% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.91% 7734ms 7.07% std::set::~set (inline) 2928ms 2.68% 32.58% 7679ms 7.02% __GI___libc_free 1374ms 1.26% 33.84% 7061ms 6.46% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 146ms 0.13% 33.97% 7000ms 6.40% std::_Rb_tree::_Rb_tree (partial-inline) 6688ms 6.11% 40.09% 6688ms 6.11% __strcmp_avx2 680ms 0.62% 40.71% 6640ms 6.07% std::_Rb_tree::_M_copy (inline) 10ms 0.0091% 40.72% 6593ms 6.03% std::set::set (inline) 2546ms 2.33% 43.04% 6398ms 5.85% std::_Rb_tree::_M_lower_bound (inline) 90ms 0.082% 43.13% 6235ms 5.70% SimpleWntCellCycleModel::GetWntLevel 6210ms 5.68% 48.80% 6210ms 5.68% boost::numeric::ublas::c_vector::operator() 167ms 0.15% 48.96% 6088ms 5.57% WntConcentration::GetWntLevel 794ms 0.73% 49.68% 5712ms 5.22% std::_Rb_tree::_M_clone_node (inline) 2679ms 2.45% 52.13% 5563ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.026% 52.16% 5528ms 5.05% MutableVertexMesh::RemoveDeletedNodes 31ms 0.028% 52.19% 5361ms 4.90% EdgeHelper::RemoveDeletedEdges 0 0% 52.19% 5340ms 4.88% std::set::insert (inline) 0 0% 52.19% 5166ms 4.72% std::_Rb_tree::lower_bound (inline) 0 0% 52.19% 5166ms 4.72% std::map::lower_bound (inline) 36ms 0.033% 52.22% 5111ms 4.67% EdgeHelper::UpdateEdgesMapKey 1479ms 1.35% 53.57% 4849ms 4.43% boost::numeric::ublas::c_vector::operator[] (inline) 199ms 0.18% 53.75% 4805ms 4.39% MutableElement::ResetIndex 2ms 0.0018% 53.75% 4730ms 4.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 4412ms 4.03% 57.79% 4730ms 4.32% _int_free 505ms 0.46% 58.25% 4554ms 4.16% std::_Rb_tree::_M_insert_ (inline) 119ms 0.11% 58.36% 4327ms 3.96% AbstractCellPopulation::GetCellUsingLocationIndex 42ms 0.038% 58.40% 4183ms 3.82% std::set_intersection (inline) 243ms 0.22% 58.62% 4141ms 3.79% std::__set_intersection 48ms 0.044% 58.66% 4026ms 3.68% Cell::GetCellProliferativeType 59ms 0.054% 58.72% 3977ms 3.64% AbstractCellProperty::IsType (inline) 3928ms 3.59% 62.31% 3928ms 3.59% boost::numeric::ublas::same_impl_ex 4ms 0.0037% 62.31% 3655ms 3.34% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3279ms 3.00% 65.31% 3279ms 3.00% std::_Rb_tree::_S_right (inline) 45ms 0.041% 65.35% 3231ms 2.95% Cell::SetCellProliferativeType 2323ms 2.12% 67.47% 3201ms 2.93% _int_malloc 753ms 0.69% 68.16% 3170ms 2.90% AbstractElement::GetNodeLocation 42ms 0.038% 68.20% 3090ms 2.82% std::_Rb_tree::erase 0 0% 68.20% 3087ms 2.82% std::insert_iterator::operator= (inline) 824ms 0.75% 68.95% 2885ms 2.64% AbstractCellProperty::IsSame 46ms 0.042% 69.00% 2770ms 2.53% CellPropertyCollection::HasProperty 6ms 0.0055% 69.00% 2733ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 418ms 0.38% 69.38% 2720ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 590ms 0.54% 69.92% 2711ms 2.48% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.92% 2664ms 2.44% Cell::HasCellProperty (inline) 0 0% 69.92% 2607ms 2.38% std::_Rb_tree::_M_insert_unique 31ms 0.028% 69.95% 2539ms 2.32% Cell::GetCellData 231ms 0.21% 70.16% 2498ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.16% 2489ms 2.28% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.16% 2400ms 2.19% AbstractCellPopulation::WriteResultsToFiles 4ms 0.0037% 70.17% 2394ms 2.19% AbstractCellPopulation::Iterator::operator++ (inline) 239ms 0.22% 70.38% 2390ms 2.18% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 70.38% 2374ms 2.17% boost::numeric::ublas::c_vector::assign (inline) 99ms 0.091% 70.47% 2303ms 2.11% VertexMesh::GetVolumeOfElement 132ms 0.12% 70.60% 2285ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 33ms 0.03% 70.63% 2202ms 2.01% std::_Rb_tree::_M_emplace_hint_unique 2118ms 1.94% 72.56% 2118ms 1.94% std::_Rb_tree_increment 1423ms 1.30% 73.86% 2112ms 1.93% std::_Rb_tree::equal_range (inline) 542ms 0.5% 74.36% 2061ms 1.88% std::type_info::operator== (inline) 0 0% 74.36% 1970ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.36% 1960ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 34ms 0.031% 74.39% 1880ms 1.72% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 66ms 0.06% 74.45% 1867ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 74.45% 1783ms 1.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.45% 1783ms 1.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.45% 1755ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 21ms 0.019% 74.47% 1683ms 1.54% VertexMesh::GetSurfaceAreaOfElement 45ms 0.041% 74.51% 1679ms 1.53% Node::RemoveElement 14ms 0.013% 74.52% 1645ms 1.50% std::set::erase (inline) 86ms 0.079% 74.60% 1622ms 1.48% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 38ms 0.035% 74.64% 1594ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.64% 1542ms 1.41% tcache_get (inline) 1542ms 1.41% 76.05% 1542ms 1.41% tcache_get_n (inline) 166ms 0.15% 76.20% 1534ms 1.40% CellPropertyCollection::AddProperty 121ms 0.11% 76.31% 1513ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.31% 1435ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 76.31% 1293ms 1.18% OffLatticeSimulation::ApplyBoundaries 68ms 0.062% 76.37% 1263ms 1.15% std::less::operator() (inline) 1261ms 1.15% 77.53% 1261ms 1.15% Node::rGetLocation 0 0% 77.53% 1217ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 999ms 0.91% 78.44% 1195ms 1.09% std::operator< (inline) 89ms 0.081% 78.52% 1183ms 1.08% std::_Rb_tree::find (inline) 0 0% 78.52% 1134ms 1.04% boost::numeric::ublas::norm_2 (inline) 78ms 0.071% 78.59% 1132ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 523ms 0.48% 79.07% 1128ms 1.03% boost::numeric::ublas::vector_norm_2::apply 1086ms 0.99% 80.06% 1086ms 0.99% std::_Rb_tree_insert_and_rebalance 18ms 0.016% 80.08% 1076ms 0.98% CellPropertyRegistry::Get 0 0% 80.08% 1076ms 0.98% std::_Rb_tree::clear (inline) 18ms 0.016% 80.10% 1059ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.10% 1057ms 0.97% std::map::clear (inline) 1045ms 0.96% 81.05% 1045ms 0.96% [libchaste_cell_based.so] 2ms 0.0018% 81.05% 1026ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1024ms 0.94% 81.99% 1024ms 0.94% std::vector::size (inline) 148ms 0.14% 82.13% 1014ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 82.13% 1014ms 0.93% boost::shared_ptr::~shared_ptr (inline) 357ms 0.33% 82.45% 1012ms 0.93% Edge::GetMapIndex 0 0% 82.45% 976ms 0.89% std::map::find (inline) 932ms 0.85% 83.30% 932ms 0.85% [libchaste_mesh.so] 0 0% 83.30% 907ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 83.31% 907ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.069% 83.38% 900ms 0.82% std::swap_ranges (inline) 33ms 0.03% 83.41% 876ms 0.8% boost::numeric::ublas::detail::expression_type_check (inline) 850ms 0.78% 84.19% 856ms 0.78% boost::detail::sp_counted_base::release 0 0% 84.19% 850ms 0.78% VertexMeshWriter::MakeVtkMesh 150ms 0.14% 84.32% 831ms 0.76% boost::numeric::ublas::detail::equals 826ms 0.76% 85.08% 826ms 0.76% std::swap (inline) 0 0% 85.08% 825ms 0.75% std::iter_swap (inline) 812ms 0.74% 85.82% 812ms 0.74% Node::GetIndex 123ms 0.11% 85.93% 798ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 95ms 0.087% 86.02% 792ms 0.72% MutableElement::GetNodeLocalIndex 23ms 0.021% 86.04% 779ms 0.71% MutableElement::RegisterWithEdges (inline) 33ms 0.03% 86.07% 777ms 0.71% Edge::AddElement 0 0% 86.07% 747ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 133ms 0.12% 86.19% 706ms 0.65% boost::shared_ptr::shared_ptr (inline) 401ms 0.37% 86.56% 693ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.56% 653ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.58% 653ms 0.6% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00091% 86.58% 652ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.58% 649ms 0.59% boost::numeric::ublas::norm_inf (inline) 339ms 0.31% 86.89% 649ms 0.59% boost::numeric::ublas::vector_norm_inf::apply (inline) 91ms 0.083% 86.97% 646ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.97% 646ms 0.59% std::allocator_traits::construct (inline) 0 0% 86.97% 628ms 0.57% vtkPolygon::New 1ms 0.00091% 86.97% 627ms 0.57% vtkPolygon::vtkPolygon 22ms 0.02% 86.99% 625ms 0.57% MutableElement::RegisterWithNodes (inline) 26ms 0.024% 87.02% 603ms 0.55% Node::AddElement 599ms 0.55% 87.56% 599ms 0.55% operator delete 0 0% 87.56% 595ms 0.54% std::_Rb_tree::_M_construct_node (inline) 28ms 0.026% 87.59% 588ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.59% 588ms 0.54% boost::numeric::ublas::vector::vector (inline) 553ms 0.51% 88.09% 573ms 0.52% boost::detail::shared_count::shared_count (inline) 560ms 0.51% 88.61% 560ms 0.51% [libstdc++.so.6.0.33]