File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94597ms, 87.52% of 108089ms total Dropped 1106 nodes (cum <= 540.45ms) flat flat% sum% cum cum% 0 0% 0% 107740ms 99.68% __libc_start_call_main 0 0% 0% 107740ms 99.68% __libc_start_main_impl 0 0% 0% 107740ms 99.68% _start 0 0% 0% 107720ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107720ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107720ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107720ms 99.66% main 0 0% 0% 107679ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107679ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107679ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 107671ms 99.61% AbstractCellBasedSimulation::Solve 25ms 0.023% 0.027% 56128ms 51.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.043% 52836ms 48.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 142ms 0.13% 0.17% 51695ms 47.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 309ms 0.29% 0.46% 39879ms 36.89% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.46% 38726ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.46% 23907ms 22.12% VertexBasedCellPopulation::Update 1ms 0.00093% 0.47% 23760ms 21.98% MutableVertexMesh::ReMesh 14722ms 13.62% 14.09% 23499ms 21.74% Cylindrical2dVertexMesh::GetVectorFromAtoB 77ms 0.071% 14.16% 17311ms 16.02% Cell::ReadyToDivide 77ms 0.071% 14.23% 16079ms 14.88% AbstractPhaseBasedCellCycleModel::ReadyToDivide 299ms 0.28% 14.50% 14489ms 13.40% NagaiHondaForce::GetAdhesionParameter 474ms 0.44% 14.94% 13983ms 12.94% boost::numeric::ublas::c_vector::c_vector (partial-inline) 154ms 0.14% 15.09% 13748ms 12.72% SimpleWntCellCycleModel::UpdateCellCyclePhase 106ms 0.098% 15.18% 13225ms 12.24% CellPropertyCollection::GetPropertiesType (inline) 293ms 0.27% 15.45% 12428ms 11.50% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.58% 11859ms 10.97% MutableVertexMesh::CheckForIntersections 3321ms 3.07% 18.65% 11259ms 10.42% __dynamic_cast 81ms 0.075% 18.73% 11253ms 10.41% VertexBasedCellPopulation::GetDampingConstant 70ms 0.065% 18.79% 11148ms 10.31% AbstractCellProperty::IsSubType (inline) 84ms 0.078% 18.87% 10337ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 45ms 0.042% 18.91% 10217ms 9.45% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 32ms 0.03% 18.94% 10113ms 9.36% AbstractCellBasedSimulation::DoCellBirth 1231ms 1.14% 20.08% 10023ms 9.27% std::__new_allocator::allocate (inline) 0 0% 20.08% 9521ms 8.81% std::_Rb_tree::_M_create_node (inline) 2958ms 2.74% 22.82% 9486ms 8.78% boost::numeric::ublas::indexing_vector_assign 0 0% 22.82% 9418ms 8.71% std::allocator_traits::allocate (inline) 353ms 0.33% 23.14% 9399ms 8.70% VertexMesh::GetNextEdgeGradientOfElementAtNode 1197ms 1.11% 24.25% 8994ms 8.32% std::_Rb_tree::_M_erase 803ms 0.74% 24.99% 8847ms 8.18% operator new 0 0% 24.99% 8780ms 8.12% std::_Rb_tree::_M_get_node (inline) 28ms 0.026% 25.02% 8764ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 793ms 0.73% 25.75% 8634ms 7.99% VertexMesh::ElementIncludesPoint 0 0% 25.75% 8326ms 7.70% std::_Rb_tree::_Alloc_node::operator() (inline) 91ms 0.084% 25.84% 8303ms 7.68% Cell::GetMutationState 451ms 0.42% 26.25% 8270ms 7.65% VertexMesh::GetCentroidOfElement 0 0% 26.25% 8146ms 7.54% std::_Rb_tree::_M_drop_node (inline) 208ms 0.19% 26.45% 8121ms 7.51% std::_Rb_tree::~_Rb_tree (inline) 232ms 0.21% 26.66% 7874ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 26.66% 7867ms 7.28% std::allocator_traits::deallocate (inline) 3009ms 2.78% 29.45% 7850ms 7.26% __GI___libc_malloc 0 0% 29.45% 7821ms 7.24% std::_Rb_tree::_M_put_node (inline) 18ms 0.017% 29.46% 7696ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.46% 7665ms 7.09% std::set::~set (inline) 494ms 0.46% 29.92% 7575ms 7.01% std::map::operator[] (partial-inline) 1468ms 1.36% 31.28% 7538ms 6.97% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2364ms 2.19% 33.46% 7349ms 6.80% __GI___libc_free 182ms 0.17% 33.63% 7316ms 6.77% std::_Rb_tree::_Rb_tree (partial-inline) 800ms 0.74% 34.37% 6871ms 6.36% std::_Rb_tree::_M_copy (inline) 37ms 0.034% 34.41% 6833ms 6.32% std::set::set (inline) 132ms 0.12% 34.53% 6299ms 5.83% SimpleWntCellCycleModel::GetWntLevel 6184ms 5.72% 40.25% 6184ms 5.72% boost::numeric::ublas::c_vector::operator() 6172ms 5.71% 45.96% 6172ms 5.71% __strcmp_avx2 163ms 0.15% 46.11% 6083ms 5.63% WntConcentration::GetWntLevel 2390ms 2.21% 48.32% 5827ms 5.39% std::_Rb_tree::_M_lower_bound (inline) 808ms 0.75% 49.07% 5823ms 5.39% std::_Rb_tree::_M_clone_node (inline) 2897ms 2.68% 51.75% 5429ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 2000ms 1.85% 53.60% 5400ms 5.00% boost::numeric::ublas::c_vector::operator[] (inline) 29ms 0.027% 53.63% 5288ms 4.89% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.63% 5189ms 4.80% std::set::insert (inline) 34ms 0.031% 53.66% 5095ms 4.71% EdgeHelper::RemoveDeletedEdges 4542ms 4.20% 57.86% 4972ms 4.60% _int_free 0 0% 57.86% 4888ms 4.52% std::_Rb_tree::lower_bound (inline) 0 0% 57.86% 4888ms 4.52% std::map::lower_bound (inline) 29ms 0.027% 57.89% 4771ms 4.41% EdgeHelper::UpdateEdgesMapKey 184ms 0.17% 58.06% 4716ms 4.36% MutableElement::ResetIndex 1ms 0.00093% 58.06% 4702ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 154ms 0.14% 58.20% 4465ms 4.13% AbstractCellPopulation::GetCellUsingLocationIndex 505ms 0.47% 58.67% 4345ms 4.02% std::_Rb_tree::_M_insert_ (inline) 96ms 0.089% 58.76% 4279ms 3.96% std::set_intersection (inline) 238ms 0.22% 58.98% 4183ms 3.87% std::__set_intersection 31ms 0.029% 59.01% 3947ms 3.65% Cell::GetCellProliferativeType 3761ms 3.48% 62.49% 3761ms 3.48% boost::numeric::ublas::same_impl_ex 45ms 0.042% 62.53% 3706ms 3.43% AbstractCellProperty::IsType (inline) 16ms 0.015% 62.54% 3593ms 3.32% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.54% 3193ms 2.95% std::insert_iterator::operator= (inline) 2257ms 2.09% 64.63% 3174ms 2.94% _int_malloc 68ms 0.063% 64.69% 3058ms 2.83% Cell::SetCellProliferativeType 65ms 0.06% 64.75% 3022ms 2.80% std::_Rb_tree::erase 845ms 0.78% 65.53% 3020ms 2.79% AbstractElement::GetNodeLocation 2931ms 2.71% 68.25% 2931ms 2.71% std::_Rb_tree::_S_right (inline) 8ms 0.0074% 68.25% 2795ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 212ms 0.2% 68.45% 2660ms 2.46% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.45% 2588ms 2.39% boost::numeric::ublas::c_vector::operator-= (inline) 618ms 0.57% 69.02% 2587ms 2.39% boost::numeric::ublas::vector_binary::size (inline) 713ms 0.66% 69.68% 2586ms 2.39% AbstractCellProperty::IsSame 22ms 0.02% 69.70% 2555ms 2.36% CellPropertyCollection::HasProperty 0 0% 69.70% 2554ms 2.36% boost::numeric::ublas::c_vector::assign (inline) 281ms 0.26% 69.96% 2509ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.96% 2467ms 2.28% Cell::HasCellProperty (inline) 0 0% 69.96% 2441ms 2.26% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00093% 69.96% 2394ms 2.21% std::_Rb_tree::_M_insert_unique 21ms 0.019% 69.98% 2325ms 2.15% Cell::GetCellData 77ms 0.071% 70.05% 2284ms 2.11% VertexMesh::GetVolumeOfElement 52ms 0.048% 70.10% 2235ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 34ms 0.031% 70.13% 2129ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0019% 70.13% 2065ms 1.91% AbstractCellPopulation::Iterator::operator++ (inline) 138ms 0.13% 70.26% 2043ms 1.89% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0019% 70.26% 2029ms 1.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.26% 2029ms 1.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1333ms 1.23% 71.50% 2013ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 71.50% 1988ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0037% 71.50% 1978ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1978ms 1.83% 73.33% 1978ms 1.83% std::_Rb_tree_increment 446ms 0.41% 73.74% 1873ms 1.73% std::type_info::operator== (inline) 71ms 0.066% 73.81% 1831ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.81% 1783ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 40ms 0.037% 73.85% 1611ms 1.49% VertexMesh::GetSurfaceAreaOfElement 26ms 0.024% 73.87% 1575ms 1.46% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 42ms 0.039% 73.91% 1561ms 1.44% Node::RemoveElement 14ms 0.013% 73.92% 1520ms 1.41% std::set::erase (inline) 0 0% 73.92% 1493ms 1.38% tcache_get (inline) 1493ms 1.38% 75.30% 1493ms 1.38% tcache_get_n (inline) 32ms 0.03% 75.33% 1431ms 1.32% AbstractCellPopulation::GetLocationIndexUsingCell 66ms 0.061% 75.39% 1383ms 1.28% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 54ms 0.05% 75.44% 1382ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 150ms 0.14% 75.58% 1365ms 1.26% CellPropertyCollection::AddProperty 1336ms 1.24% 76.82% 1336ms 1.24% [libchaste_cell_based.so] 0 0% 76.82% 1320ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 76.82% 1319ms 1.22% boost::numeric::ublas::norm_2 (inline) 562ms 0.52% 77.34% 1299ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.00093% 77.34% 1245ms 1.15% OffLatticeSimulation::ApplyBoundaries 55ms 0.051% 77.39% 1219ms 1.13% std::less::operator() (inline) 0 0% 77.39% 1195ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 967ms 0.89% 78.29% 1164ms 1.08% std::operator< (inline) 0 0% 78.29% 1142ms 1.06% boost::numeric::ublas::c_vector::assign_temporary (inline) 17ms 0.016% 78.30% 1142ms 1.06% boost::numeric::ublas::c_vector::swap (inline) 37ms 0.034% 78.34% 1141ms 1.06% CellPropertyRegistry::Get 76ms 0.07% 78.41% 1125ms 1.04% std::swap_ranges (inline) 61ms 0.056% 78.46% 1115ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.46% 1086ms 1.00% std::_Rb_tree::clear (inline) 0 0% 78.46% 1064ms 0.98% std::map::clear (inline) 11ms 0.01% 78.47% 1063ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1060ms 0.98% 79.45% 1060ms 0.98% std::_Rb_tree_insert_and_rebalance 14ms 0.013% 79.47% 1056ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.47% 1049ms 0.97% std::iter_swap (inline) 1049ms 0.97% 80.44% 1049ms 0.97% std::swap (inline) 18ms 0.017% 80.45% 1002ms 0.93% boost::numeric::ublas::detail::expression_type_check (inline) 105ms 0.097% 80.55% 1000ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.55% 1000ms 0.93% boost::shared_ptr::~shared_ptr (inline) 999ms 0.92% 81.47% 999ms 0.92% Node::rGetLocation 203ms 0.19% 81.66% 972ms 0.9% boost::numeric::ublas::detail::equals 104ms 0.096% 81.76% 956ms 0.88% std::_Rb_tree::find (inline) 85ms 0.079% 81.84% 871ms 0.81% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 81.84% 869ms 0.8% VertexMeshWriter::MakeVtkMesh 832ms 0.77% 82.61% 862ms 0.8% boost::detail::sp_counted_base::release 0 0% 82.61% 822ms 0.76% std::map::find (inline) 815ms 0.75% 83.36% 815ms 0.75% std::vector::size (inline) 239ms 0.22% 83.58% 797ms 0.74% std::__new_allocator::construct (inline) 0 0% 83.58% 797ms 0.74% std::allocator_traits::construct (inline) 37ms 0.034% 83.62% 778ms 0.72% Edge::AddElement 186ms 0.17% 83.79% 771ms 0.71% boost::shared_ptr::shared_ptr (inline) 13ms 0.012% 83.80% 768ms 0.71% MutableElement::RegisterWithEdges (inline) 761ms 0.7% 84.50% 761ms 0.7% [libchaste_mesh.so] 0 0% 84.50% 741ms 0.69% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.50% 734ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 382ms 0.35% 84.86% 730ms 0.68% Edge::GetMapIndex 406ms 0.38% 85.23% 720ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.23% 712ms 0.66% boost::numeric::ublas::norm_inf (inline) 374ms 0.35% 85.58% 712ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 710ms 0.66% 86.24% 710ms 0.66% [libstdc++.so.6.0.33] 125ms 0.12% 86.35% 676ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 86.35% 651ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.00093% 86.35% 636ms 0.59% std::_Vector_base::_M_allocate (inline) 28ms 0.026% 86.38% 633ms 0.59% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.38% 633ms 0.59% boost::numeric::ublas::vector::vector (inline) 0 0% 86.38% 631ms 0.58% vtkPolygon::New 0 0% 86.38% 631ms 0.58% vtkPolygon::vtkPolygon 0 0% 86.38% 614ms 0.57% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.017% 86.40% 614ms 0.57% std::_Rb_tree::_M_insert_node (inline) 36ms 0.033% 86.43% 604ms 0.56% MutableElement::RegisterWithNodes (inline) 567ms 0.52% 86.95% 585ms 0.54% boost::detail::shared_count::shared_count (inline) 577ms 0.53% 87.49% 577ms 0.53% Node::GetIndex 33ms 0.031% 87.52% 562ms 0.52% Node::AddElement