File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95815ms, 88.72% of 107993ms total Dropped 1083 nodes (cum <= 539.97ms) flat flat% sum% cum cum% 0 0% 0% 107510ms 99.55% __libc_start_call_main 0 0% 0% 107510ms 99.55% __libc_start_main_impl 0 0% 0% 107510ms 99.55% _start 0 0% 0% 107491ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107491ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107491ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107491ms 99.54% main 0 0% 0% 107456ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107456ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107456ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 107449ms 99.50% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.013% 55805ms 51.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 23ms 0.021% 0.034% 52606ms 48.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 135ms 0.13% 0.16% 51579ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 426ms 0.39% 0.55% 40218ms 37.24% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.55% 38851ms 35.98% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.55% 24068ms 22.29% VertexBasedCellPopulation::Update 0 0% 0.55% 23944ms 22.17% MutableVertexMesh::ReMesh 14581ms 13.50% 14.06% 23179ms 21.46% Cylindrical2dVertexMesh::GetVectorFromAtoB 88ms 0.081% 14.14% 17450ms 16.16% Cell::ReadyToDivide 133ms 0.12% 14.26% 16336ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 345ms 0.32% 14.58% 14839ms 13.74% NagaiHondaForce::GetAdhesionParameter 419ms 0.39% 14.97% 14694ms 13.61% boost::numeric::ublas::c_vector::c_vector (partial-inline) 136ms 0.13% 15.09% 13881ms 12.85% SimpleWntCellCycleModel::UpdateCellCyclePhase 126ms 0.12% 15.21% 13397ms 12.41% CellPropertyCollection::GetPropertiesType (inline) 586ms 0.54% 15.75% 13136ms 12.16% boost::numeric::ublas::vector_assign (inline) 118ms 0.11% 15.86% 12067ms 11.17% MutableVertexMesh::CheckForIntersections 3163ms 2.93% 18.79% 11199ms 10.37% __dynamic_cast 64ms 0.059% 18.85% 11077ms 10.26% AbstractCellProperty::IsSubType (inline) 57ms 0.053% 18.90% 10856ms 10.05% VertexBasedCellPopulation::GetDampingConstant 67ms 0.062% 18.97% 10387ms 9.62% AbstractTargetAreaModifier::UpdateTargetAreas 67ms 0.062% 19.03% 10305ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 17ms 0.016% 19.04% 10179ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1191ms 1.10% 20.15% 9876ms 9.15% std::__new_allocator::allocate (inline) 2751ms 2.55% 22.69% 9796ms 9.07% boost::numeric::ublas::indexing_vector_assign 1309ms 1.21% 23.91% 9262ms 8.58% std::_Rb_tree::_M_erase 0 0% 23.91% 9250ms 8.57% std::allocator_traits::allocate (inline) 0 0% 23.91% 9194ms 8.51% std::_Rb_tree::_M_create_node (inline) 377ms 0.35% 24.26% 9043ms 8.37% VertexMesh::GetNextEdgeGradientOfElementAtNode 816ms 0.76% 25.01% 9026ms 8.36% VertexMesh::ElementIncludesPoint 35ms 0.032% 25.04% 8879ms 8.22% VertexBasedCellPopulation::GetLocationOfCellCentre 809ms 0.75% 25.79% 8786ms 8.14% operator new 79ms 0.073% 25.87% 8604ms 7.97% Cell::GetMutationState 0 0% 25.87% 8587ms 7.95% std::_Rb_tree::_M_get_node (inline) 216ms 0.2% 26.07% 8501ms 7.87% std::_Rb_tree::~_Rb_tree (inline) 504ms 0.47% 26.53% 8471ms 7.84% VertexMesh::GetCentroidOfElement 0 0% 26.53% 8293ms 7.68% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.53% 8063ms 7.47% std::_Rb_tree::_Alloc_node::operator() (inline) 260ms 0.24% 26.77% 8037ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 26.77% 8035ms 7.44% std::set::~set (inline) 0 0% 26.77% 8010ms 7.42% std::allocator_traits::deallocate (inline) 0 0% 26.77% 7964ms 7.37% std::_Rb_tree::_M_put_node (inline) 3036ms 2.81% 29.58% 7805ms 7.23% __GI___libc_free 3056ms 2.83% 32.41% 7777ms 7.20% __GI___libc_malloc 1234ms 1.14% 33.56% 7451ms 6.90% AbstractMesh::GetDistanceBetweenNodes 13ms 0.012% 33.57% 7420ms 6.87% MutableVertexMesh::RemoveDeletedNodesAndElements 454ms 0.42% 33.99% 7076ms 6.55% std::map::operator[] (partial-inline) 100ms 0.093% 34.08% 6580ms 6.09% std::_Rb_tree::_Rb_tree (partial-inline) 127ms 0.12% 34.20% 6432ms 5.96% SimpleWntCellCycleModel::GetWntLevel 6381ms 5.91% 40.11% 6381ms 5.91% boost::numeric::ublas::c_vector::operator() 6320ms 5.85% 45.96% 6320ms 5.85% __strcmp_avx2 649ms 0.6% 46.56% 6239ms 5.78% std::_Rb_tree::_M_copy (inline) 129ms 0.12% 46.68% 6197ms 5.74% WntConcentration::GetWntLevel 8ms 0.0074% 46.69% 6133ms 5.68% std::set::set (inline) 2728ms 2.53% 49.21% 5574ms 5.16% __cxxabiv1::__si_class_type_info::__do_dyncast 2410ms 2.23% 51.45% 5538ms 5.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.45% 5334ms 4.94% std::set::insert (inline) 690ms 0.64% 52.08% 5327ms 4.93% std::_Rb_tree::_M_clone_node (inline) 27ms 0.025% 52.11% 5310ms 4.92% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 52.14% 5142ms 4.76% EdgeHelper::RemoveDeletedEdges 1481ms 1.37% 53.51% 4898ms 4.54% boost::numeric::ublas::c_vector::operator[] (inline) 31ms 0.029% 53.54% 4860ms 4.50% EdgeHelper::UpdateEdgesMapKey 4445ms 4.12% 57.66% 4756ms 4.40% _int_free 213ms 0.2% 57.86% 4623ms 4.28% MutableElement::ResetIndex 1ms 0.00093% 57.86% 4594ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 64ms 0.059% 57.92% 4549ms 4.21% std::set_intersection (inline) 521ms 0.48% 58.40% 4538ms 4.20% std::_Rb_tree::_M_insert_ (inline) 279ms 0.26% 58.66% 4485ms 4.15% std::__set_intersection 0 0% 58.66% 4463ms 4.13% std::_Rb_tree::lower_bound (inline) 0 0% 58.66% 4463ms 4.13% std::map::lower_bound (inline) 4085ms 3.78% 62.44% 4085ms 3.78% boost::numeric::ublas::same_impl_ex 47ms 0.044% 62.48% 3960ms 3.67% Cell::GetCellProliferativeType 104ms 0.096% 62.58% 3734ms 3.46% AbstractCellPopulation::GetCellUsingLocationIndex 81ms 0.075% 62.65% 3615ms 3.35% AbstractCellProperty::IsType (inline) 5ms 0.0046% 62.66% 3561ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 864ms 0.8% 63.46% 3340ms 3.09% AbstractElement::GetNodeLocation 0 0% 63.46% 3237ms 3.00% std::insert_iterator::operator= (inline) 59ms 0.055% 63.51% 3139ms 2.91% Cell::SetCellProliferativeType 2161ms 2.00% 65.51% 3052ms 2.83% _int_malloc 38ms 0.035% 65.55% 2912ms 2.70% std::_Rb_tree::erase 1ms 0.00093% 65.55% 2906ms 2.69% std::_Rb_tree::_M_insert_unique_ (inline) 605ms 0.56% 66.11% 2852ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 479ms 0.44% 66.55% 2679ms 2.48% std::_Rb_tree_const_iterator::operator++ (inline) 2608ms 2.41% 68.97% 2608ms 2.41% std::_Rb_tree::_S_right (inline) 747ms 0.69% 69.66% 2591ms 2.40% AbstractCellProperty::IsSame 45ms 0.042% 69.70% 2502ms 2.32% CellPropertyCollection::HasProperty 0 0% 69.70% 2488ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.70% 2470ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 215ms 0.2% 69.90% 2456ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.00093% 69.90% 2428ms 2.25% std::_Rb_tree::_M_insert_unique 0 0% 69.90% 2392ms 2.21% Cell::HasCellProperty (inline) 0 0% 69.90% 2383ms 2.21% AbstractCellPopulation::WriteResultsToFiles 101ms 0.094% 70.00% 2311ms 2.14% VertexMesh::GetVolumeOfElement 124ms 0.11% 70.11% 2297ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0028% 70.11% 2223ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.027% 70.14% 2201ms 2.04% Cell::GetCellData 205ms 0.19% 70.33% 2195ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 48ms 0.044% 70.37% 2109ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2033ms 1.88% 72.26% 2033ms 1.88% std::_Rb_tree_increment 0 0% 72.26% 1949ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 1303ms 1.21% 73.46% 1944ms 1.80% std::_Rb_tree::equal_range (inline) 2ms 0.0019% 73.47% 1939ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 67ms 0.062% 73.53% 1892ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 436ms 0.4% 73.93% 1844ms 1.71% std::type_info::operator== (inline) 0 0% 73.93% 1751ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0028% 73.93% 1711ms 1.58% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.93% 1711ms 1.58% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 14ms 0.013% 73.95% 1710ms 1.58% VertexMesh::GetSurfaceAreaOfElement 32ms 0.03% 73.98% 1693ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 124ms 0.11% 74.09% 1546ms 1.43% boost::numeric::ublas::vector_reference::operator() (inline) 40ms 0.037% 74.13% 1522ms 1.41% Node::RemoveElement 36ms 0.033% 74.16% 1497ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 13ms 0.012% 74.17% 1493ms 1.38% std::set::erase (inline) 0 0% 74.17% 1482ms 1.37% tcache_get (inline) 1482ms 1.37% 75.55% 1482ms 1.37% tcache_get_n (inline) 84ms 0.078% 75.62% 1473ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 184ms 0.17% 75.79% 1432ms 1.33% CellPropertyCollection::AddProperty 0 0% 75.79% 1409ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.79% 1314ms 1.22% OffLatticeSimulation::ApplyBoundaries 80ms 0.074% 75.87% 1177ms 1.09% std::less::operator() (inline) 1173ms 1.09% 76.95% 1173ms 1.09% Node::rGetLocation 0 0% 76.95% 1166ms 1.08% boost::numeric::ublas::norm_2 (inline) 82ms 0.076% 77.03% 1164ms 1.08% std::_Rb_tree::_M_erase_aux (partial-inline) 493ms 0.46% 77.49% 1155ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1135ms 1.05% 78.54% 1135ms 1.05% std::_Rb_tree_insert_and_rebalance 0 0% 78.54% 1131ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 21ms 0.019% 78.56% 1102ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 903ms 0.84% 79.39% 1097ms 1.02% std::operator< (inline) 88ms 0.081% 79.48% 1046ms 0.97% std::_Rb_tree::find (inline) 11ms 0.01% 79.49% 1037ms 0.96% CellPropertyRegistry::Get 1035ms 0.96% 80.44% 1035ms 0.96% [libchaste_cell_based.so] 1013ms 0.94% 81.38% 1013ms 0.94% [libchaste_mesh.so] 6ms 0.0056% 81.39% 989ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.39% 981ms 0.91% std::_Rb_tree::clear (inline) 977ms 0.9% 82.29% 977ms 0.9% std::vector::size (inline) 0 0% 82.29% 968ms 0.9% std::map::clear (inline) 396ms 0.37% 82.66% 963ms 0.89% Edge::GetMapIndex 151ms 0.14% 82.80% 960ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 82.80% 960ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.80% 925ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0065% 82.81% 925ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 81ms 0.075% 82.88% 918ms 0.85% std::swap_ranges (inline) 137ms 0.13% 83.01% 917ms 0.85% MutableElement::GetNodeLocalIndex 2ms 0.0019% 83.01% 857ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 83.01% 837ms 0.78% std::iter_swap (inline) 837ms 0.78% 83.78% 837ms 0.78% std::swap (inline) 0 0% 83.78% 835ms 0.77% std::map::find (inline) 783ms 0.73% 84.51% 788ms 0.73% boost::detail::sp_counted_base::release 18ms 0.017% 84.53% 776ms 0.72% boost::numeric::ublas::detail::expression_type_check (inline) 165ms 0.15% 84.68% 770ms 0.71% boost::shared_ptr::shared_ptr (inline) 18ms 0.017% 84.70% 760ms 0.7% MutableElement::RegisterWithEdges (inline) 114ms 0.11% 84.80% 756ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 31ms 0.029% 84.83% 751ms 0.7% Edge::AddElement 749ms 0.69% 85.52% 749ms 0.69% Node::GetIndex 0 0% 85.52% 745ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 442ms 0.41% 85.93% 741ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 151ms 0.14% 86.07% 740ms 0.69% boost::numeric::ublas::detail::equals 1ms 0.00093% 86.07% 662ms 0.61% std::_Vector_base::_M_allocate (inline) 97ms 0.09% 86.16% 660ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.16% 660ms 0.61% std::allocator_traits::construct (inline) 30ms 0.028% 86.19% 656ms 0.61% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.19% 656ms 0.61% boost::numeric::ublas::vector::vector (inline) 0 0% 86.19% 634ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.023% 86.21% 634ms 0.59% std::_Rb_tree::_M_insert_node (inline) 632ms 0.59% 86.80% 632ms 0.59% operator delete 27ms 0.025% 86.82% 621ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 86.82% 607ms 0.56% std::_Rb_tree::_M_construct_node (inline) 576ms 0.53% 87.36% 605ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 87.36% 604ms 0.56% vtkPolygon::New 1ms 0.00093% 87.36% 602ms 0.56% vtkPolygon::vtkPolygon 597ms 0.55% 87.91% 597ms 0.55% [libstdc++.so.6.0.33] 34ms 0.031% 87.94% 587ms 0.54% Node::AddElement 6ms 0.0056% 87.95% 555ms 0.51% std::vector::_M_default_append (inline) 549ms 0.51% 88.46% 549ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 88.46% 545ms 0.5% boost::numeric::ublas::norm_inf (inline) 288ms 0.27% 88.72% 545ms 0.5% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 88.72% 541ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)