File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 82327ms, 88.65% of 92870ms total Dropped 1059 nodes (cum <= 464.35ms) flat flat% sum% cum cum% 0 0% 0% 92418ms 99.51% __libc_start_call_main 0 0% 0% 92418ms 99.51% __libc_start_main_impl 0 0% 0% 92418ms 99.51% _start 0 0% 0% 92400ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 92400ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 92400ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 92400ms 99.49% main 0 0% 0% 92364ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 92364ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 92364ms 99.46% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 92357ms 99.45% AbstractCellBasedSimulation::Solve 22ms 0.024% 0.024% 40886ms 44.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.024% 38767ms 41.74% AbstractCellBasedSimulation::UpdateCellPopulation 18ms 0.019% 0.043% 37598ms 40.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.14% 0.18% 36540ms 39.35% AbstractNumericalMethod::ComputeForcesIncludingDamping 392ms 0.42% 0.6% 25286ms 27.23% NagaiHondaForce::AddForceContribution 1ms 0.0011% 0.61% 24058ms 25.91% VertexBasedCellPopulation::Update 2ms 0.0022% 0.61% 23982ms 25.82% MutableVertexMesh::ReMesh 14560ms 15.68% 16.29% 22789ms 24.54% Cylindrical2dVertexMesh::GetVectorFromAtoB 67ms 0.072% 16.36% 17407ms 18.74% Cell::ReadyToDivide 44ms 0.047% 16.40% 16214ms 17.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 427ms 0.46% 16.86% 14035ms 15.11% boost::numeric::ublas::c_vector::c_vector (partial-inline) 153ms 0.16% 17.03% 13815ms 14.88% SimpleWntCellCycleModel::UpdateCellCyclePhase 129ms 0.14% 17.17% 13744ms 14.80% CellPropertyCollection::GetPropertiesType (inline) 344ms 0.37% 17.54% 12453ms 13.41% boost::numeric::ublas::vector_assign (inline) 154ms 0.17% 17.70% 12172ms 13.11% MutableVertexMesh::CheckForIntersections 3728ms 4.01% 21.72% 11364ms 12.24% __dynamic_cast 81ms 0.087% 21.81% 11231ms 12.09% AbstractCellProperty::IsSubType (inline) 454ms 0.49% 22.29% 10804ms 11.63% VertexBasedCellPopulation::GetDampingConstant 73ms 0.079% 22.37% 10302ms 11.09% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.043% 22.42% 10195ms 10.98% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.027% 22.44% 10193ms 10.98% AbstractCellBasedSimulation::DoCellBirth 2519ms 2.71% 25.16% 9248ms 9.96% boost::numeric::ublas::indexing_vector_assign 801ms 0.86% 26.02% 9004ms 9.70% VertexMesh::ElementIncludesPoint 442ms 0.48% 26.49% 8890ms 9.57% VertexMesh::GetNextEdgeGradientOfElementAtNode 87ms 0.094% 26.59% 8835ms 9.51% Cell::GetMutationState 30ms 0.032% 26.62% 8570ms 9.23% VertexBasedCellPopulation::GetLocationOfCellCentre 485ms 0.52% 27.14% 8109ms 8.73% VertexMesh::GetCentroidOfElement 22ms 0.024% 27.17% 7387ms 7.95% MutableVertexMesh::RemoveDeletedNodesAndElements 445ms 0.48% 27.65% 7179ms 7.73% std::map::operator[] (partial-inline) 1252ms 1.35% 28.99% 7025ms 7.56% AbstractMesh::GetDistanceBetweenNodes 2541ms 2.74% 31.73% 6250ms 6.73% std::_Rb_tree::_M_lower_bound (inline) 107ms 0.12% 31.84% 6223ms 6.70% SimpleWntCellCycleModel::GetWntLevel 6186ms 6.66% 38.51% 6186ms 6.66% boost::numeric::ublas::c_vector::operator() 6019ms 6.48% 44.99% 6019ms 6.48% __strcmp_avx2 121ms 0.13% 45.12% 6015ms 6.48% WntConcentration::GetWntLevel 26ms 0.028% 45.14% 5343ms 5.75% MutableVertexMesh::RemoveDeletedNodes 2620ms 2.82% 47.97% 5217ms 5.62% __cxxabiv1::__si_class_type_info::__do_dyncast 34ms 0.037% 48.00% 5191ms 5.59% EdgeHelper::RemoveDeletedEdges 35ms 0.038% 48.04% 4896ms 5.27% EdgeHelper::UpdateEdgesMapKey 1453ms 1.56% 49.60% 4756ms 5.12% boost::numeric::ublas::c_vector::operator[] (inline) 2ms 0.0022% 49.61% 4508ms 4.85% AbstractCellBasedSimulation::DoCellRemoval (inline) 178ms 0.19% 49.80% 4508ms 4.85% MutableElement::ResetIndex 0 0% 49.80% 4474ms 4.82% std::_Rb_tree::lower_bound (inline) 0 0% 49.80% 4474ms 4.82% std::map::lower_bound (inline) 330ms 0.36% 50.15% 4369ms 4.70% std::__new_allocator::allocate (inline) 372ms 0.4% 50.55% 4251ms 4.58% operator new 46ms 0.05% 50.60% 4018ms 4.33% Cell::GetCellProliferativeType 3947ms 4.25% 54.85% 3947ms 4.25% boost::numeric::ublas::same_impl_ex 0 0% 54.85% 3866ms 4.16% std::allocator_traits::allocate (inline) 105ms 0.11% 54.97% 3841ms 4.14% AbstractCellPopulation::GetCellUsingLocationIndex 1310ms 1.41% 56.38% 3831ms 4.13% __GI___libc_malloc 0 0% 56.38% 3764ms 4.05% std::_Rb_tree::_M_create_node (inline) 60ms 0.065% 56.44% 3755ms 4.04% AbstractCellProperty::IsType (inline) 7ms 0.0075% 56.45% 3455ms 3.72% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 72ms 0.078% 56.53% 3258ms 3.51% Cell::SetCellProliferativeType 0 0% 56.53% 3224ms 3.47% std::_Rb_tree::_M_get_node (inline) 809ms 0.87% 57.40% 3117ms 3.36% AbstractElement::GetNodeLocation 3068ms 3.30% 60.70% 3068ms 3.30% std::_Rb_tree::_S_right (inline) 34ms 0.037% 60.74% 2842ms 3.06% std::_Rb_tree::erase 607ms 0.65% 61.39% 2799ms 3.01% boost::numeric::ublas::vector_binary::size (inline) 921ms 0.99% 62.38% 2762ms 2.97% AbstractCellProperty::IsSame 984ms 1.06% 63.44% 2709ms 2.92% __GI___libc_free 873ms 0.94% 64.38% 2690ms 2.90% std::_Rb_tree::_M_erase 0 0% 64.38% 2619ms 2.82% std::set::insert (inline) 1ms 0.0011% 64.38% 2618ms 2.82% std::_Rb_tree::_M_insert_unique 0 0% 64.38% 2617ms 2.82% std::_Rb_tree::_Alloc_node::operator() (inline) 48ms 0.052% 64.44% 2516ms 2.71% CellPropertyCollection::HasProperty 0 0% 64.44% 2449ms 2.64% std::_Rb_tree::_M_drop_node (inline) 259ms 0.28% 64.72% 2422ms 2.61% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 64.72% 2410ms 2.60% Cell::HasCellProperty (inline) 0 0% 64.72% 2386ms 2.57% boost::numeric::ublas::c_vector::assign (inline) 0 0% 64.72% 2380ms 2.56% AbstractCellPopulation::WriteResultsToFiles 0 0% 64.72% 2369ms 2.55% boost::numeric::ublas::c_vector::operator-= (inline) 91ms 0.098% 64.81% 2323ms 2.50% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 25ms 0.027% 64.84% 2307ms 2.48% Cell::GetCellData 128ms 0.14% 64.98% 2241ms 2.41% std::__new_allocator::deallocate (inline) 350ms 0.38% 65.35% 2235ms 2.41% std::_Rb_tree::_M_insert_ (inline) 0 0% 65.35% 2212ms 2.38% std::allocator_traits::deallocate (inline) 40ms 0.043% 65.40% 2210ms 2.38% std::_Rb_tree::_M_emplace_hint_unique 82ms 0.088% 65.49% 2206ms 2.38% VertexMesh::GetVolumeOfElement 6ms 0.0065% 65.49% 2173ms 2.34% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.49% 2167ms 2.33% std::_Rb_tree::_M_put_node (inline) 262ms 0.28% 65.77% 2166ms 2.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 180ms 0.19% 65.97% 2113ms 2.28% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 65.97% 1957ms 2.11% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0011% 65.97% 1949ms 2.10% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1321ms 1.42% 67.39% 1927ms 2.07% std::_Rb_tree::equal_range (inline) 13ms 0.014% 67.41% 1924ms 2.07% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 67.41% 1924ms 2.07% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1168ms 1.26% 68.66% 1915ms 2.06% _int_malloc 449ms 0.48% 69.15% 1841ms 1.98% std::type_info::operator== (inline) 198ms 0.21% 69.36% 1838ms 1.98% std::_Rb_tree::~_Rb_tree (inline) 1838ms 1.98% 71.34% 1838ms 1.98% std::_Rb_tree_increment 180ms 0.19% 71.53% 1817ms 1.96% std::_Rb_tree::find (inline) 62ms 0.067% 71.60% 1810ms 1.95% MutableVertexMesh::CheckForSwapsFromShortEdges 89ms 0.096% 71.70% 1753ms 1.89% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0011% 71.70% 1748ms 1.88% VertexMeshWriter::WriteVtkUsingMesh 1552ms 1.67% 73.37% 1719ms 1.85% _int_free 26ms 0.028% 73.40% 1677ms 1.81% VertexMesh::GetSurfaceAreaOfElement 34ms 0.037% 73.43% 1650ms 1.78% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 177ms 0.19% 73.62% 1621ms 1.75% CellPropertyCollection::AddProperty 119ms 0.13% 73.75% 1582ms 1.70% std::_Rb_tree::_M_copy (inline) 227ms 0.24% 74.00% 1550ms 1.67% NagaiHondaForce::GetAdhesionParameter 47ms 0.051% 74.05% 1501ms 1.62% Node::RemoveElement 13ms 0.014% 74.06% 1461ms 1.57% std::set::erase (inline) 478ms 0.51% 74.58% 1460ms 1.57% std::_Rb_tree::_M_clone_node (inline) 40ms 0.043% 74.62% 1445ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 86ms 0.093% 74.71% 1410ms 1.52% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 126ms 0.14% 74.85% 1391ms 1.50% boost::numeric::ublas::vector_reference::operator() (inline) 16ms 0.017% 74.86% 1347ms 1.45% std::set::set (inline) 0 0% 74.86% 1343ms 1.45% std::set::~set (inline) 0 0% 74.86% 1342ms 1.45% OffLatticeSimulation::ApplyBoundaries 0 0% 74.86% 1285ms 1.38% boost::numeric::ublas::vector_binary::operator() (inline) 209ms 0.23% 75.09% 1277ms 1.38% std::less::operator() (inline) 0 0% 75.09% 1164ms 1.25% boost::numeric::ublas::norm_2 (inline) 0 0% 75.09% 1147ms 1.24% std::_Rb_tree::_Auto_node::_Auto_node (inline) 485ms 0.52% 75.61% 1143ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 24ms 0.026% 75.64% 1119ms 1.20% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1109ms 1.19% 76.83% 1109ms 1.19% Node::rGetLocation 86ms 0.093% 76.92% 1082ms 1.17% std::_Rb_tree::_M_erase_aux (partial-inline) 877ms 0.94% 77.87% 1068ms 1.15% std::operator< (inline) 1ms 0.0011% 77.87% 1053ms 1.13% std::_Rb_tree::clear (inline) 31ms 0.033% 77.90% 1044ms 1.12% CellPropertyRegistry::Get 0 0% 77.90% 1036ms 1.12% std::map::clear (inline) 11ms 0.012% 77.91% 1006ms 1.08% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 18ms 0.019% 77.93% 1002ms 1.08% boost::numeric::ublas::detail::expression_type_check (inline) 124ms 0.13% 78.07% 989ms 1.06% boost::detail::shared_count::~shared_count (inline) 0 0% 78.07% 989ms 1.06% boost::shared_ptr::~shared_ptr (inline) 160ms 0.17% 78.24% 973ms 1.05% boost::numeric::ublas::detail::equals 972ms 1.05% 79.29% 972ms 1.05% std::vector::size (inline) 398ms 0.43% 79.71% 926ms 1% Edge::GetMapIndex 0 0% 79.71% 905ms 0.97% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0043% 79.72% 905ms 0.97% boost::numeric::ublas::c_vector::swap (inline) 901ms 0.97% 80.69% 901ms 0.97% std::_Rb_tree_insert_and_rebalance 66ms 0.071% 80.76% 901ms 0.97% std::swap_ranges (inline) 0 0% 80.76% 888ms 0.96% std::map::find (inline) 884ms 0.95% 81.71% 884ms 0.95% [libchaste_mesh.so] 0 0% 81.71% 849ms 0.91% VertexMeshWriter::MakeVtkMesh 0 0% 81.71% 838ms 0.9% std::set::count (inline) 0 0% 81.71% 835ms 0.9% std::iter_swap (inline) 835ms 0.9% 82.61% 835ms 0.9% std::swap (inline) 826ms 0.89% 83.50% 831ms 0.89% boost::detail::sp_counted_base::release 829ms 0.89% 84.39% 829ms 0.89% [libchaste_cell_based.so] 134ms 0.14% 84.54% 822ms 0.89% MutableElement::GetNodeLocalIndex 123ms 0.13% 84.67% 779ms 0.84% boost::numeric::ublas::c_vector::operator= (inline) 142ms 0.15% 84.82% 777ms 0.84% boost::shared_ptr::shared_ptr (inline) 19ms 0.02% 84.84% 768ms 0.83% MutableElement::RegisterWithEdges (inline) 0 0% 84.84% 762ms 0.82% boost::numeric::ublas::norm_inf (inline) 382ms 0.41% 85.25% 762ms 0.82% boost::numeric::ublas::vector_norm_inf::apply (inline) 24ms 0.026% 85.28% 761ms 0.82% Edge::AddElement 0 0% 85.28% 739ms 0.8% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.28% 722ms 0.78% std::_Rb_tree::_Auto_node::_M_insert (inline) 31ms 0.033% 85.31% 722ms 0.78% std::_Rb_tree::_M_insert_node (inline) 675ms 0.73% 86.04% 675ms 0.73% Node::GetIndex 0 0% 86.04% 639ms 0.69% std::_Vector_base::_M_allocate (inline) 611ms 0.66% 86.70% 635ms 0.68% boost::detail::shared_count::shared_count (inline) 0 0% 86.70% 616ms 0.66% vtkPolygon::New 3ms 0.0032% 86.70% 616ms 0.66% vtkPolygon::vtkPolygon 7ms 0.0075% 86.71% 601ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.71% 601ms 0.65% std::allocator_traits::construct (inline) 34ms 0.037% 86.75% 594ms 0.64% MutableElement::RegisterWithNodes (inline) 32ms 0.034% 86.78% 554ms 0.6% Node::AddElement 0 0% 86.78% 541ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.78% 540ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.78% 535ms 0.58% tcache_get (inline) 535ms 0.58% 87.36% 535ms 0.58% tcache_get_n (inline) 6ms 0.0065% 87.36% 531ms 0.57% std::vector::_M_default_append (inline) 18ms 0.019% 87.38% 521ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.38% 521ms 0.56% boost::numeric::ublas::vector::vector (inline) 513ms 0.55% 87.93% 513ms 0.55% boost::shared_ptr::operator-> (inline) 0 0% 87.93% 495ms 0.53% std::map::~map (inline) 25ms 0.027% 87.96% 492ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 291ms 0.31% 88.28% 490ms 0.53% CellPropertyCollection::GetProperty 346ms 0.37% 88.65% 471ms 0.51% malloc_consolidate