File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16560ms, 82.31% of 20119ms total Dropped 795 nodes (cum <= 100.59ms) flat flat% sum% cum cum% 0 0% 0% 20077ms 99.79% __libc_start_call_main 0 0% 0% 20077ms 99.79% __libc_start_main_impl 0 0% 0% 20077ms 99.79% _start 0 0% 0% 20058ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20058ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20058ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20058ms 99.70% main 0 0% 0% 20021ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20021ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20021ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19996ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 15480ms 76.94% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10160ms 50.50% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.035% 10050ms 49.95% Cell::ReadyToDivide 5ms 0.025% 0.06% 9974ms 49.58% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.06% 9811ms 48.76% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.065% 0.12% 9803ms 48.73% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.13% 9785ms 48.64% CellCycleModelOdeHandler::SolveOdeToTime 65ms 0.32% 0.45% 9602ms 47.73% AbstractOneStepIvpOdeSolver::InternalSolve 887ms 4.41% 4.86% 8756ms 43.52% RungeKutta4IvpOdeSolver::CalculateNextYValue 3612ms 17.95% 22.81% 7667ms 38.11% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 22.82% 5204ms 25.87% MeshBasedCellPopulation::Update 206ms 1.02% 23.84% 4120ms 20.48% AbstractCellProperty::IsType (inline) 3ms 0.015% 23.86% 4015ms 19.96% Cylindrical2dMesh::ReMesh 567ms 2.82% 26.68% 2828ms 14.06% AbstractCellProperty::IsSame 1ms 0.005% 26.68% 2518ms 12.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 377ms 1.87% 28.56% 2261ms 11.24% std::type_info::operator== (inline) 0 0% 28.56% 2220ms 11.03% MutableMesh::ReMesh 0 0% 28.56% 2207ms 10.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.05% 28.60% 2154ms 10.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.60% 1991ms 9.90% AbstractCellPopulation::WriteResultsToFiles 1908ms 9.48% 38.09% 1908ms 9.48% __strcmp_avx2 821ms 4.08% 42.17% 1876ms 9.32% std::_Rb_tree::_M_lower_bound (inline) 135ms 0.67% 42.84% 1728ms 8.59% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.33% 43.17% 1398ms 6.95% std::_Rb_tree::find (inline) 2ms 0.0099% 43.18% 1155ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 43.22% 1129ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 49ms 0.24% 43.46% 1127ms 5.60% operator new 15ms 0.075% 43.54% 1115ms 5.54% TetrahedralMesh::ImportFromMesher 257ms 1.28% 44.81% 1058ms 5.26% __GI___libc_malloc 8ms 0.04% 44.85% 1055ms 5.24% std::set::insert (inline) 8ms 0.04% 44.89% 1047ms 5.20% std::_Rb_tree::_M_insert_unique 10ms 0.05% 44.94% 1035ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 52ms 0.26% 45.20% 1005ms 5.00% std::__new_allocator::allocate (inline) 0 0% 45.20% 1000ms 4.97% std::allocator_traits::allocate (inline) 0 0% 45.20% 869ms 4.32% std::set::count (inline) 0 0% 45.20% 826ms 4.11% triangulate 0 0% 45.20% 742ms 3.69% delaunay 3ms 0.015% 45.22% 742ms 3.69% divconqdelaunay 2ms 0.0099% 45.23% 737ms 3.66% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.23% 730ms 3.63% AbstractTwoBodyInteractionForce::AddForceContribution 53ms 0.26% 45.49% 716ms 3.56% std::map::operator[] (partial-inline) 413ms 2.05% 47.54% 708ms 3.52% _int_malloc 202ms 1.00% 48.55% 695ms 3.45% __dynamic_cast 0 0% 48.55% 674ms 3.35% std::_Rb_tree::_M_create_node (inline) 668ms 3.32% 51.87% 668ms 3.32% std::_Rb_tree::_S_right (inline) 34ms 0.17% 52.04% 667ms 3.32% std::_Rb_tree::_M_insert_ (inline) 13ms 0.065% 52.10% 663ms 3.30% CellPopulationElementWriter::Visit 641ms 3.19% 55.29% 654ms 3.25% WntCellCycleOdeSystem::CalculateStoppingEvent 12ms 0.06% 55.35% 653ms 3.25% std::less::operator() (inline) 0 0% 55.35% 643ms 3.20% std::_Rb_tree::_M_get_node (inline) 641ms 3.19% 58.53% 641ms 3.19% std::operator< (inline) 20ms 0.099% 58.63% 629ms 3.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.63% 613ms 3.05% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 58.65% 592ms 2.94% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.025% 58.68% 582ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 9ms 0.045% 58.72% 578ms 2.87% Element::Element 0 0% 58.72% 578ms 2.87% std::_Rb_tree::lower_bound (inline) 0 0% 58.72% 578ms 2.87% std::map::lower_bound (inline) 18ms 0.089% 58.81% 561ms 2.79% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.81% 527ms 2.62% std::map::find (inline) 10ms 0.05% 58.86% 508ms 2.52% MutableMesh::ReIndex 10ms 0.05% 58.91% 505ms 2.51% Element::RegisterWithNodes (inline) 2ms 0.0099% 58.92% 502ms 2.50% AbstractCellProperty::IsSubType (inline) 334ms 1.66% 60.58% 501ms 2.49% AbstractCellMutationState::AbstractCellMutationState 8ms 0.04% 60.62% 497ms 2.47% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.06% 60.68% 486ms 2.42% Node::AddElement 19ms 0.094% 60.77% 463ms 2.30% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 60.77% 462ms 2.30% std::ostream::operator<< (inline) 55ms 0.27% 61.05% 461ms 2.29% std::ostream::_M_insert 148ms 0.74% 61.78% 422ms 2.10% __GI___libc_free 14ms 0.07% 61.85% 385ms 1.91% divconqrecurse 156ms 0.78% 62.63% 372ms 1.85% std::_Rb_tree::_M_get_insert_unique_pos 102ms 0.51% 63.13% 366ms 1.82% mergehulls 1ms 0.005% 63.14% 358ms 1.78% std::_Vector_base::_M_allocate (inline) 7ms 0.035% 63.17% 357ms 1.77% std::_Rb_tree::erase 2ms 0.0099% 63.18% 357ms 1.77% std::set::erase (inline) 9ms 0.045% 63.23% 354ms 1.76% Node::RemoveElement 118ms 0.59% 63.82% 351ms 1.74% std::_Rb_tree::_M_erase 164ms 0.82% 64.63% 333ms 1.66% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.11% 64.74% 325ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 14ms 0.07% 64.81% 325ms 1.62% std::__new_allocator::deallocate (inline) 23ms 0.11% 64.92% 323ms 1.61% Element::ResetIndex 3ms 0.015% 64.94% 320ms 1.59% Cell::GetCellProliferativeType 0 0% 64.94% 316ms 1.57% std::allocator_traits::deallocate (inline) 1ms 0.005% 64.94% 314ms 1.56% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 64.96% 313ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.0099% 64.97% 307ms 1.53% Cell::GetMutationState 3ms 0.015% 64.98% 305ms 1.52% NodeLocationWriter::Visit 0 0% 64.98% 302ms 1.50% std::set::~set (inline) 10ms 0.05% 65.03% 296ms 1.47% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 29ms 0.14% 65.18% 293ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.18% 293ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.18% 292ms 1.45% std::_Rb_tree::_M_drop_node (inline) 281ms 1.40% 66.57% 281ms 1.40% std::type_info::name (inline) 274ms 1.36% 67.94% 274ms 1.36% [libchaste_cell_based.so] 207ms 1.03% 68.96% 273ms 1.36% _int_free 14ms 0.07% 69.03% 269ms 1.34% std::num_put::_M_insert_float 15ms 0.075% 69.11% 263ms 1.31% AbstractTetrahedralElement::CalculateJacobian 21ms 0.1% 69.21% 262ms 1.30% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.21% 252ms 1.25% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 69.23% 248ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.045% 69.28% 248ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 243ms 1.21% 70.49% 244ms 1.21% std::vector::operator[] (inline) 12ms 0.06% 70.55% 244ms 1.21% std::vector::push_back (inline) 65ms 0.32% 70.87% 242ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.0099% 70.88% 240ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.005% 70.88% 239ms 1.19% std::set::set (inline) 3ms 0.015% 70.90% 232ms 1.15% alternateaxes 215ms 1.07% 71.97% 229ms 1.14% vertexmedian 0 0% 71.97% 227ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 70ms 0.35% 72.31% 227ms 1.13% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.045% 72.36% 224ms 1.11% std::vector::_M_realloc_insert 23ms 0.11% 72.47% 221ms 1.10% std::_Rb_tree::_M_copy (inline) 10ms 0.05% 72.52% 221ms 1.10% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.035% 72.56% 216ms 1.07% std::__cxx11::collate::do_transform 21ms 0.1% 72.66% 212ms 1.05% AbstractTetrahedralElement::RefreshJacobian 9ms 0.045% 72.71% 210ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 43ms 0.21% 72.92% 202ms 1.00% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.025% 72.95% 201ms 1% ___vsnprintf 0 0% 72.95% 196ms 0.97% OffLatticeSimulation::ApplyBoundaries 14ms 0.07% 73.02% 196ms 0.97% __printf_buffer 0 0% 73.02% 196ms 0.97% __vsnprintf_internal (inline) 58ms 0.29% 73.30% 196ms 0.97% std::_Rb_tree::_M_clone_node (inline) 140ms 0.7% 74.00% 194ms 0.96% malloc_consolidate 142ms 0.71% 74.71% 193ms 0.96% AbstractElement::GetNodeGlobalIndex 18ms 0.089% 74.79% 193ms 0.96% TetrahedralMesh::Clear 14ms 0.07% 74.86% 184ms 0.91% Element::MarkAsDeleted 2ms 0.0099% 74.87% 183ms 0.91% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.87% 181ms 0.9% AbstractCentreBasedCellPopulation::GetDampingConstant 175ms 0.87% 75.74% 175ms 0.87% Node::GetIndex 65ms 0.32% 76.07% 172ms 0.85% AbstractElement::GetNodeLocation 2ms 0.0099% 76.08% 172ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 167ms 0.83% 76.91% 167ms 0.83% std::_Rb_tree_insert_and_rebalance 11ms 0.055% 76.96% 166ms 0.83% __printf_fp_l_buffer 0 0% 76.96% 166ms 0.83% __printf_fp_spec (inline) 2ms 0.0099% 76.97% 162ms 0.81% CellProliferativeTypesWriter::VisitCell 158ms 0.79% 77.76% 158ms 0.79% incircle 158ms 0.79% 78.54% 158ms 0.79% std::vector::size (inline) 1ms 0.005% 78.55% 157ms 0.78% CellPropertyCollection::HasProperty 0 0% 78.55% 155ms 0.77% Cell::HasCellProperty (inline) 61ms 0.3% 78.85% 155ms 0.77% __printf_fp_buffer_1 1ms 0.005% 78.86% 152ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.02% 78.88% 150ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 148ms 0.74% 79.61% 148ms 0.74% unlink_chunk 0 0% 79.61% 142ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.005% 79.62% 142ms 0.71% boost::numeric::ublas::vector_assign (inline) 0 0% 79.62% 140ms 0.7% OutputFileHandler::OpenOutputFile 87ms 0.43% 80.05% 139ms 0.69% std::_Rb_tree::equal_range (inline) 2ms 0.0099% 80.06% 135ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 44ms 0.22% 80.28% 134ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 7ms 0.035% 80.31% 134ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 13ms 0.065% 80.38% 134ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.005% 80.38% 131ms 0.65% Cell::SetCellProliferativeType 0 0% 80.38% 124ms 0.62% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 16ms 0.08% 80.46% 119ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 80.46% 119ms 0.59% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.46% 115ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 70ms 0.35% 80.81% 115ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 104ms 0.52% 81.33% 113ms 0.56% vertexsort 25ms 0.12% 81.45% 112ms 0.56% TetrahedralMesh::EdgesEnd 38ms 0.19% 81.64% 109ms 0.54% boost::numeric::ublas::indexing_vector_assign 0 0% 81.64% 108ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 23ms 0.11% 81.75% 108ms 0.54% std::num_put::_M_insert_int 7ms 0.035% 81.79% 104ms 0.52% Node::~Node 4ms 0.02% 81.81% 103ms 0.51% MeshBasedCellPopulation::SpringsEnd (inline) 101ms 0.5% 82.31% 101ms 0.5% std::_Rb_tree_rebalance_for_erase