File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16552ms, 84.89% of 19499ms total Dropped 819 nodes (cum <= 97.50ms) flat flat% sum% cum cum% 0 0% 0% 19455ms 99.77% __libc_start_call_main 0 0% 0% 19455ms 99.77% __libc_start_main_impl 0 0% 0% 19455ms 99.77% _start 0 0% 0% 19433ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19433ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19433ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19433ms 99.66% main 0 0% 0% 19390ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19390ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19390ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19362ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14793ms 75.87% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 9328ms 47.84% AbstractCellBasedSimulation::DoCellBirth 7ms 0.036% 0.046% 9225ms 47.31% Cell::ReadyToDivide 5ms 0.026% 0.072% 9134ms 46.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.087% 8980ms 46.05% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.13% 8969ms 46.00% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.026% 0.15% 8959ms 45.95% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.4% 0.55% 8767ms 44.96% AbstractOneStepIvpOdeSolver::InternalSolve 1033ms 5.30% 5.85% 7844ms 40.23% RungeKutta4IvpOdeSolver::CalculateNextYValue 2700ms 13.85% 19.70% 6611ms 33.90% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.70% 5352ms 27.45% MeshBasedCellPopulation::Update 3ms 0.015% 19.72% 4143ms 21.25% Cylindrical2dMesh::ReMesh 64ms 0.33% 20.05% 3939ms 20.20% AbstractCellProperty::IsType (inline) 321ms 1.65% 21.69% 2595ms 13.31% AbstractCellProperty::IsSame 0 0% 21.69% 2555ms 13.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 234ms 1.20% 22.89% 2274ms 11.66% std::type_info::operator== (inline) 1ms 0.0051% 22.90% 2232ms 11.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 22.90% 2222ms 11.40% MutableMesh::ReMesh 7ms 0.036% 22.93% 2180ms 11.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 2171ms 11.13% 34.07% 2171ms 11.13% __strcmp_avx2 0 0% 34.07% 2008ms 10.30% AbstractCellPopulation::WriteResultsToFiles 789ms 4.05% 38.11% 1932ms 9.91% std::_Rb_tree::_M_lower_bound (inline) 174ms 0.89% 39.01% 1693ms 8.68% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.32% 39.33% 1416ms 7.26% std::_Rb_tree::find (inline) 1ms 0.0051% 39.33% 1166ms 5.98% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 39.35% 1147ms 5.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.077% 39.43% 1117ms 5.73% TetrahedralMesh::ImportFromMesher 6ms 0.031% 39.46% 1029ms 5.28% MeshBasedCellPopulation::SpringIterator::operator++ 33ms 0.17% 39.63% 1023ms 5.25% operator new 11ms 0.056% 39.68% 979ms 5.02% std::set::insert (inline) 243ms 1.25% 40.93% 977ms 5.01% __GI___libc_malloc 15ms 0.077% 41.01% 968ms 4.96% std::_Rb_tree::_M_insert_unique 51ms 0.26% 41.27% 888ms 4.55% std::__new_allocator::allocate (inline) 0 0% 41.27% 882ms 4.52% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.27% 871ms 4.47% triangulate 0 0% 41.27% 857ms 4.40% std::set::count (inline) 0 0% 41.27% 789ms 4.05% delaunay 3ms 0.015% 41.29% 785ms 4.03% divconqdelaunay 769ms 3.94% 45.23% 769ms 3.94% std::_Rb_tree::_S_right (inline) 5ms 0.026% 45.26% 755ms 3.87% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 62ms 0.32% 45.58% 748ms 3.84% std::map::operator[] (partial-inline) 731ms 3.75% 49.33% 731ms 3.75% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 49.33% 707ms 3.63% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.046% 49.37% 707ms 3.63% CellPopulationElementWriter::Visit 196ms 1.01% 50.38% 691ms 3.54% __dynamic_cast 17ms 0.087% 50.46% 667ms 3.42% std::less::operator() (inline) 373ms 1.91% 52.38% 652ms 3.34% _int_malloc 650ms 3.33% 55.71% 650ms 3.33% std::operator< (inline) 22ms 0.11% 55.82% 639ms 3.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.036% 55.86% 623ms 3.20% CellPropertyCollection::GetPropertiesType (inline) 20ms 0.1% 55.96% 606ms 3.11% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.036% 56.00% 604ms 3.10% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.00% 602ms 3.09% std::_Rb_tree::_M_create_node (inline) 0 0% 56.00% 593ms 3.04% std::_Rb_tree::lower_bound (inline) 0 0% 56.00% 593ms 3.04% std::map::lower_bound (inline) 0 0% 56.00% 584ms 3.00% std::_Rb_tree::_M_get_node (inline) 12ms 0.062% 56.06% 573ms 2.94% MutableMesh::ReIndex 25ms 0.13% 56.19% 569ms 2.92% std::_Rb_tree::_M_insert_ (inline) 9ms 0.046% 56.23% 563ms 2.89% Element::Element 0 0% 56.23% 553ms 2.84% std::map::find (inline) 9ms 0.046% 56.28% 532ms 2.73% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 56.28% 531ms 2.72% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.021% 56.30% 508ms 2.61% AbstractCellProperty::IsSubType (inline) 10ms 0.051% 56.35% 485ms 2.49% Element::RegisterWithNodes (inline) 11ms 0.056% 56.41% 477ms 2.45% Node::AddElement 1ms 0.0051% 56.41% 470ms 2.41% std::ostream::operator<< (inline) 63ms 0.32% 56.74% 467ms 2.39% std::ostream::_M_insert 15ms 0.077% 56.81% 460ms 2.36% Cylindrical2dMesh::ReconstructCylindricalMesh 123ms 0.63% 57.44% 449ms 2.30% __GI___libc_free 299ms 1.53% 58.98% 428ms 2.19% AbstractCellMutationState::AbstractCellMutationState 10ms 0.051% 59.03% 425ms 2.18% std::_Rb_tree::erase 0 0% 59.03% 425ms 2.18% std::set::erase (inline) 14ms 0.072% 59.10% 416ms 2.13% Node::RemoveElement 31ms 0.16% 59.26% 385ms 1.97% Element::ResetIndex 128ms 0.66% 59.92% 384ms 1.97% std::_Rb_tree::_M_get_insert_unique_pos 107ms 0.55% 60.46% 383ms 1.96% std::_Rb_tree::_M_erase 12ms 0.062% 60.53% 370ms 1.90% divconqrecurse 8ms 0.041% 60.57% 363ms 1.86% std::__new_allocator::deallocate (inline) 0 0% 60.57% 359ms 1.84% std::allocator_traits::deallocate (inline) 7ms 0.036% 60.60% 356ms 1.83% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 182ms 0.93% 61.54% 352ms 1.81% __cxxabiv1::__si_class_type_info::__do_dyncast 93ms 0.48% 62.01% 349ms 1.79% mergehulls 0 0% 62.01% 347ms 1.78% std::_Rb_tree::_M_drop_node (inline) 28ms 0.14% 62.16% 345ms 1.77% std::_Rb_tree::~_Rb_tree (inline) 339ms 1.74% 63.90% 339ms 1.74% [libchaste_cell_based.so] 3ms 0.015% 63.91% 330ms 1.69% Cell::GetMutationState 261ms 1.34% 65.25% 324ms 1.66% _int_free 2ms 0.01% 65.26% 321ms 1.65% Cell::GetCellProliferativeType 0 0% 65.26% 315ms 1.62% std::set::~set (inline) 4ms 0.021% 65.28% 314ms 1.61% LegacyCellProliferativeTypesWriter::VisitCell 6ms 0.031% 65.31% 304ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.31% 303ms 1.55% std::_Rb_tree::_M_put_node (inline) 1ms 0.0051% 65.32% 299ms 1.53% std::_Vector_base::_M_allocate (inline) 289ms 1.48% 66.80% 292ms 1.50% std::vector::operator[] (inline) 35ms 0.18% 66.98% 288ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.98% 288ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 66.99% 281ms 1.44% NodeLocationWriter::Visit 4ms 0.021% 67.01% 270ms 1.38% alternateaxes 17ms 0.087% 67.10% 268ms 1.37% std::vector::push_back (inline) 236ms 1.21% 68.31% 265ms 1.36% vertexmedian 18ms 0.092% 68.40% 257ms 1.32% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.1% 68.50% 256ms 1.31% AbstractTetrahedralElement::CalculateJacobian 20ms 0.1% 68.60% 255ms 1.31% std::num_put::_M_insert_float 6ms 0.031% 68.63% 253ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 13ms 0.067% 68.70% 251ms 1.29% std::_Rb_tree::_M_erase_aux (inline) 102ms 0.52% 69.22% 240ms 1.23% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 69.24% 240ms 1.23% std::set::set (inline) 23ms 0.12% 69.36% 239ms 1.23% std::vector::_M_realloc_insert 83ms 0.43% 69.78% 238ms 1.22% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 69ms 0.35% 70.14% 237ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 8ms 0.041% 70.18% 232ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 70.18% 222ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.18% 222ms 1.14% MeshBasedCellPopulation::GetDampingConstant 7ms 0.036% 70.21% 220ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 13ms 0.067% 70.28% 210ms 1.08% Element::MarkAsDeleted 12ms 0.062% 70.34% 210ms 1.08% std::_Rb_tree::_M_copy (inline) 4ms 0.021% 70.36% 208ms 1.07% std::__cxx11::collate::do_transform 0 0% 70.36% 207ms 1.06% TetrahedralMesh::RefreshJacobianCachedData 0 0% 70.36% 203ms 1.04% OffLatticeSimulation::ApplyBoundaries 1ms 0.0051% 70.37% 201ms 1.03% ___vsnprintf 0 0% 70.37% 200ms 1.03% __vsnprintf_internal (inline) 138ms 0.71% 71.08% 197ms 1.01% AbstractElement::GetNodeGlobalIndex 13ms 0.067% 71.14% 197ms 1.01% TetrahedralMesh::Clear 19ms 0.097% 71.24% 196ms 1.01% __printf_buffer 67ms 0.34% 71.58% 196ms 1.01% std::_Rb_tree::_M_clone_node (inline) 27ms 0.14% 71.72% 194ms 0.99% AbstractTetrahedralElement::RefreshJacobian 5ms 0.026% 71.75% 193ms 0.99% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.046% 71.79% 189ms 0.97% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.021% 71.81% 175ms 0.9% CellPropertyCollection::HasProperty 117ms 0.6% 72.41% 173ms 0.89% std::_Rb_tree::equal_range (inline) 0 0% 72.41% 171ms 0.88% Cell::HasCellProperty (inline) 5ms 0.026% 72.44% 170ms 0.87% __printf_fp_l_buffer 0 0% 72.44% 170ms 0.87% __printf_fp_spec (inline) 3ms 0.015% 72.45% 169ms 0.87% CellProliferativeTypesWriter::VisitCell 168ms 0.86% 73.32% 168ms 0.86% incircle 2ms 0.01% 73.33% 166ms 0.85% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 163ms 0.84% 74.16% 163ms 0.84% Node::GetIndex 72ms 0.37% 74.53% 160ms 0.82% __printf_fp_buffer_1 111ms 0.57% 75.10% 160ms 0.82% malloc_consolidate 11ms 0.056% 75.16% 160ms 0.82% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 154ms 0.79% 75.95% 154ms 0.79% std::_Rb_tree_insert_and_rebalance 151ms 0.77% 76.72% 151ms 0.77% std::type_info::name (inline) 151ms 0.77% 77.50% 151ms 0.77% unlink_chunk 61ms 0.31% 77.81% 150ms 0.77% AbstractElement::GetNodeLocation 51ms 0.26% 78.07% 150ms 0.77% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 37ms 0.19% 78.26% 146ms 0.75% TetrahedralMesh::EdgesEnd 2ms 0.01% 78.27% 145ms 0.74% boost::numeric::ublas::vector_assign (inline) 5ms 0.026% 78.30% 144ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.0051% 78.30% 141ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 91ms 0.47% 78.77% 137ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 130ms 0.67% 79.43% 135ms 0.69% vertexsort 12ms 0.062% 79.50% 134ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 49ms 0.25% 79.75% 133ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 133ms 0.68% 80.43% 133ms 0.68% std::vector::size (inline) 19ms 0.097% 80.53% 132ms 0.68% boost::detail::shared_count::~shared_count (inline) 0 0% 80.53% 132ms 0.68% boost::shared_ptr::~shared_ptr (inline) 41ms 0.21% 80.74% 131ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 129ms 0.66% 81.40% 129ms 0.66% AbstractCellMutationState::~AbstractCellMutationState 10ms 0.051% 81.45% 125ms 0.64% Node::~Node 123ms 0.63% 82.08% 123ms 0.63% [libchaste_crypt.so] 1ms 0.0051% 82.09% 121ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.01% 82.10% 121ms 0.62% Cell::SetCellProliferativeType 8ms 0.041% 82.14% 120ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 120ms 0.62% 82.75% 120ms 0.62% std::_Rb_tree_increment 3ms 0.015% 82.77% 118ms 0.61% OutputFileHandler::OpenOutputFile 1ms 0.0051% 82.77% 113ms 0.58% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 82.77% 111ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 82.78% 111ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 30ms 0.15% 82.94% 111ms 0.57% boost::numeric::ublas::indexing_vector_assign 108ms 0.55% 83.49% 108ms 0.55% std::_Rb_tree_rebalance_for_erase 47ms 0.24% 83.73% 104ms 0.53% boost::shared_ptr::shared_ptr (inline) 2ms 0.01% 83.74% 103ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 96ms 0.49% 84.24% 103ms 0.53% boost::detail::sp_counted_base::release 75ms 0.38% 84.62% 101ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 31ms 0.16% 84.78% 101ms 0.52% std::num_put::_M_insert_int 14ms 0.072% 84.85% 99ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.036% 84.89% 98ms 0.5% Cylindrical2dMesh::CreateMirrorNodes