File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16604ms, 84.59% of 19628ms total Dropped 822 nodes (cum <= 98.14ms) flat flat% sum% cum cum% 0 0% 0% 19580ms 99.76% __libc_start_call_main 0 0% 0% 19580ms 99.76% __libc_start_main_impl 0 0% 0% 19580ms 99.76% _start 0 0% 0% 19557ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19557ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19557ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19557ms 99.64% main 0 0% 0% 19509ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19509ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19509ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.01% 0.01% 19482ms 99.26% AbstractCellBasedSimulation::Solve 0 0% 0.01% 14887ms 75.85% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.015% 9387ms 47.82% AbstractCellBasedSimulation::DoCellBirth 7ms 0.036% 0.051% 9271ms 47.23% Cell::ReadyToDivide 5ms 0.025% 0.076% 9182ms 46.78% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.092% 9042ms 46.07% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.056% 0.15% 9034ms 46.03% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.16% 9018ms 45.94% CellCycleModelOdeHandler::SolveOdeToTime 54ms 0.28% 0.44% 8828ms 44.98% AbstractOneStepIvpOdeSolver::InternalSolve 1012ms 5.16% 5.59% 7941ms 40.46% RungeKutta4IvpOdeSolver::CalculateNextYValue 2678ms 13.64% 19.24% 6754ms 34.41% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.24% 5373ms 27.37% MeshBasedCellPopulation::Update 3ms 0.015% 19.25% 4156ms 21.17% Cylindrical2dMesh::ReMesh 50ms 0.25% 19.51% 4086ms 20.82% AbstractCellProperty::IsType (inline) 357ms 1.82% 21.33% 2665ms 13.58% AbstractCellProperty::IsSame 1ms 0.0051% 21.33% 2558ms 13.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 231ms 1.18% 22.51% 2308ms 11.76% std::type_info::operator== (inline) 0 0% 22.51% 2268ms 11.55% MutableMesh::ReMesh 1ms 0.0051% 22.51% 2218ms 11.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.056% 22.57% 2175ms 11.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 2153ms 10.97% 33.54% 2153ms 10.97% __strcmp_avx2 0 0% 33.54% 2030ms 10.34% AbstractCellPopulation::WriteResultsToFiles 812ms 4.14% 37.68% 1888ms 9.62% std::_Rb_tree::_M_lower_bound (inline) 192ms 0.98% 38.65% 1750ms 8.92% TetrahedralMesh::EdgeIterator::operator++ 59ms 0.3% 38.95% 1412ms 7.19% std::_Rb_tree::find (inline) 0 0% 38.95% 1183ms 6.03% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.01% 38.96% 1166ms 5.94% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.076% 39.04% 1136ms 5.79% TetrahedralMesh::ImportFromMesher 40ms 0.2% 39.24% 1113ms 5.67% operator new 7ms 0.036% 39.28% 1058ms 5.39% MeshBasedCellPopulation::SpringIterator::operator++ 252ms 1.28% 40.56% 1058ms 5.39% __GI___libc_malloc 20ms 0.1% 40.67% 1031ms 5.25% std::set::insert (inline) 16ms 0.082% 40.75% 1011ms 5.15% std::_Rb_tree::_M_insert_unique 39ms 0.2% 40.95% 947ms 4.82% std::__new_allocator::allocate (inline) 0 0% 40.95% 942ms 4.80% std::allocator_traits::allocate (inline) 2ms 0.01% 40.96% 866ms 4.41% triangulate 0 0% 40.96% 847ms 4.32% std::set::count (inline) 0 0% 40.96% 784ms 3.99% delaunay 3ms 0.015% 40.97% 782ms 3.98% divconqdelaunay 89ms 0.45% 41.43% 763ms 3.89% std::map::operator[] (partial-inline) 1ms 0.0051% 41.43% 727ms 3.70% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 725ms 3.69% 45.12% 725ms 3.69% WntCellCycleOdeSystem::CalculateStoppingEvent 411ms 2.09% 47.22% 725ms 3.69% _int_malloc 707ms 3.60% 50.82% 707ms 3.60% std::_Rb_tree::_S_right (inline) 3ms 0.015% 50.84% 671ms 3.42% CellPopulationElementWriter::Visit 0 0% 50.84% 665ms 3.39% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.082% 50.92% 645ms 3.29% std::less::operator() (inline) 629ms 3.20% 54.12% 629ms 3.20% std::operator< (inline) 199ms 1.01% 55.14% 625ms 3.18% __dynamic_cast 0 0% 55.14% 623ms 3.17% std::_Rb_tree::_M_create_node (inline) 0 0% 55.14% 601ms 3.06% std::_Rb_tree::_M_get_node (inline) 25ms 0.13% 55.26% 596ms 3.04% std::_Rb_tree::_M_insert_ (inline) 2ms 0.01% 55.27% 589ms 3.00% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.13% 55.41% 585ms 2.98% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 24ms 0.12% 55.53% 574ms 2.92% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 55.55% 568ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.55% 561ms 2.86% std::map::find (inline) 0 0% 55.55% 559ms 2.85% std::_Rb_tree::lower_bound (inline) 0 0% 55.55% 559ms 2.85% std::map::lower_bound (inline) 0 0% 55.55% 555ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.031% 55.58% 549ms 2.80% Element::Element 11ms 0.056% 55.63% 530ms 2.70% MutableMesh::ReIndex 11ms 0.056% 55.69% 519ms 2.64% Element::RegisterWithNodes (inline) 17ms 0.087% 55.78% 505ms 2.57% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.051% 55.83% 504ms 2.57% Node::AddElement 12ms 0.061% 55.89% 479ms 2.44% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.01% 55.90% 477ms 2.43% AbstractCellProperty::IsSubType (inline) 1ms 0.0051% 55.90% 476ms 2.43% std::ostream::operator<< (inline) 146ms 0.74% 56.65% 472ms 2.40% __GI___libc_free 57ms 0.29% 56.94% 472ms 2.40% std::ostream::_M_insert 323ms 1.65% 58.58% 462ms 2.35% AbstractCellMutationState::AbstractCellMutationState 159ms 0.81% 59.39% 400ms 2.04% std::_Rb_tree::_M_get_insert_unique_pos 121ms 0.62% 60.01% 387ms 1.97% std::_Rb_tree::_M_erase 13ms 0.066% 60.08% 381ms 1.94% divconqrecurse 10ms 0.051% 60.13% 379ms 1.93% std::_Rb_tree::erase 1ms 0.0051% 60.13% 378ms 1.93% std::set::erase (inline) 15ms 0.076% 60.21% 377ms 1.92% Node::RemoveElement 11ms 0.056% 60.27% 377ms 1.92% std::__new_allocator::deallocate (inline) 0 0% 60.27% 370ms 1.89% std::allocator_traits::deallocate (inline) 368ms 1.87% 62.14% 368ms 1.87% [libchaste_cell_based.so] 96ms 0.49% 62.63% 363ms 1.85% mergehulls 26ms 0.13% 62.76% 356ms 1.81% Element::ResetIndex 21ms 0.11% 62.87% 347ms 1.77% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 62.88% 343ms 1.75% std::_Vector_base::_M_allocate (inline) 0 0% 62.88% 341ms 1.74% std::_Rb_tree::_M_drop_node (inline) 11ms 0.056% 62.94% 337ms 1.72% AbstractCellPopulation::GetLocationIndexUsingCell 45ms 0.23% 63.16% 327ms 1.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.16% 327ms 1.67% AbstractCellPopulation::Iterator::operator++ (inline) 267ms 1.36% 64.53% 326ms 1.66% _int_free 10ms 0.051% 64.58% 324ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.58% 323ms 1.65% std::set::~set (inline) 4ms 0.02% 64.60% 315ms 1.60% NodeLocationWriter::Visit 0 0% 64.60% 314ms 1.60% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 64.61% 312ms 1.59% Cell::GetMutationState 153ms 0.78% 65.39% 303ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 65.41% 301ms 1.53% Cell::GetCellProliferativeType 267ms 1.36% 66.77% 273ms 1.39% std::vector::operator[] (inline) 11ms 0.056% 66.82% 271ms 1.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 20ms 0.1% 66.92% 270ms 1.38% std::num_put::_M_insert_float 10ms 0.051% 66.98% 268ms 1.37% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.015% 66.99% 262ms 1.33% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 67.00% 262ms 1.33% alternateaxes 246ms 1.25% 68.25% 260ms 1.32% vertexmedian 90ms 0.46% 68.71% 257ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.031% 68.74% 256ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 19ms 0.097% 68.84% 256ms 1.30% AbstractTetrahedralElement::CalculateJacobian 11ms 0.056% 68.90% 252ms 1.28% std::vector::push_back (inline) 1ms 0.0051% 68.90% 249ms 1.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 104ms 0.53% 69.43% 246ms 1.25% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 53ms 0.27% 69.70% 243ms 1.24% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 69.70% 240ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 69.72% 236ms 1.20% std::set::set (inline) 21ms 0.11% 69.82% 232ms 1.18% std::vector::_M_realloc_insert 1ms 0.0051% 69.83% 230ms 1.17% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 69.84% 229ms 1.17% AbstractCentreBasedCellPopulation::GetDampingConstant 24ms 0.12% 69.96% 228ms 1.16% std::_Rb_tree::_M_copy (inline) 8ms 0.041% 70.00% 225ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 144ms 0.73% 70.74% 221ms 1.13% AbstractElement::GetNodeGlobalIndex 6ms 0.031% 70.77% 221ms 1.13% std::__cxx11::collate::do_transform 13ms 0.066% 70.83% 218ms 1.11% TetrahedralMesh::Clear 0 0% 70.83% 215ms 1.10% OffLatticeSimulation::ApplyBoundaries 1ms 0.0051% 70.84% 211ms 1.07% ___vsnprintf 9ms 0.046% 70.88% 210ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.061% 70.94% 210ms 1.07% Element::MarkAsDeleted 0 0% 70.94% 210ms 1.07% __vsnprintf_internal (inline) 17ms 0.087% 71.03% 207ms 1.05% __printf_buffer 49ms 0.25% 71.28% 201ms 1.02% std::_Rb_tree::_M_clone_node (inline) 199ms 1.01% 72.29% 199ms 1.01% std::_Rb_tree_insert_and_rebalance 195ms 0.99% 73.29% 195ms 0.99% [libchaste_crypt.so] 32ms 0.16% 73.45% 194ms 0.99% AbstractTetrahedralElement::RefreshJacobian 125ms 0.64% 74.09% 188ms 0.96% malloc_consolidate 184ms 0.94% 75.03% 184ms 0.94% std::vector::size (inline) 7ms 0.036% 75.06% 179ms 0.91% __printf_fp_l_buffer 0 0% 75.06% 179ms 0.91% __printf_fp_spec (inline) 5ms 0.025% 75.09% 175ms 0.89% CellPropertyCollection::HasProperty 0 0% 75.09% 170ms 0.87% Cell::HasCellProperty (inline) 170ms 0.87% 75.95% 170ms 0.87% unlink_chunk 169ms 0.86% 76.81% 169ms 0.86% incircle 66ms 0.34% 77.15% 167ms 0.85% __printf_fp_buffer_1 5ms 0.025% 77.18% 165ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 13ms 0.066% 77.24% 163ms 0.83% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 77.24% 163ms 0.83% CellProliferativeTypesWriter::VisitCell 158ms 0.8% 78.05% 158ms 0.8% Node::GetIndex 1ms 0.0051% 78.05% 156ms 0.79% boost::numeric::ublas::vector_assign (inline) 104ms 0.53% 78.58% 156ms 0.79% std::_Rb_tree::equal_range (inline) 153ms 0.78% 79.36% 153ms 0.78% std::type_info::name (inline) 3ms 0.015% 79.38% 152ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 12ms 0.061% 79.44% 152ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 62ms 0.32% 79.75% 144ms 0.73% AbstractElement::GetNodeLocation 51ms 0.26% 80.01% 140ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 7ms 0.036% 80.05% 139ms 0.71% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.05% 138ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.05% 138ms 0.7% OutputFileHandler::OpenOutputFile 26ms 0.13% 80.18% 138ms 0.7% TetrahedralMesh::EdgesEnd 45ms 0.23% 80.41% 137ms 0.7% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 72ms 0.37% 80.78% 134ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 7ms 0.036% 80.81% 132ms 0.67% Node::~Node 8ms 0.041% 80.85% 130ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.041% 80.89% 129ms 0.66% Cylindrical2dMesh::CreateMirrorNodes 2ms 0.01% 80.90% 129ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.90% 126ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 80.92% 123ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 114ms 0.58% 81.50% 123ms 0.63% vertexsort 3ms 0.015% 81.51% 118ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 81.51% 117ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 16ms 0.082% 81.59% 116ms 0.59% boost::detail::shared_count::~shared_count (inline) 36ms 0.18% 81.78% 116ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 81.78% 116ms 0.59% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 81.79% 114ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.02% 81.81% 109ms 0.56% Cell::SetCellProliferativeType 3ms 0.015% 81.83% 105ms 0.53% CellLocationIndexWriter::VisitCell 8ms 0.041% 81.87% 105ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 32ms 0.16% 82.03% 105ms 0.53% std::__ostream_insert 104ms 0.53% 82.56% 104ms 0.53% AbstractCellMutationState::~AbstractCellMutationState 10ms 0.051% 82.61% 103ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 69ms 0.35% 82.96% 102ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 102ms 0.52% 83.48% 102ms 0.52% std::_Rb_tree_increment 100ms 0.51% 83.99% 100ms 0.51% boost::shared_ptr::operator-> (inline) 19ms 0.097% 84.09% 100ms 0.51% std::num_put::_M_insert_int 99ms 0.5% 84.59% 99ms 0.5% AbstractElement::IsDeleted