File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16727ms, 84.83% of 19718ms total Dropped 753 nodes (cum <= 98.59ms) flat flat% sum% cum cum% 0 0% 0% 19669ms 99.75% __libc_start_call_main 0 0% 0% 19669ms 99.75% __libc_start_main_impl 0 0% 0% 19669ms 99.75% _start 0 0% 0% 19645ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19645ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19645ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19645ms 99.63% main 0 0% 0% 19598ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19598ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19598ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19572ms 99.26% AbstractCellBasedSimulation::Solve 0 0% 0% 14980ms 75.97% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 9507ms 48.21% AbstractCellBasedSimulation::DoCellBirth 6ms 0.03% 0.036% 9401ms 47.68% Cell::ReadyToDivide 7ms 0.036% 0.071% 9326ms 47.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.076% 9174ms 46.53% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.086% 0.16% 9170ms 46.51% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.16% 9148ms 46.39% CellCycleModelOdeHandler::SolveOdeToTime 55ms 0.28% 0.44% 8988ms 45.58% AbstractOneStepIvpOdeSolver::InternalSolve 1016ms 5.15% 5.59% 8058ms 40.87% RungeKutta4IvpOdeSolver::CalculateNextYValue 2495ms 12.65% 18.25% 6846ms 34.72% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 18.25% 5347ms 27.12% MeshBasedCellPopulation::Update 52ms 0.26% 18.51% 4365ms 22.14% AbstractCellProperty::IsType (inline) 2ms 0.01% 18.52% 4148ms 21.04% Cylindrical2dMesh::ReMesh 333ms 1.69% 20.21% 3081ms 15.63% AbstractCellProperty::IsSame 633ms 3.21% 23.42% 2748ms 13.94% std::type_info::operator== (inline) 0 0% 23.42% 2526ms 12.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.42% 2279ms 11.56% MutableMesh::ReMesh 1ms 0.0051% 23.43% 2207ms 11.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.076% 23.50% 2159ms 10.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0051% 23.51% 2058ms 10.44% AbstractCellPopulation::WriteResultsToFiles 2035ms 10.32% 33.83% 2035ms 10.32% __strcmp_avx2 817ms 4.14% 37.97% 1893ms 9.60% std::_Rb_tree::_M_lower_bound (inline) 167ms 0.85% 38.82% 1707ms 8.66% TetrahedralMesh::EdgeIterator::operator++ 57ms 0.29% 39.11% 1419ms 7.20% std::_Rb_tree::find (inline) 1ms 0.0051% 39.11% 1162ms 5.89% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 39.14% 1150ms 5.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.071% 39.21% 1131ms 5.74% TetrahedralMesh::ImportFromMesher 43ms 0.22% 39.43% 1103ms 5.59% operator new 280ms 1.42% 40.85% 1053ms 5.34% __GI___libc_malloc 4ms 0.02% 40.87% 1029ms 5.22% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.056% 40.92% 1001ms 5.08% std::set::insert (inline) 16ms 0.081% 41.00% 990ms 5.02% std::_Rb_tree::_M_insert_unique 42ms 0.21% 41.22% 969ms 4.91% std::__new_allocator::allocate (inline) 0 0% 41.22% 965ms 4.89% std::allocator_traits::allocate (inline) 0 0% 41.22% 884ms 4.48% triangulate 0 0% 41.22% 832ms 4.22% std::set::count (inline) 0 0% 41.22% 803ms 4.07% delaunay 3ms 0.015% 41.23% 803ms 4.07% divconqdelaunay 3ms 0.015% 41.25% 788ms 4.00% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 760ms 3.85% 45.10% 760ms 3.85% WntCellCycleOdeSystem::CalculateStoppingEvent 715ms 3.63% 48.73% 715ms 3.63% std::_Rb_tree::_S_right (inline) 67ms 0.34% 49.07% 711ms 3.61% std::map::operator[] (partial-inline) 6ms 0.03% 49.10% 702ms 3.56% CellPopulationElementWriter::Visit 388ms 1.97% 51.07% 686ms 3.48% _int_malloc 1ms 0.0051% 51.07% 677ms 3.43% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.056% 51.13% 649ms 3.29% std::less::operator() (inline) 0 0% 51.13% 639ms 3.24% std::_Rb_tree::_M_create_node (inline) 638ms 3.24% 54.36% 638ms 3.24% std::operator< (inline) 5ms 0.025% 54.39% 636ms 3.23% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.041% 54.43% 632ms 3.21% CellPropertyCollection::GetPropertiesType (inline) 201ms 1.02% 55.45% 631ms 3.20% __dynamic_cast 50ms 0.25% 55.70% 618ms 3.13% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.70% 610ms 3.09% std::_Rb_tree::_M_get_node (inline) 0 0% 55.70% 584ms 2.96% std::map::find (inline) 0 0% 55.70% 579ms 2.94% std::_Rb_tree::_Alloc_node::operator() (inline) 30ms 0.15% 55.85% 570ms 2.89% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 18ms 0.091% 55.94% 567ms 2.88% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.94% 557ms 2.82% std::_Rb_tree::lower_bound (inline) 0 0% 55.94% 557ms 2.82% std::map::lower_bound (inline) 9ms 0.046% 55.99% 548ms 2.78% Element::Element 10ms 0.051% 56.04% 533ms 2.70% MutableMesh::ReIndex 15ms 0.076% 56.12% 497ms 2.52% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 56.12% 495ms 2.51% AbstractCellProperty::IsSubType (inline) 15ms 0.076% 56.19% 490ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 56.19% 483ms 2.45% std::ostream::operator<< (inline) 73ms 0.37% 56.56% 480ms 2.43% std::ostream::_M_insert 16ms 0.081% 56.64% 475ms 2.41% Element::RegisterWithNodes (inline) 13ms 0.066% 56.71% 453ms 2.30% Node::AddElement 143ms 0.73% 57.43% 430ms 2.18% __GI___libc_free 286ms 1.45% 58.89% 427ms 2.17% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0051% 58.89% 399ms 2.02% std::set::erase (inline) 11ms 0.056% 58.95% 398ms 2.02% std::_Rb_tree::erase 9ms 0.046% 58.99% 394ms 2.00% Node::RemoveElement 116ms 0.59% 59.58% 383ms 1.94% std::_Rb_tree::_M_erase 376ms 1.91% 61.49% 376ms 1.91% [libchaste_cell_based.so] 15ms 0.076% 61.56% 372ms 1.89% divconqrecurse 12ms 0.061% 61.62% 358ms 1.82% std::__new_allocator::deallocate (inline) 36ms 0.18% 61.81% 356ms 1.81% Element::ResetIndex 127ms 0.64% 62.45% 356ms 1.81% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0051% 62.46% 356ms 1.81% std::_Vector_base::_M_allocate (inline) 0 0% 62.46% 354ms 1.80% std::allocator_traits::deallocate (inline) 105ms 0.53% 62.99% 346ms 1.75% mergehulls 24ms 0.12% 63.11% 345ms 1.75% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 63.13% 337ms 1.71% Cell::GetCellProliferativeType 8ms 0.041% 63.17% 336ms 1.70% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 63.17% 331ms 1.68% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 63.18% 330ms 1.67% Cell::GetMutationState 2ms 0.01% 63.19% 325ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 63.19% 323ms 1.64% AbstractCellPopulation::Iterator::operator++ (inline) 323ms 1.64% 64.82% 323ms 1.64% std::type_info::name (inline) 0 0% 64.82% 320ms 1.62% std::set::~set (inline) 11ms 0.056% 64.88% 317ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 32ms 0.16% 65.04% 315ms 1.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 149ms 0.76% 65.80% 300ms 1.52% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.80% 295ms 1.50% std::_Rb_tree::_M_put_node (inline) 290ms 1.47% 67.27% 293ms 1.49% std::vector::operator[] (inline) 1ms 0.0051% 67.27% 287ms 1.46% alternateaxes 24ms 0.12% 67.40% 287ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 231ms 1.17% 68.57% 285ms 1.45% _int_free 268ms 1.36% 69.93% 285ms 1.45% vertexmedian 0 0% 69.93% 278ms 1.41% NodeLocationWriter::Visit 12ms 0.061% 69.99% 264ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 23ms 0.12% 70.10% 260ms 1.32% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 70.11% 260ms 1.32% std::set::set (inline) 6ms 0.03% 70.14% 258ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 10ms 0.051% 70.19% 257ms 1.30% std::vector::push_back (inline) 3ms 0.015% 70.21% 250ms 1.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 26ms 0.13% 70.34% 248ms 1.26% std::num_put::_M_insert_float 13ms 0.066% 70.41% 247ms 1.25% std::_Rb_tree::_M_erase_aux (inline) 67ms 0.34% 70.75% 244ms 1.24% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.046% 70.79% 240ms 1.22% std::vector::_M_realloc_insert 77ms 0.39% 71.18% 237ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 71.18% 234ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 22ms 0.11% 71.30% 229ms 1.16% std::_Rb_tree::_M_copy (inline) 0 0% 71.30% 226ms 1.15% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.30% 226ms 1.15% MeshBasedCellPopulation::GetDampingConstant 9ms 0.046% 71.34% 211ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 21ms 0.11% 71.45% 210ms 1.07% TetrahedralMesh::Clear 153ms 0.78% 72.22% 207ms 1.05% AbstractElement::GetNodeGlobalIndex 5ms 0.025% 72.25% 207ms 1.05% Element::MarkAsDeleted 71ms 0.36% 72.61% 206ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 63ms 0.32% 72.93% 204ms 1.03% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 72.93% 199ms 1.01% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 72.95% 198ms 1.00% std::__cxx11::collate::do_transform 1ms 0.0051% 72.96% 189ms 0.96% ___vsnprintf 0 0% 72.96% 189ms 0.96% __vsnprintf_internal (inline) 16ms 0.081% 73.04% 188ms 0.95% __printf_buffer 26ms 0.13% 73.17% 184ms 0.93% AbstractTetrahedralElement::RefreshJacobian 4ms 0.02% 73.19% 182ms 0.92% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.025% 73.22% 182ms 0.92% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 73.23% 180ms 0.91% CellPropertyCollection::HasProperty 117ms 0.59% 73.83% 177ms 0.9% malloc_consolidate 0 0% 73.83% 176ms 0.89% Cell::HasCellProperty (inline) 5ms 0.025% 73.85% 172ms 0.87% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 73.88% 163ms 0.83% __printf_fp_l_buffer 0 0% 73.88% 163ms 0.83% __printf_fp_spec (inline) 159ms 0.81% 74.68% 159ms 0.81% std::vector::size (inline) 159ms 0.81% 75.49% 159ms 0.81% unlink_chunk 6ms 0.03% 75.52% 156ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 153ms 0.78% 76.30% 153ms 0.78% Node::GetIndex 152ms 0.77% 77.07% 152ms 0.77% [libchaste_crypt.so] 152ms 0.77% 77.84% 152ms 0.77% incircle 65ms 0.33% 78.17% 151ms 0.77% __printf_fp_buffer_1 8ms 0.041% 78.21% 145ms 0.74% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.02% 78.23% 144ms 0.73% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 98ms 0.5% 78.73% 143ms 0.73% std::_Rb_tree::equal_range (inline) 39ms 0.2% 78.92% 141ms 0.72% boost::numeric::ublas::indexing_vector_assign 141ms 0.72% 79.64% 141ms 0.72% std::_Rb_tree_insert_and_rebalance 69ms 0.35% 79.99% 140ms 0.71% AbstractElement::GetNodeLocation 12ms 0.061% 80.05% 138ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 18ms 0.091% 80.14% 137ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 84ms 0.43% 80.57% 135ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 37ms 0.19% 80.75% 132ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 121ms 0.61% 81.37% 132ms 0.67% vertexsort 0 0% 81.37% 125ms 0.63% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.37% 123ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0051% 81.37% 123ms 0.62% Cell::SetCellProliferativeType 0 0% 81.37% 122ms 0.62% OutputFileHandler::OpenOutputFile 2ms 0.01% 81.38% 122ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 43ms 0.22% 81.60% 117ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 117ms 0.59% 82.19% 117ms 0.59% std::_Rb_tree_increment 2ms 0.01% 82.20% 116ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.025% 82.23% 115ms 0.58% Node::~Node 5ms 0.025% 82.25% 115ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 114ms 0.58% 82.83% 114ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 14ms 0.071% 82.90% 111ms 0.56% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.061% 82.96% 111ms 0.56% boost::detail::shared_count::~shared_count (inline) 0 0% 82.96% 111ms 0.56% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.96% 110ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 82.96% 108ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 107ms 0.54% 83.51% 107ms 0.54% std::_Rb_tree_rebalance_for_erase 8ms 0.041% 83.55% 103ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 103ms 0.52% 84.07% 103ms 0.52% TetrahedralMesh::EdgeIterator::operator!= 50ms 0.25% 84.32% 102ms 0.52% boost::shared_ptr::shared_ptr (inline) 100ms 0.51% 84.83% 100ms 0.51% boost::shared_ptr::operator-> (inline)