File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16848ms, 85.43% of 19721ms total Dropped 799 nodes (cum <= 98.61ms) flat flat% sum% cum cum% 0 0% 0% 19677ms 99.78% __libc_start_call_main 0 0% 0% 19677ms 99.78% __libc_start_main_impl 0 0% 0% 19677ms 99.78% _start 0 0% 0% 19655ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19655ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19655ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19655ms 99.67% main 0 0% 0% 19612ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19612ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19612ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19585ms 99.31% AbstractCellBasedSimulation::Solve 3ms 0.015% 0.015% 14979ms 75.95% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.03% 0.046% 9483ms 48.09% AbstractCellBasedSimulation::DoCellBirth 7ms 0.035% 0.081% 9368ms 47.50% Cell::ReadyToDivide 6ms 0.03% 0.11% 9277ms 47.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.12% 9138ms 46.34% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.056% 0.18% 9129ms 46.29% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.19% 9114ms 46.21% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.31% 0.5% 8939ms 45.33% AbstractOneStepIvpOdeSolver::InternalSolve 1013ms 5.14% 5.64% 8047ms 40.80% RungeKutta4IvpOdeSolver::CalculateNextYValue 2735ms 13.87% 19.51% 6848ms 34.72% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.51% 5379ms 27.28% MeshBasedCellPopulation::Update 3ms 0.015% 19.53% 4139ms 20.99% Cylindrical2dMesh::ReMesh 67ms 0.34% 19.87% 4123ms 20.91% AbstractCellProperty::IsType (inline) 321ms 1.63% 21.49% 2724ms 13.81% AbstractCellProperty::IsSame 2ms 0.01% 21.50% 2582ms 13.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 243ms 1.23% 22.74% 2403ms 12.18% std::type_info::operator== (inline) 0 0% 22.74% 2275ms 11.54% MutableMesh::ReMesh 0 0% 22.74% 2255ms 11.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 2223ms 11.27% 34.01% 2223ms 11.27% __strcmp_avx2 12ms 0.061% 34.07% 2210ms 11.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0051% 34.08% 2020ms 10.24% AbstractCellPopulation::WriteResultsToFiles 814ms 4.13% 38.20% 1896ms 9.61% std::_Rb_tree::_M_lower_bound (inline) 170ms 0.86% 39.06% 1695ms 8.59% TetrahedralMesh::EdgeIterator::operator++ 80ms 0.41% 39.47% 1434ms 7.27% std::_Rb_tree::find (inline) 2ms 0.01% 39.48% 1192ms 6.04% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 39.51% 1157ms 5.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 21ms 0.11% 39.62% 1146ms 5.81% TetrahedralMesh::ImportFromMesher 55ms 0.28% 39.90% 1088ms 5.52% operator new 18ms 0.091% 39.99% 1048ms 5.31% MeshBasedCellPopulation::SpringIterator::operator++ 250ms 1.27% 41.26% 1031ms 5.23% __GI___libc_malloc 13ms 0.066% 41.32% 987ms 5.00% std::set::insert (inline) 16ms 0.081% 41.40% 974ms 4.94% std::_Rb_tree::_M_insert_unique 37ms 0.19% 41.59% 933ms 4.73% std::__new_allocator::allocate (inline) 0 0% 41.59% 928ms 4.71% std::allocator_traits::allocate (inline) 0 0% 41.59% 874ms 4.43% triangulate 0 0% 41.59% 823ms 4.17% std::set::count (inline) 0 0% 41.59% 790ms 4.01% delaunay 790ms 4.01% 45.60% 790ms 4.01% std::_Rb_tree::_S_right (inline) 6ms 0.03% 45.63% 787ms 3.99% divconqdelaunay 62ms 0.31% 45.94% 736ms 3.73% std::map::operator[] (partial-inline) 1ms 0.0051% 45.95% 727ms 3.69% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.01% 45.96% 712ms 3.61% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 706ms 3.58% 49.54% 706ms 3.58% WntCellCycleOdeSystem::CalculateStoppingEvent 381ms 1.93% 51.47% 697ms 3.53% _int_malloc 11ms 0.056% 51.52% 694ms 3.52% CellPopulationElementWriter::Visit 210ms 1.06% 52.59% 667ms 3.38% __dynamic_cast 0 0% 52.59% 631ms 3.20% std::_Rb_tree::_M_create_node (inline) 18ms 0.091% 52.68% 629ms 3.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.061% 52.74% 614ms 3.11% std::less::operator() (inline) 28ms 0.14% 52.88% 609ms 3.09% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.88% 604ms 3.06% std::map::find (inline) 602ms 3.05% 55.94% 602ms 3.05% std::operator< (inline) 0 0% 55.94% 601ms 3.05% std::_Rb_tree::_M_get_node (inline) 4ms 0.02% 55.96% 599ms 3.04% CellPropertyCollection::GetPropertiesType (inline) 29ms 0.15% 56.10% 577ms 2.93% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.10% 576ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 56.10% 576ms 2.92% std::map::lower_bound (inline) 5ms 0.025% 56.13% 565ms 2.86% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.041% 56.17% 564ms 2.86% Element::Element 0 0% 56.17% 563ms 2.85% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.051% 56.22% 543ms 2.75% MutableMesh::ReIndex 11ms 0.056% 56.28% 519ms 2.63% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 56.28% 500ms 2.54% std::ostream::operator<< (inline) 84ms 0.43% 56.71% 499ms 2.53% std::ostream::_M_insert 3ms 0.015% 56.72% 492ms 2.49% AbstractCellProperty::IsSubType (inline) 11ms 0.056% 56.78% 484ms 2.45% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.076% 56.85% 478ms 2.42% Element::RegisterWithNodes (inline) 10ms 0.051% 56.90% 459ms 2.33% Node::AddElement 130ms 0.66% 57.56% 433ms 2.20% __GI___libc_free 279ms 1.41% 58.98% 424ms 2.15% AbstractCellMutationState::AbstractCellMutationState 14ms 0.071% 59.05% 414ms 2.10% std::_Rb_tree::erase 0 0% 59.05% 411ms 2.08% std::set::erase (inline) 11ms 0.056% 59.10% 408ms 2.07% Node::RemoveElement 14ms 0.071% 59.18% 383ms 1.94% divconqrecurse 138ms 0.7% 59.88% 381ms 1.93% std::_Rb_tree::_M_get_insert_unique_pos 127ms 0.64% 60.52% 368ms 1.87% std::_Rb_tree::_M_erase 112ms 0.57% 61.09% 361ms 1.83% mergehulls 36ms 0.18% 61.27% 348ms 1.76% Element::ResetIndex 19ms 0.096% 61.37% 339ms 1.72% std::__new_allocator::deallocate (inline) 10ms 0.051% 61.42% 338ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 337ms 1.71% 63.13% 337ms 1.71% [libchaste_cell_based.so] 22ms 0.11% 63.24% 336ms 1.70% std::_Rb_tree::~_Rb_tree (inline) 170ms 0.86% 64.10% 335ms 1.70% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.035% 64.13% 333ms 1.69% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.13% 332ms 1.68% std::allocator_traits::deallocate (inline) 1ms 0.0051% 64.14% 328ms 1.66% std::_Vector_base::_M_allocate (inline) 4ms 0.02% 64.16% 323ms 1.64% Cell::GetMutationState 2ms 0.01% 64.17% 318ms 1.61% NodeLocationWriter::Visit 0 0% 64.17% 316ms 1.60% std::set::~set (inline) 1ms 0.0051% 64.18% 312ms 1.58% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 64.19% 310ms 1.57% Cell::GetCellProliferativeType 35ms 0.18% 64.36% 309ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 234ms 1.19% 65.55% 300ms 1.52% _int_free 0 0% 65.55% 295ms 1.50% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 65.55% 287ms 1.46% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 65.55% 269ms 1.36% alternateaxes 21ms 0.11% 65.66% 269ms 1.36% std::num_put::_M_insert_float 247ms 1.25% 66.91% 269ms 1.36% vertexmedian 24ms 0.12% 67.04% 268ms 1.36% AbstractTetrahedralElement::CalculateJacobian 267ms 1.35% 68.39% 268ms 1.36% std::vector::operator[] (inline) 10ms 0.051% 68.44% 267ms 1.35% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.44% 266ms 1.35% std::_Rb_tree::_M_put_node (inline) 95ms 0.48% 68.92% 261ms 1.32% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.051% 68.97% 251ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 13ms 0.066% 69.04% 251ms 1.27% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 69.07% 245ms 1.24% std::vector::push_back (inline) 59ms 0.3% 69.37% 237ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 13ms 0.066% 69.43% 237ms 1.20% std::vector::_M_realloc_insert 22ms 0.11% 69.55% 236ms 1.20% std::_Rb_tree::_M_copy (inline) 3ms 0.015% 69.56% 235ms 1.19% std::set::set (inline) 1ms 0.0051% 69.57% 234ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.041% 69.61% 233ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 106ms 0.54% 70.14% 230ms 1.17% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.01% 70.15% 225ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.15% 225ms 1.14% MeshBasedCellPopulation::GetDampingConstant 14ms 0.071% 70.22% 224ms 1.14% TetrahedralMesh::Clear 8ms 0.041% 70.27% 223ms 1.13% Element::MarkAsDeleted 0 0% 70.27% 222ms 1.13% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.02% 70.29% 214ms 1.09% std::__cxx11::collate::do_transform 0 0% 70.29% 213ms 1.08% OffLatticeSimulation::ApplyBoundaries 65ms 0.33% 70.62% 212ms 1.07% std::_Rb_tree::_M_clone_node (inline) 0 0% 70.62% 203ms 1.03% ___vsnprintf 0 0% 70.62% 203ms 1.03% __vsnprintf_internal (inline) 23ms 0.12% 70.73% 201ms 1.02% __printf_buffer 199ms 1.01% 71.74% 199ms 1.01% std::type_info::name (inline) 24ms 0.12% 71.86% 198ms 1.00% AbstractTetrahedralElement::RefreshJacobian 13ms 0.066% 71.93% 194ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 8ms 0.041% 71.97% 190ms 0.96% AbstractTetrahedralElement::AbstractTetrahedralElement 143ms 0.73% 72.69% 189ms 0.96% AbstractElement::GetNodeGlobalIndex 135ms 0.68% 73.38% 185ms 0.94% malloc_consolidate 4ms 0.02% 73.40% 166ms 0.84% __printf_fp_l_buffer 0 0% 73.40% 166ms 0.84% __printf_fp_spec (inline) 2ms 0.01% 73.41% 165ms 0.84% CellPropertyCollection::HasProperty 165ms 0.84% 74.25% 165ms 0.84% Node::GetIndex 163ms 0.83% 75.07% 163ms 0.83% unlink_chunk 0 0% 75.07% 162ms 0.82% Cell::HasCellProperty (inline) 69ms 0.35% 75.42% 159ms 0.81% AbstractElement::GetNodeLocation 76ms 0.39% 75.81% 159ms 0.81% __printf_fp_buffer_1 6ms 0.03% 75.84% 158ms 0.8% boost::numeric::ublas::vector_assign (inline) 99ms 0.5% 76.34% 156ms 0.79% std::_Rb_tree::equal_range (inline) 5ms 0.025% 76.37% 155ms 0.79% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 76.38% 154ms 0.78% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 51ms 0.26% 76.64% 152ms 0.77% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 13ms 0.066% 76.71% 151ms 0.77% MeshBasedCellPopulation::SpringsEnd (inline) 148ms 0.75% 77.46% 148ms 0.75% [libchaste_crypt.so] 14ms 0.071% 77.53% 148ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 146ms 0.74% 78.27% 146ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 28ms 0.14% 78.41% 145ms 0.74% TetrahedralMesh::EdgesEnd (partial-inline) 144ms 0.73% 79.14% 144ms 0.73% std::vector::size (inline) 141ms 0.71% 79.85% 141ms 0.71% std::_Rb_tree_insert_and_rebalance 139ms 0.7% 80.56% 139ms 0.7% incircle 43ms 0.22% 80.78% 138ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 89ms 0.45% 81.23% 138ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.051% 81.28% 137ms 0.69% Node::~Node 35ms 0.18% 81.46% 136ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.46% 133ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0051% 81.46% 129ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0051% 81.47% 127ms 0.64% OutputFileHandler::OpenOutputFile 2ms 0.01% 81.48% 126ms 0.64% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 6ms 0.03% 81.51% 125ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 41ms 0.21% 81.71% 122ms 0.62% boost::numeric::ublas::indexing_vector_assign 115ms 0.58% 82.30% 122ms 0.62% vertexsort 118ms 0.6% 82.90% 118ms 0.6% std::_Rb_tree_rebalance_for_erase 37ms 0.19% 83.08% 116ms 0.59% std::__ostream_insert 115ms 0.58% 83.67% 115ms 0.58% TetrahedralMesh::EdgeIterator::operator!= 0 0% 83.67% 114ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 83.67% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0051% 83.67% 111ms 0.56% Cell::SetCellProliferativeType 12ms 0.061% 83.73% 108ms 0.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 18ms 0.091% 83.82% 108ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.82% 108ms 0.55% boost::shared_ptr::~shared_ptr (inline) 76ms 0.39% 84.21% 107ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator 107ms 0.54% 84.75% 107ms 0.54% std::_Rb_tree_increment 1ms 0.0051% 84.76% 105ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.51% 85.27% 101ms 0.51% counterclockwise 8ms 0.041% 85.31% 100ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 3ms 0.015% 85.33% 99ms 0.5% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.11% 85.43% 99ms 0.5% std::num_put::_M_insert_int