File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16615ms, 84.41% of 19684ms total Dropped 774 nodes (cum <= 98.42ms) flat flat% sum% cum cum% 0 0% 0% 19636ms 99.76% __libc_start_call_main 0 0% 0% 19636ms 99.76% __libc_start_main_impl 0 0% 0% 19636ms 99.76% _start 0 0% 0% 19615ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19615ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19615ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19615ms 99.65% main 0 0% 0% 19579ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19579ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19579ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19551ms 99.32% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 15166ms 77.05% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0051% 9974ms 50.67% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 9892ms 50.25% Cell::ReadyToDivide 2ms 0.01% 0.03% 9811ms 49.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.03% 9685ms 49.20% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.046% 0.076% 9671ms 49.13% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.091% 9662ms 49.09% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.4% 0.49% 9497ms 48.25% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.46% 4.94% 8636ms 43.87% RungeKutta4IvpOdeSolver::CalculateNextYValue 3608ms 18.33% 23.27% 7543ms 38.32% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 23.28% 5075ms 25.78% MeshBasedCellPopulation::Update 82ms 0.42% 23.69% 3989ms 20.27% AbstractCellProperty::IsType (inline) 7ms 0.036% 23.73% 3954ms 20.09% Cylindrical2dMesh::ReMesh 579ms 2.94% 26.67% 2773ms 14.09% AbstractCellProperty::IsSame 1ms 0.0051% 26.68% 2403ms 12.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 401ms 2.04% 28.71% 2194ms 11.15% std::type_info::operator== (inline) 0 0% 28.71% 2130ms 10.82% MutableMesh::ReMesh 0 0% 28.71% 2090ms 10.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.046% 28.76% 2042ms 10.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.76% 1975ms 10.03% AbstractCellPopulation::WriteResultsToFiles 762ms 3.87% 32.63% 1756ms 8.92% std::_Rb_tree::_M_lower_bound (inline) 1739ms 8.83% 41.47% 1739ms 8.83% __strcmp_avx2 136ms 0.69% 42.16% 1534ms 7.79% TetrahedralMesh::EdgeIterator::operator++ 57ms 0.29% 42.45% 1262ms 6.41% std::_Rb_tree::find (partial-inline) 3ms 0.015% 42.46% 1098ms 5.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 66ms 0.34% 42.80% 1094ms 5.56% operator new 15ms 0.076% 42.87% 1080ms 5.49% TetrahedralMesh::ImportFromMesher 0 0% 42.87% 1068ms 5.43% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 42.90% 1008ms 5.12% std::set::insert (inline) 234ms 1.19% 44.09% 1004ms 5.10% __GI___libc_malloc 14ms 0.071% 44.16% 1002ms 5.09% std::_Rb_tree::_M_insert_unique 34ms 0.17% 44.34% 968ms 4.92% std::__new_allocator::allocate (inline) 0 0% 44.34% 962ms 4.89% std::allocator_traits::allocate (inline) 8ms 0.041% 44.38% 936ms 4.76% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0051% 44.38% 817ms 4.15% triangulate 0 0% 44.38% 745ms 3.78% std::set::count (inline) 5ms 0.025% 44.41% 738ms 3.75% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.41% 736ms 3.74% delaunay 2ms 0.01% 44.42% 736ms 3.74% divconqdelaunay 406ms 2.06% 46.48% 698ms 3.55% _int_malloc 22ms 0.11% 46.59% 689ms 3.50% CellPopulationElementWriter::Visit 47ms 0.24% 46.83% 684ms 3.47% std::map::operator[] (partial-inline) 2ms 0.01% 46.84% 673ms 3.42% AbstractTwoBodyInteractionForce::AddForceContribution 648ms 3.29% 50.13% 659ms 3.35% WntCellCycleOdeSystem::CalculateStoppingEvent 649ms 3.30% 53.43% 649ms 3.30% std::_Rb_tree::_S_right (inline) 33ms 0.17% 53.60% 643ms 3.27% std::_Rb_tree::_M_insert_ (inline) 0 0% 53.60% 629ms 3.20% std::_Rb_tree::_M_create_node (inline) 0 0% 53.60% 603ms 3.06% std::_Rb_tree::_M_get_node (inline) 18ms 0.091% 53.69% 583ms 2.96% std::less::operator() (inline) 5ms 0.025% 53.71% 579ms 2.94% MeshBasedCellPopulation::AcceptCellWriter 0 0% 53.71% 575ms 2.92% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.03% 53.74% 571ms 2.90% Element::Element 564ms 2.87% 56.61% 565ms 2.87% std::operator< (inline) 0 0% 56.61% 549ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 56.61% 549ms 2.79% std::map::lower_bound (inline) 5ms 0.025% 56.63% 545ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 23ms 0.12% 56.75% 537ms 2.73% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 139ms 0.71% 57.46% 534ms 2.71% __dynamic_cast 17ms 0.086% 57.54% 533ms 2.71% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.041% 57.58% 515ms 2.62% Element::RegisterWithNodes (inline) 0 0% 57.58% 510ms 2.59% std::map::find (inline) 6ms 0.03% 57.62% 505ms 2.57% MutableMesh::ReIndex 12ms 0.061% 57.68% 505ms 2.57% Node::AddElement 14ms 0.071% 57.75% 502ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 18ms 0.091% 57.84% 489ms 2.48% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.0051% 57.84% 480ms 2.44% std::ostream::operator<< (inline) 63ms 0.32% 58.16% 478ms 2.43% std::ostream::_M_insert 322ms 1.64% 59.80% 476ms 2.42% AbstractCellMutationState::AbstractCellMutationState 143ms 0.73% 60.53% 431ms 2.19% __GI___libc_free 3ms 0.015% 60.54% 393ms 2.00% AbstractCellProperty::IsSubType (inline) 118ms 0.6% 61.14% 369ms 1.87% std::_Rb_tree::_M_erase 5ms 0.025% 61.17% 368ms 1.87% std::_Rb_tree::erase 1ms 0.0051% 61.17% 368ms 1.87% std::set::erase (inline) 12ms 0.061% 61.23% 365ms 1.85% Node::RemoveElement 2ms 0.01% 61.24% 361ms 1.83% std::_Vector_base::_M_allocate (inline) 14ms 0.071% 61.31% 357ms 1.81% std::__new_allocator::deallocate (inline) 17ms 0.086% 61.40% 353ms 1.79% divconqrecurse 0 0% 61.40% 353ms 1.79% std::allocator_traits::deallocate (inline) 142ms 0.72% 62.12% 345ms 1.75% std::_Rb_tree::_M_get_insert_unique_pos 23ms 0.12% 62.24% 340ms 1.73% Element::ResetIndex 98ms 0.5% 62.74% 329ms 1.67% mergehulls 3ms 0.015% 62.75% 324ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.086% 62.84% 322ms 1.64% std::_Rb_tree::~_Rb_tree (inline) 314ms 1.60% 64.43% 314ms 1.60% std::type_info::name (inline) 0 0% 64.43% 313ms 1.59% std::_Rb_tree::_M_drop_node (inline) 14ms 0.071% 64.50% 308ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 137ms 0.7% 65.20% 305ms 1.55% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 65.22% 300ms 1.52% NodeLocationWriter::Visit 3ms 0.015% 65.24% 295ms 1.50% Cell::GetMutationState 243ms 1.23% 66.47% 286ms 1.45% _int_free 2ms 0.01% 66.48% 280ms 1.42% Cell::GetCellProliferativeType 0 0% 66.48% 280ms 1.42% std::set::~set (inline) 8ms 0.041% 66.52% 274ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.52% 273ms 1.39% std::_Rb_tree::_M_put_node (inline) 266ms 1.35% 67.87% 267ms 1.36% std::vector::operator[] (inline) 1ms 0.0051% 67.88% 265ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.14% 68.02% 263ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 7ms 0.036% 68.06% 262ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.076% 68.13% 258ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.056% 68.19% 258ms 1.31% std::vector::push_back (inline) 4ms 0.02% 68.21% 255ms 1.30% alternateaxes 14ms 0.071% 68.28% 252ms 1.28% AbstractTetrahedralElement::CalculateJacobian 233ms 1.18% 69.46% 251ms 1.28% vertexmedian 16ms 0.081% 69.54% 249ms 1.26% std::num_put::_M_insert_float 16ms 0.081% 69.63% 242ms 1.23% std::vector::_M_realloc_insert 71ms 0.36% 69.99% 241ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 15ms 0.076% 70.06% 239ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 70.07% 235ms 1.19% std::set::set (inline) 5ms 0.025% 70.10% 223ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 166ms 0.84% 70.94% 217ms 1.10% AbstractElement::GetNodeGlobalIndex 0 0% 70.94% 214ms 1.09% TetrahedralMesh::RefreshJacobianCachedData 214ms 1.09% 72.03% 214ms 1.09% [libchaste_cell_based.so] 26ms 0.13% 72.16% 212ms 1.08% std::_Rb_tree::_M_copy (inline) 44ms 0.22% 72.38% 210ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.041% 72.42% 207ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.2% 72.62% 201ms 1.02% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 21ms 0.11% 72.73% 199ms 1.01% AbstractTetrahedralElement::RefreshJacobian 11ms 0.056% 72.79% 194ms 0.99% Element::MarkAsDeleted 2ms 0.01% 72.80% 189ms 0.96% std::__cxx11::collate::do_transform 188ms 0.96% 73.75% 188ms 0.96% Node::GetIndex 187ms 0.95% 74.70% 187ms 0.95% std::_Rb_tree_insert_and_rebalance 52ms 0.26% 74.96% 186ms 0.94% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.96% 183ms 0.93% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.96% 183ms 0.93% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.96% 180ms 0.91% OffLatticeSimulation::ApplyBoundaries 14ms 0.071% 75.04% 179ms 0.91% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 75.04% 176ms 0.89% Cell::HasCellProperty (inline) 1ms 0.0051% 75.04% 175ms 0.89% CellPropertyCollection::HasProperty 124ms 0.63% 75.67% 175ms 0.89% malloc_consolidate 4ms 0.02% 75.69% 172ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0051% 75.70% 171ms 0.87% ___vsnprintf 0 0% 75.70% 170ms 0.86% __vsnprintf_internal (inline) 22ms 0.11% 75.81% 168ms 0.85% __printf_buffer 17ms 0.086% 75.89% 159ms 0.81% TetrahedralMesh::Clear 7ms 0.036% 75.93% 156ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 69ms 0.35% 76.28% 152ms 0.77% AbstractElement::GetNodeLocation 28ms 0.14% 76.42% 152ms 0.77% TetrahedralMesh::EdgesEnd 152ms 0.77% 77.19% 152ms 0.77% std::vector::size (inline) 3ms 0.015% 77.21% 147ms 0.75% CellProliferativeTypesWriter::VisitCell 1ms 0.0051% 77.21% 140ms 0.71% boost::numeric::ublas::vector_assign (inline) 140ms 0.71% 77.93% 140ms 0.71% incircle 42ms 0.21% 78.14% 139ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 139ms 0.71% 78.85% 139ms 0.71% unlink_chunk 2ms 0.01% 78.86% 137ms 0.7% __printf_fp_l_buffer 0 0% 78.86% 137ms 0.7% __printf_fp_spec (inline) 80ms 0.41% 79.26% 136ms 0.69% std::_Rb_tree::equal_range (inline) 45ms 0.23% 79.49% 135ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 130ms 0.66% 80.15% 130ms 0.66% AbstractCellMutationState::~AbstractCellMutationState 5ms 0.025% 80.18% 130ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 69ms 0.35% 80.53% 130ms 0.66% __printf_fp_buffer_1 5ms 0.025% 80.55% 129ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 73ms 0.37% 80.92% 125ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.92% 123ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.92% 122ms 0.62% OutputFileHandler::OpenOutputFile 14ms 0.071% 80.99% 122ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 39ms 0.2% 81.19% 120ms 0.61% std::__ostream_insert 118ms 0.6% 81.79% 118ms 0.6% AbstractCellProperty::~AbstractCellProperty 38ms 0.19% 81.99% 118ms 0.6% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0051% 81.99% 118ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 12ms 0.061% 82.05% 118ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 113ms 0.57% 82.63% 118ms 0.6% vertexsort 26ms 0.13% 82.76% 117ms 0.59% std::num_put::_M_insert_int 115ms 0.58% 83.34% 115ms 0.58% std::_Rb_tree_increment 0 0% 83.34% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 68ms 0.35% 83.69% 110ms 0.56% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0051% 83.69% 109ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.69% 107ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 83.69% 104ms 0.53% Cell::SetCellProliferativeType 36ms 0.18% 83.88% 103ms 0.52% boost::numeric::ublas::indexing_vector_assign 99ms 0.5% 84.38% 99ms 0.5% [libchaste_mesh.so] 6ms 0.03% 84.41% 99ms 0.5% boost::detail::shared_count::~shared_count (inline) 0 0% 84.41% 99ms 0.5% boost::shared_ptr::~shared_ptr (inline)