File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17411ms, 84.05% of 20716ms total Dropped 810 nodes (cum <= 103.58ms) flat flat% sum% cum cum% 0 0% 0% 20671ms 99.78% __libc_start_call_main 0 0% 0% 20671ms 99.78% __libc_start_main_impl 0 0% 0% 20671ms 99.78% _start 0 0% 0% 20652ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20652ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20652ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20652ms 99.69% main 0 0% 0% 20613ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20613ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20612ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20586ms 99.37% AbstractCellBasedSimulation::Solve 1ms 0.0048% 0.0048% 15928ms 76.89% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0048% 0.0097% 10247ms 49.46% AbstractCellBasedSimulation::DoCellBirth 4ms 0.019% 0.029% 10152ms 49.01% Cell::ReadyToDivide 5ms 0.024% 0.053% 10070ms 48.61% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0097% 0.063% 9925ms 47.91% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.077% 0.14% 9914ms 47.86% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.014% 0.15% 9893ms 47.76% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.34% 0.49% 9735ms 46.99% AbstractOneStepIvpOdeSolver::InternalSolve 889ms 4.29% 4.78% 8907ms 43.00% RungeKutta4IvpOdeSolver::CalculateNextYValue 3645ms 17.60% 22.38% 7784ms 37.57% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.38% 5553ms 26.81% MeshBasedCellPopulation::Update 9ms 0.043% 22.42% 4331ms 20.91% Cylindrical2dMesh::ReMesh 173ms 0.84% 23.26% 4182ms 20.19% AbstractCellProperty::IsType (inline) 582ms 2.81% 26.07% 2968ms 14.33% AbstractCellProperty::IsSame 0 0% 26.07% 2603ms 12.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0048% 26.07% 2412ms 11.64% MutableMesh::ReMesh 450ms 2.17% 28.24% 2386ms 11.52% std::type_info::operator== (inline) 0 0% 28.24% 2294ms 11.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 18ms 0.087% 28.33% 2239ms 10.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.33% 2046ms 9.88% AbstractCellPopulation::WriteResultsToFiles 796ms 3.84% 32.17% 1894ms 9.14% std::_Rb_tree::_M_lower_bound (inline) 1873ms 9.04% 41.21% 1873ms 9.04% __strcmp_avx2 168ms 0.81% 42.03% 1698ms 8.20% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.32% 42.34% 1418ms 6.84% std::_Rb_tree::find (inline) 14ms 0.068% 42.41% 1248ms 6.02% TetrahedralMesh::ImportFromMesher 0 0% 42.41% 1170ms 5.65% MeshBasedCellPopulation::UpdateNodePairs 41ms 0.2% 42.61% 1170ms 5.65% operator new 5ms 0.024% 42.63% 1142ms 5.51% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 238ms 1.15% 43.78% 1113ms 5.37% __GI___libc_malloc 25ms 0.12% 43.90% 1040ms 5.02% MeshBasedCellPopulation::SpringIterator::operator++ 44ms 0.21% 44.12% 1040ms 5.02% std::__new_allocator::allocate (inline) 0 0% 44.12% 1032ms 4.98% std::allocator_traits::allocate (inline) 11ms 0.053% 44.17% 927ms 4.47% std::set::insert (inline) 21ms 0.1% 44.27% 916ms 4.42% std::_Rb_tree::_M_insert_unique 0 0% 44.27% 893ms 4.31% std::set::count (inline) 1ms 0.0048% 44.27% 821ms 3.96% triangulate 462ms 2.23% 46.51% 797ms 3.85% _int_malloc 0 0% 46.51% 749ms 3.62% delaunay 3ms 0.014% 46.52% 747ms 3.61% divconqdelaunay 49ms 0.24% 46.76% 713ms 3.44% std::map::operator[] (partial-inline) 1ms 0.0048% 46.76% 712ms 3.44% AbstractTwoBodyInteractionForce::AddForceContribution 251ms 1.21% 47.97% 710ms 3.43% __dynamic_cast 7ms 0.034% 48.01% 709ms 3.42% CellPopulationElementWriter::Visit 4ms 0.019% 48.03% 707ms 3.41% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 689ms 3.33% 51.35% 689ms 3.33% std::_Rb_tree::_S_right (inline) 20ms 0.097% 51.45% 669ms 3.23% std::less::operator() (inline) 16ms 0.077% 51.53% 659ms 3.18% CellPropertyCollection::GetPropertiesType (inline) 649ms 3.13% 54.66% 649ms 3.13% std::operator< (inline) 636ms 3.07% 57.73% 648ms 3.13% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 57.73% 633ms 3.06% std::_Rb_tree::_M_create_node (inline) 17ms 0.082% 57.81% 612ms 2.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 57.81% 610ms 2.94% std::_Rb_tree::_M_get_node (inline) 0 0% 57.81% 567ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 20ms 0.097% 57.91% 566ms 2.73% std::_Rb_tree::_M_insert_ (inline) 4ms 0.019% 57.93% 561ms 2.71% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.93% 560ms 2.70% std::_Rb_tree::lower_bound (inline) 0 0% 57.93% 560ms 2.70% std::map::lower_bound (inline) 10ms 0.048% 57.97% 551ms 2.66% MutableMesh::ReIndex 25ms 0.12% 58.10% 546ms 2.64% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.034% 58.13% 543ms 2.62% Element::Element 7ms 0.034% 58.16% 535ms 2.58% AbstractCellProperty::IsSubType (inline) 0 0% 58.16% 520ms 2.51% std::map::find (inline) 177ms 0.85% 59.02% 501ms 2.42% __GI___libc_free 54ms 0.26% 59.28% 497ms 2.40% std::ostream::_M_insert 0 0% 59.28% 497ms 2.40% std::ostream::operator<< (inline) 10ms 0.048% 59.33% 487ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 337ms 1.63% 60.95% 485ms 2.34% AbstractCellMutationState::AbstractCellMutationState 7ms 0.034% 60.99% 468ms 2.26% Element::RegisterWithNodes (inline) 13ms 0.063% 61.05% 464ms 2.24% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.058% 61.11% 456ms 2.20% Node::AddElement 1ms 0.0048% 61.11% 423ms 2.04% std::_Vector_base::_M_allocate (inline) 143ms 0.69% 61.80% 410ms 1.98% std::_Rb_tree::_M_erase 7ms 0.034% 61.84% 370ms 1.79% std::_Rb_tree::erase 1ms 0.0048% 61.84% 370ms 1.79% std::set::erase (inline) 4ms 0.019% 61.86% 363ms 1.75% Cell::GetMutationState 10ms 0.048% 61.91% 363ms 1.75% std::__new_allocator::deallocate (inline) 14ms 0.068% 61.98% 362ms 1.75% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 12ms 0.058% 62.03% 360ms 1.74% Node::RemoveElement 0 0% 62.03% 360ms 1.74% std::allocator_traits::deallocate (inline) 14ms 0.068% 62.10% 357ms 1.72% divconqrecurse 11ms 0.053% 62.15% 354ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 31ms 0.15% 62.30% 345ms 1.67% Element::ResetIndex 172ms 0.83% 63.13% 342ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 89ms 0.43% 63.56% 339ms 1.64% mergehulls 135ms 0.65% 64.22% 330ms 1.59% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 64.22% 330ms 1.59% std::set::~set (inline) 4ms 0.019% 64.24% 326ms 1.57% Cell::GetCellProliferativeType 0 0% 64.24% 321ms 1.55% NodeLocationWriter::Visit 38ms 0.18% 64.42% 321ms 1.55% TetrahedralMesh::Clear 244ms 1.18% 65.60% 321ms 1.55% _int_free 0 0% 65.60% 316ms 1.53% std::_Rb_tree::_M_drop_node (inline) 311ms 1.50% 67.10% 311ms 1.50% std::type_info::name (inline) 0 0% 67.10% 299ms 1.44% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.077% 67.18% 298ms 1.44% std::_Rb_tree::_Rb_tree (partial-inline) 294ms 1.42% 68.59% 294ms 1.42% std::vector::operator[] (inline) 20ms 0.097% 68.69% 292ms 1.41% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0048% 68.70% 289ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.082% 68.78% 288ms 1.39% std::num_put::_M_insert_float 32ms 0.15% 68.93% 286ms 1.38% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.93% 285ms 1.38% std::_Rb_tree::_M_put_node (inline) 17ms 0.082% 69.01% 283ms 1.37% std::vector::push_back (inline) 5ms 0.024% 69.04% 282ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.019% 69.06% 282ms 1.36% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0048% 69.06% 282ms 1.36% MeshBasedCellPopulation::GetDampingConstant 0 0% 69.06% 281ms 1.36% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.06% 272ms 1.31% std::set::set (inline) 6ms 0.029% 69.09% 268ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.068% 69.16% 262ms 1.26% std::vector::_M_realloc_insert 247ms 1.19% 70.35% 247ms 1.19% [libchaste_cell_based.so] 27ms 0.13% 70.48% 247ms 1.19% std::_Rb_tree::_M_copy (inline) 1ms 0.0048% 70.49% 243ms 1.17% alternateaxes 14ms 0.068% 70.55% 242ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 57ms 0.28% 70.83% 242ms 1.17% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 230ms 1.11% 71.94% 242ms 1.17% vertexmedian 29ms 0.14% 72.08% 238ms 1.15% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0097% 72.09% 234ms 1.13% std::__cxx11::collate::do_transform 5ms 0.024% 72.11% 229ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 169ms 0.82% 72.93% 226ms 1.09% malloc_consolidate 1ms 0.0048% 72.93% 223ms 1.08% ___vsnprintf 0 0% 72.93% 222ms 1.07% __vsnprintf_internal (inline) 10ms 0.048% 72.98% 222ms 1.07% std::_Rb_tree::_M_erase_aux (inline) 53ms 0.26% 73.24% 220ms 1.06% ApcOneHitCellMutationState::ApcOneHitCellMutationState 23ms 0.11% 73.35% 218ms 1.05% __printf_buffer 3ms 0.014% 73.36% 216ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 64ms 0.31% 73.67% 215ms 1.04% std::_Rb_tree::_M_clone_node (inline) 154ms 0.74% 74.42% 195ms 0.94% AbstractElement::GetNodeGlobalIndex 66ms 0.32% 74.73% 195ms 0.94% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 74.73% 194ms 0.94% OffLatticeSimulation::ApplyBoundaries 3ms 0.014% 74.75% 188ms 0.91% CellProliferativeTypesWriter::VisitCell 90ms 0.43% 75.18% 186ms 0.9% AbstractElement::GetNodeLocation 19ms 0.092% 75.28% 183ms 0.88% Node::~Node 182ms 0.88% 76.15% 182ms 0.88% unlink_chunk 5ms 0.024% 76.18% 173ms 0.84% __printf_fp_l_buffer 0 0% 76.18% 173ms 0.84% __printf_fp_spec (inline) 15ms 0.072% 76.25% 172ms 0.83% Element::MarkAsDeleted 4ms 0.019% 76.27% 170ms 0.82% CellPropertyCollection::HasProperty 3ms 0.014% 76.28% 169ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 76.28% 166ms 0.8% Cell::HasCellProperty (inline) 165ms 0.8% 77.08% 165ms 0.8% Node::GetIndex 67ms 0.32% 77.40% 162ms 0.78% __printf_fp_buffer_1 28ms 0.14% 77.54% 156ms 0.75% TetrahedralMesh::EdgesEnd (partial-inline) 156ms 0.75% 78.29% 156ms 0.75% incircle 4ms 0.019% 78.31% 154ms 0.74% boost::numeric::ublas::vector_assign (inline) 151ms 0.73% 79.04% 151ms 0.73% std::_Rb_tree_insert_and_rebalance 9ms 0.043% 79.08% 147ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 89ms 0.43% 79.51% 145ms 0.7% std::_Rb_tree::equal_range (inline) 142ms 0.69% 80.20% 143ms 0.69% std::vector::size (inline) 0 0% 80.20% 139ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.20% 138ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.20% 135ms 0.65% std::vector::resize (inline) 1ms 0.0048% 80.20% 134ms 0.65% std::vector::_M_default_append 128ms 0.62% 80.82% 134ms 0.65% vertexsort 133ms 0.64% 81.46% 133ms 0.64% AbstractElement::IsDeleted 6ms 0.029% 81.49% 132ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.49% 132ms 0.64% OutputFileHandler::OpenOutputFile 83ms 0.4% 81.89% 131ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 6ms 0.029% 81.92% 129ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.92% 127ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.92% 126ms 0.61% NodeMap::NodeMap 33ms 0.16% 82.08% 124ms 0.6% boost::numeric::ublas::indexing_vector_assign 1ms 0.0048% 82.09% 123ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 14ms 0.068% 82.15% 123ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.25% 82.40% 121ms 0.58% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.0097% 82.41% 121ms 0.58% Cell::SetCellProliferativeType 118ms 0.57% 82.98% 118ms 0.57% std::_Rb_tree_increment 7ms 0.034% 83.02% 117ms 0.56% Cylindrical2dMesh::CreateMirrorNodes 73ms 0.35% 83.37% 117ms 0.56% TetrahedralMesh::EdgeIterator::EdgeIterator 6ms 0.029% 83.40% 117ms 0.56% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 37ms 0.18% 83.58% 116ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.024% 83.60% 116ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 14ms 0.068% 83.67% 114ms 0.55% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 56ms 0.27% 83.94% 112ms 0.54% std::__ostream_insert 1ms 0.0048% 83.94% 111ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0048% 83.95% 108ms 0.52% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 10ms 0.048% 84.00% 107ms 0.52% boost::detail::shared_count::~shared_count (inline) 0 0% 84.00% 107ms 0.52% boost::shared_ptr::~shared_ptr (inline) 6ms 0.029% 84.03% 106ms 0.51% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 4ms 0.019% 84.05% 104ms 0.5% std::_Rb_tree::_M_emplace_hint_unique