File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16425ms, 84.38% of 19465ms total Dropped 798 nodes (cum <= 97.33ms) flat flat% sum% cum cum% 0 0% 0% 19418ms 99.76% __libc_start_call_main 0 0% 0% 19418ms 99.76% __libc_start_main_impl 0 0% 0% 19418ms 99.76% _start 0 0% 0% 19395ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19395ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19395ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19395ms 99.64% main 0 0% 0% 19352ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19352ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19352ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19326ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 14768ms 75.87% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9345ms 48.01% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.031% 9250ms 47.52% Cell::ReadyToDivide 5ms 0.026% 0.057% 9175ms 47.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.062% 9039ms 46.44% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.067% 0.13% 9030ms 46.39% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.13% 9011ms 46.29% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.4% 0.53% 8857ms 45.50% AbstractOneStepIvpOdeSolver::InternalSolve 1044ms 5.36% 5.90% 7959ms 40.89% RungeKutta4IvpOdeSolver::CalculateNextYValue 2754ms 14.15% 20.05% 6732ms 34.59% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.05% 5305ms 27.25% MeshBasedCellPopulation::Update 6ms 0.031% 20.08% 4093ms 21.03% Cylindrical2dMesh::ReMesh 72ms 0.37% 20.45% 3994ms 20.52% AbstractCellProperty::IsType (inline) 337ms 1.73% 22.18% 2623ms 13.48% AbstractCellProperty::IsSame 0 0% 22.18% 2541ms 13.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 263ms 1.35% 23.53% 2286ms 11.74% std::type_info::operator== (inline) 0 0% 23.53% 2236ms 11.49% MutableMesh::ReMesh 0 0% 23.53% 2191ms 11.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 23.58% 2148ms 11.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 2093ms 10.75% 34.33% 2093ms 10.75% __strcmp_avx2 0 0% 34.33% 2010ms 10.33% AbstractCellPopulation::WriteResultsToFiles 785ms 4.03% 38.37% 1858ms 9.55% std::_Rb_tree::_M_lower_bound (inline) 181ms 0.93% 39.30% 1726ms 8.87% TetrahedralMesh::EdgeIterator::operator++ 89ms 0.46% 39.75% 1416ms 7.27% std::_Rb_tree::find (inline) 0 0% 39.75% 1172ms 6.02% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.041% 39.79% 1147ms 5.89% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 22ms 0.11% 39.91% 1104ms 5.67% TetrahedralMesh::ImportFromMesher 37ms 0.19% 40.10% 1053ms 5.41% operator new 14ms 0.072% 40.17% 1026ms 5.27% MeshBasedCellPopulation::SpringIterator::operator++ 236ms 1.21% 41.38% 997ms 5.12% __GI___libc_malloc 13ms 0.067% 41.45% 964ms 4.95% std::set::insert (inline) 22ms 0.11% 41.56% 951ms 4.89% std::_Rb_tree::_M_insert_unique 38ms 0.2% 41.76% 921ms 4.73% std::__new_allocator::allocate (inline) 0 0% 41.76% 915ms 4.70% std::allocator_traits::allocate (inline) 0 0% 41.76% 881ms 4.53% triangulate 0 0% 41.76% 843ms 4.33% std::set::count (inline) 0 0% 41.76% 798ms 4.10% delaunay 1ms 0.0051% 41.76% 797ms 4.09% divconqdelaunay 2ms 0.01% 41.77% 734ms 3.77% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 719ms 3.69% 45.47% 719ms 3.69% std::_Rb_tree::_S_right (inline) 52ms 0.27% 45.73% 703ms 3.61% std::map::operator[] (partial-inline) 700ms 3.60% 49.33% 700ms 3.60% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.021% 49.35% 696ms 3.58% CellPopulationElementWriter::Visit 1ms 0.0051% 49.36% 690ms 3.54% AbstractTwoBodyInteractionForce::AddForceContribution 381ms 1.96% 51.31% 670ms 3.44% _int_malloc 21ms 0.11% 51.42% 654ms 3.36% std::less::operator() (inline) 633ms 3.25% 54.67% 633ms 3.25% std::operator< (inline) 16ms 0.082% 54.75% 620ms 3.19% AbstractCellPopulation::GetCellUsingLocationIndex 185ms 0.95% 55.71% 598ms 3.07% __dynamic_cast 32ms 0.16% 55.87% 597ms 3.07% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 55.87% 588ms 3.02% std::_Rb_tree::_M_create_node (inline) 5ms 0.026% 55.90% 585ms 3.01% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.041% 55.94% 581ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.94% 567ms 2.91% std::map::find (inline) 0 0% 55.94% 560ms 2.88% std::_Rb_tree::_M_get_node (inline) 11ms 0.057% 55.99% 554ms 2.85% Element::Element 0 0% 55.99% 551ms 2.83% std::_Rb_tree::lower_bound (inline) 0 0% 55.99% 551ms 2.83% std::map::lower_bound (inline) 30ms 0.15% 56.15% 543ms 2.79% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.15% 529ms 2.72% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.036% 56.18% 517ms 2.66% MutableMesh::ReIndex 14ms 0.072% 56.25% 514ms 2.64% Cylindrical2dMesh::ReconstructCylindricalMesh 16ms 0.082% 56.34% 492ms 2.53% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 56.35% 472ms 2.42% AbstractCellProperty::IsSubType (inline) 69ms 0.35% 56.71% 467ms 2.40% std::ostream::_M_insert 0 0% 56.71% 467ms 2.40% std::ostream::operator<< (inline) 15ms 0.077% 56.78% 466ms 2.39% Element::RegisterWithNodes (inline) 11ms 0.057% 56.84% 443ms 2.28% Node::AddElement 258ms 1.33% 58.17% 419ms 2.15% AbstractCellMutationState::AbstractCellMutationState 105ms 0.54% 58.71% 418ms 2.15% __GI___libc_free 8ms 0.041% 58.75% 398ms 2.04% std::_Rb_tree::erase 0 0% 58.75% 394ms 2.02% std::set::erase (inline) 15ms 0.077% 58.82% 392ms 2.01% divconqrecurse 136ms 0.7% 59.52% 387ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.057% 59.58% 384ms 1.97% Node::RemoveElement 112ms 0.58% 60.15% 380ms 1.95% std::_Rb_tree::_M_erase 370ms 1.90% 62.05% 370ms 1.90% [libchaste_cell_based.so] 98ms 0.5% 62.56% 367ms 1.89% mergehulls 27ms 0.14% 62.70% 363ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0051% 62.70% 356ms 1.83% std::_Vector_base::_M_allocate (inline) 4ms 0.021% 62.72% 349ms 1.79% Cell::GetMutationState 29ms 0.15% 62.87% 342ms 1.76% Element::ResetIndex 8ms 0.041% 62.91% 341ms 1.75% std::__new_allocator::deallocate (inline) 0 0% 62.91% 334ms 1.72% std::allocator_traits::deallocate (inline) 0 0% 62.91% 332ms 1.71% std::set::~set (inline) 1ms 0.0051% 62.92% 325ms 1.67% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 62.92% 325ms 1.67% std::_Rb_tree::_M_drop_node (inline) 12ms 0.062% 62.98% 322ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 21ms 0.11% 63.09% 314ms 1.61% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 63.09% 312ms 1.60% NodeLocationWriter::Visit 248ms 1.27% 64.36% 312ms 1.60% _int_free 150ms 0.77% 65.13% 305ms 1.57% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.031% 65.16% 293ms 1.51% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 65.17% 290ms 1.49% AbstractCellPopulation::Iterator::operator++ (inline) 34ms 0.17% 65.34% 285ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.031% 65.37% 285ms 1.46% std::set::set (inline) 1ms 0.0051% 65.38% 282ms 1.45% Cell::GetCellProliferativeType 0 0% 65.38% 278ms 1.43% std::_Rb_tree::_M_put_node (inline) 271ms 1.39% 66.77% 274ms 1.41% std::vector::operator[] (inline) 1ms 0.0051% 66.78% 267ms 1.37% alternateaxes 244ms 1.25% 68.03% 265ms 1.36% vertexmedian 27ms 0.14% 68.17% 264ms 1.36% std::_Rb_tree::_M_copy (inline) 10ms 0.051% 68.22% 264ms 1.36% std::vector::push_back (inline) 18ms 0.092% 68.31% 253ms 1.30% std::num_put::_M_insert_float 20ms 0.1% 68.42% 248ms 1.27% AbstractTetrahedralElement::CalculateJacobian 20ms 0.1% 68.52% 244ms 1.25% std::vector::_M_realloc_insert 7ms 0.036% 68.55% 243ms 1.25% AbstractCellPopulation::IsCellAttachedToLocationIndex 91ms 0.47% 69.02% 241ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 61ms 0.31% 69.33% 240ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 99ms 0.51% 69.84% 233ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.046% 69.89% 232ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 85ms 0.44% 70.33% 231ms 1.19% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 70.33% 222ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.087% 70.42% 220ms 1.13% Element::MarkAsDeleted 1ms 0.0051% 70.42% 218ms 1.12% MeshBasedCellPopulation::GetDampingConstant 15ms 0.077% 70.50% 216ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 70.51% 215ms 1.10% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0051% 70.52% 211ms 1.08% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 70.53% 210ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 15ms 0.077% 70.61% 204ms 1.05% TetrahedralMesh::Clear 7ms 0.036% 70.64% 200ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 70.66% 200ms 1.03% std::__cxx11::collate::do_transform 0 0% 70.66% 193ms 0.99% ___vsnprintf 0 0% 70.66% 193ms 0.99% __vsnprintf_internal (inline) 4ms 0.021% 70.68% 192ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.046% 70.72% 190ms 0.98% __printf_buffer 129ms 0.66% 71.38% 187ms 0.96% AbstractElement::GetNodeGlobalIndex 139ms 0.71% 72.10% 186ms 0.96% malloc_consolidate 123ms 0.63% 72.73% 181ms 0.93% std::_Rb_tree::equal_range (inline) 21ms 0.11% 72.84% 176ms 0.9% AbstractTetrahedralElement::RefreshJacobian 176ms 0.9% 73.74% 176ms 0.9% [libchaste_crypt.so] 174ms 0.89% 74.64% 174ms 0.89% Node::GetIndex 4ms 0.021% 74.66% 172ms 0.88% __printf_fp_l_buffer 0 0% 74.66% 172ms 0.88% __printf_fp_spec (inline) 167ms 0.86% 75.52% 167ms 0.86% incircle 2ms 0.01% 75.53% 165ms 0.85% CellPropertyCollection::HasProperty 0 0% 75.53% 163ms 0.84% Cell::HasCellProperty (inline) 64ms 0.33% 75.85% 162ms 0.83% __printf_fp_buffer_1 1ms 0.0051% 75.86% 156ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 155ms 0.8% 76.66% 155ms 0.8% std::type_info::name (inline) 152ms 0.78% 77.44% 152ms 0.78% std::_Rb_tree_insert_and_rebalance 152ms 0.78% 78.22% 152ms 0.78% std::vector::size (inline) 50ms 0.26% 78.47% 150ms 0.77% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 52ms 0.27% 78.74% 145ms 0.74% std::__ostream_insert 144ms 0.74% 79.48% 144ms 0.74% unlink_chunk 1ms 0.0051% 79.49% 142ms 0.73% boost::numeric::ublas::vector_assign (inline) 60ms 0.31% 79.79% 140ms 0.72% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 40ms 0.21% 80.00% 138ms 0.71% TetrahedralMesh::EdgesEnd (partial-inline) 49ms 0.25% 80.25% 136ms 0.7% AbstractElement::GetNodeLocation 4ms 0.021% 80.27% 136ms 0.7% CellProliferativeTypesWriter::VisitCell 84ms 0.43% 80.70% 134ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.041% 80.74% 131ms 0.67% Node::~Node 20ms 0.1% 80.85% 130ms 0.67% boost::detail::shared_count::~shared_count (inline) 0 0% 80.85% 130ms 0.67% boost::shared_ptr::~shared_ptr (inline) 5ms 0.026% 80.87% 129ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.026% 80.90% 128ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.90% 125ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 115ms 0.59% 81.49% 125ms 0.64% vertexsort 11ms 0.057% 81.55% 124ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 8ms 0.041% 81.59% 123ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.015% 81.60% 122ms 0.63% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 81.60% 121ms 0.62% std::operator<< (inline) 0 0% 81.60% 119ms 0.61% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 81.60% 118ms 0.61% OutputFileHandler::OpenOutputFile 0 0% 81.60% 117ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 31ms 0.16% 81.76% 113ms 0.58% boost::numeric::ublas::indexing_vector_assign 1ms 0.0051% 81.77% 112ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.01% 81.78% 108ms 0.55% Cell::SetCellProliferativeType 106ms 0.54% 82.32% 106ms 0.54% AbstractCellMutationState::~AbstractCellMutationState 46ms 0.24% 82.56% 106ms 0.54% std::basic_filebuf::xsputn 0 0% 82.56% 103ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 8ms 0.041% 82.60% 103ms 0.53% Cylindrical2dMesh::CreateMirrorNodes 95ms 0.49% 83.09% 103ms 0.53% boost::detail::sp_counted_base::release 101ms 0.52% 83.61% 101ms 0.52% std::_Rb_tree_increment 4ms 0.021% 83.63% 100ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 99ms 0.51% 84.14% 99ms 0.51% [libchaste_mesh.so] 48ms 0.25% 84.38% 99ms 0.51% boost::shared_ptr::shared_ptr (inline)