File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17106ms, 85.64% of 19975ms total Dropped 803 nodes (cum <= 99.88ms) flat flat% sum% cum cum% 0 0% 0% 19923ms 99.74% __libc_start_call_main 0 0% 0% 19923ms 99.74% __libc_start_main_impl 0 0% 0% 19923ms 99.74% _start 0 0% 0% 19900ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19900ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19900ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19900ms 99.62% main 0 0% 0% 19855ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19855ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19855ms 99.40% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19829ms 99.27% AbstractCellBasedSimulation::Solve 0 0% 0% 15090ms 75.54% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9537ms 47.74% AbstractCellBasedSimulation::DoCellBirth 8ms 0.04% 0.055% 9445ms 47.28% Cell::ReadyToDivide 3ms 0.015% 0.07% 9338ms 46.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.02% 0.09% 9182ms 45.97% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.075% 0.17% 9175ms 45.93% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.19% 9159ms 45.85% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.4% 0.58% 8944ms 44.78% AbstractOneStepIvpOdeSolver::InternalSolve 997ms 4.99% 5.57% 8042ms 40.26% RungeKutta4IvpOdeSolver::CalculateNextYValue 2868ms 14.36% 19.93% 6881ms 34.45% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.93% 5430ms 27.18% MeshBasedCellPopulation::Update 6ms 0.03% 19.96% 4210ms 21.08% Cylindrical2dMesh::ReMesh 58ms 0.29% 20.25% 4069ms 20.37% AbstractCellProperty::IsType (inline) 437ms 2.19% 22.44% 2649ms 13.26% AbstractCellProperty::IsSame 0 0% 22.44% 2606ms 13.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.005% 22.44% 2323ms 11.63% MutableMesh::ReMesh 1ms 0.005% 22.45% 2261ms 11.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.04% 22.49% 2212ms 11.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 260ms 1.30% 23.79% 2212ms 11.07% std::type_info::operator== (inline) 2ms 0.01% 23.80% 2122ms 10.62% AbstractCellPopulation::WriteResultsToFiles 2074ms 10.38% 34.18% 2074ms 10.38% __strcmp_avx2 843ms 4.22% 38.40% 1878ms 9.40% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.79% 39.19% 1718ms 8.60% TetrahedralMesh::EdgeIterator::operator++ 86ms 0.43% 39.62% 1412ms 7.07% std::_Rb_tree::find (inline) 0 0% 39.62% 1182ms 5.92% MeshBasedCellPopulation::UpdateNodePairs 15ms 0.075% 39.70% 1159ms 5.80% TetrahedralMesh::ImportFromMesher 6ms 0.03% 39.73% 1155ms 5.78% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 43ms 0.22% 39.94% 1079ms 5.40% operator new 15ms 0.075% 40.02% 1058ms 5.30% MeshBasedCellPopulation::SpringIterator::operator++ 232ms 1.16% 41.18% 1022ms 5.12% __GI___libc_malloc 18ms 0.09% 41.27% 1021ms 5.11% std::set::insert (inline) 13ms 0.065% 41.34% 1003ms 5.02% std::_Rb_tree::_M_insert_unique 50ms 0.25% 41.59% 969ms 4.85% std::__new_allocator::allocate (inline) 0 0% 41.59% 965ms 4.83% std::allocator_traits::allocate (inline) 2ms 0.01% 41.60% 903ms 4.52% triangulate 0 0% 41.60% 870ms 4.36% std::set::count (inline) 0 0% 41.60% 823ms 4.12% delaunay 6ms 0.03% 41.63% 823ms 4.12% divconqdelaunay 6ms 0.03% 41.66% 800ms 4.01% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 47ms 0.24% 41.89% 746ms 3.73% std::map::operator[] (partial-inline) 725ms 3.63% 45.52% 725ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.02% 45.54% 718ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.055% 45.60% 700ms 3.50% CellPopulationElementWriter::Visit 397ms 1.99% 47.58% 686ms 3.43% _int_malloc 26ms 0.13% 47.71% 684ms 3.42% CellPropertyCollection::GetPropertiesType (inline) 672ms 3.36% 51.08% 672ms 3.36% std::_Rb_tree::_S_right (inline) 0 0% 51.08% 661ms 3.31% std::_Rb_tree::_M_create_node (inline) 207ms 1.04% 52.12% 658ms 3.29% __dynamic_cast 6ms 0.03% 52.15% 644ms 3.22% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.05% 52.20% 642ms 3.21% std::less::operator() (inline) 11ms 0.055% 52.25% 637ms 3.19% AbstractCellPopulation::GetCellUsingLocationIndex 632ms 3.16% 55.41% 632ms 3.16% std::operator< (inline) 0 0% 55.41% 625ms 3.13% std::_Rb_tree::_M_get_node (inline) 28ms 0.14% 55.55% 611ms 3.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 30ms 0.15% 55.70% 611ms 3.06% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.70% 581ms 2.91% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.70% 581ms 2.91% std::_Rb_tree::lower_bound (inline) 0 0% 55.70% 581ms 2.91% std::map::lower_bound (inline) 4ms 0.02% 55.72% 559ms 2.80% Element::Element 8ms 0.04% 55.76% 541ms 2.71% MutableMesh::ReIndex 0 0% 55.76% 536ms 2.68% std::map::find (inline) 2ms 0.01% 55.77% 529ms 2.65% AbstractCellProperty::IsSubType (inline) 16ms 0.08% 55.85% 517ms 2.59% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.005% 55.86% 508ms 2.54% std::ostream::operator<< (inline) 66ms 0.33% 56.19% 506ms 2.53% std::ostream::_M_insert 11ms 0.055% 56.25% 492ms 2.46% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.06% 56.31% 478ms 2.39% Element::RegisterWithNodes (inline) 295ms 1.48% 57.78% 474ms 2.37% AbstractCellMutationState::AbstractCellMutationState 9ms 0.045% 57.83% 469ms 2.35% Node::AddElement 142ms 0.71% 58.54% 456ms 2.28% __GI___libc_free 22ms 0.11% 58.65% 424ms 2.12% Node::RemoveElement 10ms 0.05% 58.70% 417ms 2.09% std::_Rb_tree::erase 0 0% 58.70% 414ms 2.07% std::set::erase (inline) 413ms 2.07% 60.77% 413ms 2.07% [libchaste_cell_based.so] 14ms 0.07% 60.84% 412ms 2.06% divconqrecurse 106ms 0.53% 61.37% 390ms 1.95% mergehulls 159ms 0.8% 62.16% 379ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.055% 62.22% 372ms 1.86% std::__new_allocator::deallocate (inline) 93ms 0.47% 62.68% 366ms 1.83% std::_Rb_tree::_M_erase 35ms 0.18% 62.86% 366ms 1.83% std::_Rb_tree::~_Rb_tree (inline) 0 0% 62.86% 366ms 1.83% std::allocator_traits::deallocate (inline) 0 0% 62.86% 362ms 1.81% Cell::GetCellProliferativeType 35ms 0.18% 63.03% 358ms 1.79% Element::ResetIndex 1ms 0.005% 63.04% 352ms 1.76% Cell::GetMutationState 0 0% 63.04% 349ms 1.75% std::_Rb_tree::_M_drop_node (inline) 1ms 0.005% 63.04% 341ms 1.71% std::_Vector_base::_M_allocate (inline) 0 0% 63.04% 336ms 1.68% std::set::~set (inline) 5ms 0.025% 63.07% 331ms 1.66% LegacyCellProliferativeTypesWriter::VisitCell 159ms 0.8% 63.86% 330ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.035% 63.90% 315ms 1.58% AbstractCellPopulation::GetLocationIndexUsingCell 255ms 1.28% 65.18% 312ms 1.56% _int_free 0 0% 65.18% 311ms 1.56% NodeLocationWriter::Visit 8ms 0.04% 65.22% 310ms 1.55% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 21ms 0.11% 65.32% 304ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 65.32% 299ms 1.50% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 65.33% 286ms 1.43% alternateaxes 25ms 0.13% 65.46% 285ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 274ms 1.37% 66.83% 283ms 1.42% vertexmedian 0 0% 66.83% 282ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.055% 66.88% 281ms 1.41% std::vector::push_back (inline) 0 0% 66.88% 275ms 1.38% std::set::set (inline) 18ms 0.09% 66.97% 271ms 1.36% std::num_put::_M_insert_float 18ms 0.09% 67.06% 260ms 1.30% std::vector::_M_realloc_insert 63ms 0.32% 67.38% 258ms 1.29% ApcOneHitCellMutationState::ApcOneHitCellMutationState 101ms 0.51% 67.88% 255ms 1.28% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 19ms 0.095% 67.98% 254ms 1.27% AbstractTetrahedralElement::CalculateJacobian 28ms 0.14% 68.12% 253ms 1.27% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 68.13% 249ms 1.25% MeshBasedCellPopulation::GetDampingConstant 11ms 0.055% 68.19% 249ms 1.25% std::_Rb_tree::_M_erase_aux (inline) 8ms 0.04% 68.23% 246ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 68.24% 245ms 1.23% AbstractCentreBasedCellPopulation::GetDampingConstant 89ms 0.45% 68.68% 245ms 1.23% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.045% 68.73% 242ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 237ms 1.19% 69.91% 238ms 1.19% std::vector::operator[] (inline) 17ms 0.085% 70.00% 237ms 1.19% Element::MarkAsDeleted 0 0% 70.00% 227ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 24ms 0.12% 70.12% 224ms 1.12% TetrahedralMesh::Clear 79ms 0.4% 70.51% 222ms 1.11% std::_Rb_tree::_M_clone_node (inline) 4ms 0.02% 70.53% 220ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 70.55% 218ms 1.09% std::__cxx11::collate::do_transform 0 0% 70.55% 216ms 1.08% OffLatticeSimulation::ApplyBoundaries 5ms 0.025% 70.58% 211ms 1.06% CellPropertyCollection::HasProperty 3ms 0.015% 70.59% 209ms 1.05% ___vsnprintf 1ms 0.005% 70.60% 206ms 1.03% __vsnprintf_internal (inline) 0 0% 70.60% 205ms 1.03% Cell::HasCellProperty (inline) 12ms 0.06% 70.66% 204ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.025% 70.68% 204ms 1.02% CellProliferativeTypesWriter::VisitCell 14ms 0.07% 70.75% 203ms 1.02% __printf_buffer 142ms 0.71% 71.46% 196ms 0.98% AbstractElement::GetNodeGlobalIndex 33ms 0.17% 71.63% 191ms 0.96% AbstractTetrahedralElement::RefreshJacobian 8ms 0.04% 71.67% 185ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 175ms 0.88% 72.55% 175ms 0.88% incircle 4ms 0.02% 72.57% 174ms 0.87% __printf_fp_l_buffer 0 0% 72.57% 174ms 0.87% __printf_fp_spec (inline) 172ms 0.86% 73.43% 172ms 0.86% Node::GetIndex 55ms 0.28% 73.70% 166ms 0.83% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 110ms 0.55% 74.25% 165ms 0.83% std::_Rb_tree::equal_range (inline) 119ms 0.6% 74.85% 162ms 0.81% malloc_consolidate 161ms 0.81% 75.65% 161ms 0.81% std::_Rb_tree_insert_and_rebalance 75ms 0.38% 76.03% 160ms 0.8% __printf_fp_buffer_1 9ms 0.045% 76.08% 160ms 0.8% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 156ms 0.78% 76.86% 156ms 0.78% std::vector::size (inline) 7ms 0.035% 76.89% 155ms 0.78% MeshBasedCellPopulation::SpringsEnd (inline) 152ms 0.76% 77.65% 152ms 0.76% [libchaste_crypt.so] 38ms 0.19% 77.84% 151ms 0.76% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.01% 77.85% 149ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.02% 77.87% 147ms 0.74% boost::numeric::ublas::vector_assign (inline) 147ms 0.74% 78.61% 147ms 0.74% unlink_chunk 33ms 0.17% 78.77% 144ms 0.72% TetrahedralMesh::EdgesEnd (partial-inline) 62ms 0.31% 79.08% 141ms 0.71% AbstractElement::GetNodeLocation 9ms 0.045% 79.13% 139ms 0.7% Node::~Node 17ms 0.085% 79.21% 138ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 138ms 0.69% 79.90% 138ms 0.69% std::type_info::name (inline) 1ms 0.005% 79.91% 135ms 0.68% AbstractCellBasedWriter::OpenOutputFileForAppend 14ms 0.07% 79.98% 135ms 0.68% boost::detail::shared_count::~shared_count (inline) 0 0% 79.98% 135ms 0.68% boost::shared_ptr::~shared_ptr (inline) 84ms 0.42% 80.40% 134ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.40% 133ms 0.67% OutputFileHandler::OpenOutputFile 12ms 0.06% 80.46% 132ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.005% 80.47% 131ms 0.66% Cell::SetCellProliferativeType 4ms 0.02% 80.49% 131ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 131ms 0.66% 81.14% 131ms 0.66% std::_Rb_tree_increment 3ms 0.015% 81.16% 127ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 81.16% 121ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 19ms 0.095% 81.25% 121ms 0.61% MeshBasedCellPopulation::SpringIterator::SpringIterator 26ms 0.13% 81.38% 121ms 0.61% std::num_put::_M_insert_int 7ms 0.035% 81.42% 118ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 117ms 0.59% 82.00% 117ms 0.59% AbstractCellMutationState::~AbstractCellMutationState 110ms 0.55% 82.55% 115ms 0.58% boost::detail::sp_counted_base::release 4ms 0.02% 82.57% 114ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 2ms 0.01% 82.58% 114ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 102ms 0.51% 83.09% 114ms 0.57% vertexsort 0 0% 83.09% 113ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 78ms 0.39% 83.48% 110ms 0.55% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 48ms 0.24% 83.72% 108ms 0.54% std::basic_filebuf::xsputn 33ms 0.17% 83.89% 107ms 0.54% boost::numeric::ublas::indexing_vector_assign 103ms 0.52% 84.41% 103ms 0.52% AbstractCellProperty::AbstractCellProperty 4ms 0.02% 84.43% 103ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 103ms 0.52% 84.94% 103ms 0.52% counterclockwise 39ms 0.2% 85.14% 103ms 0.52% std::__ostream_insert 0 0% 85.14% 102ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 100ms 0.5% 85.64% 100ms 0.5% boost::shared_ptr::operator-> (inline)