File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16922ms, 83.59% of 20245ms total Dropped 799 nodes (cum <= 101.22ms) flat flat% sum% cum cum% 0 0% 0% 20200ms 99.78% __libc_start_call_main 0 0% 0% 20200ms 99.78% __libc_start_main_impl 0 0% 0% 20200ms 99.78% _start 0 0% 0% 20182ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20182ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20182ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20182ms 99.69% main 0 0% 0% 20141ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20141ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20141ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0049% 0.0049% 20114ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0.0049% 15555ms 76.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0049% 10178ms 50.27% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0049% 0.0099% 10092ms 49.85% Cell::ReadyToDivide 5ms 0.025% 0.035% 10014ms 49.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0099% 0.044% 9871ms 48.76% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 21ms 0.1% 0.15% 9861ms 48.71% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.15% 9837ms 48.59% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.39% 0.54% 9657ms 47.70% AbstractOneStepIvpOdeSolver::InternalSolve 871ms 4.30% 4.84% 8832ms 43.63% RungeKutta4IvpOdeSolver::CalculateNextYValue 3626ms 17.91% 22.75% 7723ms 38.15% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.75% 5261ms 25.99% MeshBasedCellPopulation::Update 176ms 0.87% 23.62% 4108ms 20.29% AbstractCellProperty::IsType (inline) 6ms 0.03% 23.65% 4058ms 20.04% Cylindrical2dMesh::ReMesh 591ms 2.92% 26.57% 2860ms 14.13% AbstractCellProperty::IsSame 1ms 0.0049% 26.57% 2511ms 12.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 427ms 2.11% 28.68% 2269ms 11.21% std::type_info::operator== (inline) 1ms 0.0049% 28.69% 2224ms 10.99% MutableMesh::ReMesh 0 0% 28.69% 2204ms 10.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.044% 28.73% 2172ms 10.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.73% 2041ms 10.08% AbstractCellPopulation::WriteResultsToFiles 812ms 4.01% 32.74% 1892ms 9.35% std::_Rb_tree::_M_lower_bound (inline) 1825ms 9.01% 41.76% 1825ms 9.01% __strcmp_avx2 173ms 0.85% 42.61% 1687ms 8.33% TetrahedralMesh::EdgeIterator::operator++ 69ms 0.34% 42.95% 1420ms 7.01% std::_Rb_tree::find (inline) 2ms 0.0099% 42.96% 1161ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 42.98% 1139ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 7ms 0.035% 43.02% 1114ms 5.50% TetrahedralMesh::ImportFromMesher 46ms 0.23% 43.25% 1092ms 5.39% operator new 245ms 1.21% 44.46% 1036ms 5.12% __GI___libc_malloc 12ms 0.059% 44.51% 1005ms 4.96% MeshBasedCellPopulation::SpringIterator::operator++ 51ms 0.25% 44.77% 973ms 4.81% std::__new_allocator::allocate (inline) 9ms 0.044% 44.81% 973ms 4.81% std::set::insert (inline) 0 0% 44.81% 967ms 4.78% std::allocator_traits::allocate (inline) 14ms 0.069% 44.88% 964ms 4.76% std::_Rb_tree::_M_insert_unique 0 0% 44.88% 859ms 4.24% std::set::count (inline) 1ms 0.0049% 44.89% 831ms 4.10% triangulate 0 0% 44.89% 753ms 3.72% delaunay 3ms 0.015% 44.90% 752ms 3.71% divconqdelaunay 4ms 0.02% 44.92% 745ms 3.68% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 63ms 0.31% 45.23% 737ms 3.64% std::map::operator[] (partial-inline) 1ms 0.0049% 45.24% 712ms 3.52% AbstractTwoBodyInteractionForce::AddForceContribution 711ms 3.51% 48.75% 711ms 3.51% std::_Rb_tree::_S_right (inline) 7ms 0.035% 48.78% 697ms 3.44% CellPopulationElementWriter::Visit 392ms 1.94% 50.72% 695ms 3.43% _int_malloc 186ms 0.92% 51.64% 689ms 3.40% __dynamic_cast 660ms 3.26% 54.90% 668ms 3.30% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 54.90% 631ms 3.12% std::_Rb_tree::_M_create_node (inline) 34ms 0.17% 55.07% 627ms 3.10% std::_Rb_tree::_M_insert_ (inline) 13ms 0.064% 55.13% 625ms 3.09% std::less::operator() (inline) 4ms 0.02% 55.15% 614ms 3.03% CellPropertyCollection::GetPropertiesType (inline) 612ms 3.02% 58.17% 612ms 3.02% std::operator< (inline) 0 0% 58.17% 602ms 2.97% std::_Rb_tree::_M_get_node (inline) 31ms 0.15% 58.33% 599ms 2.96% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.015% 58.34% 592ms 2.92% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.1% 58.44% 571ms 2.82% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.44% 571ms 2.82% std::_Rb_tree::lower_bound (inline) 0 0% 58.44% 571ms 2.82% std::map::lower_bound (inline) 0 0% 58.44% 567ms 2.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.44% 557ms 2.75% std::map::find (inline) 12ms 0.059% 58.50% 547ms 2.70% Element::Element 4ms 0.02% 58.52% 520ms 2.57% AbstractCellProperty::IsSubType (inline) 15ms 0.074% 58.60% 506ms 2.50% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 58.61% 503ms 2.48% MutableMesh::ReIndex 8ms 0.04% 58.65% 477ms 2.36% Element::RegisterWithNodes (inline) 9ms 0.044% 58.70% 475ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.0099% 58.71% 469ms 2.32% std::ostream::operator<< (inline) 64ms 0.32% 59.02% 466ms 2.30% std::ostream::_M_insert 7ms 0.035% 59.06% 465ms 2.30% Node::AddElement 313ms 1.55% 60.60% 451ms 2.23% AbstractCellMutationState::AbstractCellMutationState 146ms 0.72% 61.32% 415ms 2.05% __GI___libc_free 15ms 0.074% 61.40% 388ms 1.92% divconqrecurse 3ms 0.015% 61.41% 376ms 1.86% std::set::erase (inline) 11ms 0.054% 61.47% 373ms 1.84% Node::RemoveElement 13ms 0.064% 61.53% 373ms 1.84% std::_Rb_tree::erase 179ms 0.88% 62.42% 372ms 1.84% __cxxabiv1::__si_class_type_info::__do_dyncast 105ms 0.52% 62.93% 367ms 1.81% mergehulls 2ms 0.0099% 62.94% 366ms 1.81% std::_Vector_base::_M_allocate (inline) 122ms 0.6% 63.55% 362ms 1.79% std::_Rb_tree::_M_erase 18ms 0.089% 63.64% 347ms 1.71% std::__new_allocator::deallocate (inline) 0 0% 63.64% 342ms 1.69% std::allocator_traits::deallocate (inline) 24ms 0.12% 63.75% 336ms 1.66% Element::ResetIndex 3ms 0.015% 63.77% 332ms 1.64% Cell::GetMutationState 6ms 0.03% 63.80% 331ms 1.63% Cell::GetCellProliferativeType 17ms 0.084% 63.88% 327ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 118ms 0.58% 64.47% 323ms 1.60% std::_Rb_tree::_M_get_insert_unique_pos 312ms 1.54% 66.01% 312ms 1.54% std::type_info::name (inline) 7ms 0.035% 66.04% 311ms 1.54% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 66.06% 311ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 297ms 1.47% 67.52% 298ms 1.47% std::vector::operator[] (inline) 0 0% 67.52% 297ms 1.47% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.52% 294ms 1.45% std::set::~set (inline) 3ms 0.015% 67.54% 292ms 1.44% NodeLocationWriter::Visit 23ms 0.11% 67.65% 281ms 1.39% std::vector::push_back (inline) 5ms 0.025% 67.68% 277ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 224ms 1.11% 68.78% 269ms 1.33% _int_free 20ms 0.099% 68.88% 269ms 1.33% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.88% 268ms 1.32% std::_Rb_tree::_M_put_node (inline) 19ms 0.094% 68.98% 268ms 1.32% std::num_put::_M_insert_float 0 0% 68.98% 262ms 1.29% AbstractCellPopulation::Iterator::operator++ (inline) 34ms 0.17% 69.14% 261ms 1.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.11% 69.25% 261ms 1.29% AbstractTetrahedralElement::CalculateJacobian 2ms 0.0099% 69.26% 259ms 1.28% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 69.26% 253ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.059% 69.32% 252ms 1.24% std::vector::_M_realloc_insert 9ms 0.044% 69.37% 250ms 1.23% alternateaxes 0 0% 69.37% 245ms 1.21% std::set::set (inline) 234ms 1.16% 70.52% 241ms 1.19% vertexmedian 238ms 1.18% 71.70% 238ms 1.18% [libchaste_cell_based.so] 60ms 0.3% 71.99% 229ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 72.01% 228ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.01% 228ms 1.13% MeshBasedCellPopulation::GetDampingConstant 15ms 0.074% 72.09% 226ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 20ms 0.099% 72.19% 220ms 1.09% std::_Rb_tree::_M_copy (inline) 10ms 0.049% 72.24% 214ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.04% 72.27% 213ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 33ms 0.16% 72.44% 210ms 1.04% TetrahedralMesh::Clear 2ms 0.0099% 72.45% 203ms 1.00% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 78ms 0.39% 72.83% 203ms 1.00% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.0099% 72.84% 201ms 0.99% std::__cxx11::collate::do_transform 62ms 0.31% 73.15% 196ms 0.97% std::_Rb_tree::_M_clone_node (inline) 36ms 0.18% 73.33% 193ms 0.95% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 12ms 0.059% 73.39% 193ms 0.95% Element::MarkAsDeleted 27ms 0.13% 73.52% 192ms 0.95% AbstractTetrahedralElement::RefreshJacobian 144ms 0.71% 74.23% 192ms 0.95% malloc_consolidate 3ms 0.015% 74.25% 189ms 0.93% ___vsnprintf 0 0% 74.25% 186ms 0.92% __vsnprintf_internal (inline) 19ms 0.094% 74.34% 185ms 0.91% __printf_buffer 129ms 0.64% 74.98% 180ms 0.89% AbstractElement::GetNodeGlobalIndex 0 0% 74.98% 176ms 0.87% OffLatticeSimulation::ApplyBoundaries 175ms 0.86% 75.84% 175ms 0.86% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 75.87% 174ms 0.86% CellProliferativeTypesWriter::VisitCell 171ms 0.84% 76.72% 171ms 0.84% Node::GetIndex 4ms 0.02% 76.73% 166ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 158ms 0.78% 77.52% 158ms 0.78% incircle 7ms 0.035% 77.55% 157ms 0.78% CellPropertyCollection::HasProperty 0 0% 77.55% 153ms 0.76% Cell::HasCellProperty (inline) 3ms 0.015% 77.56% 152ms 0.75% __printf_fp_l_buffer 0 0% 77.56% 152ms 0.75% __printf_fp_spec (inline) 55ms 0.27% 77.84% 151ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 151ms 0.75% 78.58% 151ms 0.75% unlink_chunk 71ms 0.35% 78.93% 149ms 0.74% AbstractElement::GetNodeLocation 8ms 0.04% 78.97% 146ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 107ms 0.53% 79.50% 144ms 0.71% std::_Rb_tree::equal_range (inline) 71ms 0.35% 79.85% 141ms 0.7% __printf_fp_buffer_1 141ms 0.7% 80.55% 141ms 0.7% std::vector::size (inline) 6ms 0.03% 80.58% 133ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 48ms 0.24% 80.82% 132ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.02% 80.83% 131ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 82ms 0.41% 81.24% 130ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 17ms 0.084% 81.32% 129ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 34ms 0.17% 81.49% 129ms 0.64% TetrahedralMesh::EdgesEnd 5ms 0.025% 81.52% 128ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.52% 126ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0049% 81.52% 126ms 0.62% boost::numeric::ublas::vector_assign (inline) 2ms 0.0099% 81.53% 125ms 0.62% OutputFileHandler::OpenOutputFile 49ms 0.24% 81.77% 117ms 0.58% std::__ostream_insert 10ms 0.049% 81.82% 116ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 0 0% 81.82% 115ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.82% 115ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 81.82% 115ms 0.57% Cell::SetCellProliferativeType 17ms 0.084% 81.91% 112ms 0.55% Node::~Node 111ms 0.55% 82.45% 111ms 0.55% AbstractCellProperty::~AbstractCellProperty 3ms 0.015% 82.47% 110ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 7ms 0.035% 82.50% 109ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.50% 108ms 0.53% std::vector::resize (inline) 5ms 0.025% 82.53% 107ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 105ms 0.52% 83.05% 105ms 0.52% std::_Rb_tree_rebalance_for_erase 1ms 0.0049% 83.05% 104ms 0.51% std::vector::_M_default_append 103ms 0.51% 83.56% 103ms 0.51% boost::shared_ptr::operator-> (inline) 5ms 0.025% 83.59% 103ms 0.51% std::_Rb_tree::_M_emplace_hint_unique