File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16936ms, 84.67% of 20002ms total Dropped 814 nodes (cum <= 100.01ms) flat flat% sum% cum cum% 0 0% 0% 19956ms 99.77% __libc_start_call_main 0 0% 0% 19956ms 99.77% __libc_start_main_impl 0 0% 0% 19956ms 99.77% _start 0 0% 0% 19933ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19933ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19933ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19933ms 99.66% main 0 0% 0% 19892ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19892ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19892ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 19865ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.005% 15151ms 75.75% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.01% 9527ms 47.63% AbstractCellBasedSimulation::DoCellBirth 8ms 0.04% 0.05% 9419ms 47.09% Cell::ReadyToDivide 4ms 0.02% 0.07% 9304ms 46.52% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.02% 0.09% 9121ms 45.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 23ms 0.11% 0.2% 9112ms 45.56% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.22% 9086ms 45.43% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.31% 0.53% 8884ms 44.42% AbstractOneStepIvpOdeSolver::InternalSolve 1007ms 5.03% 5.56% 8003ms 40.01% RungeKutta4IvpOdeSolver::CalculateNextYValue 2834ms 14.17% 19.73% 6821ms 34.10% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 19.74% 5492ms 27.46% MeshBasedCellPopulation::Update 4ms 0.02% 19.76% 4270ms 21.35% Cylindrical2dMesh::ReMesh 74ms 0.37% 20.13% 4029ms 20.14% AbstractCellProperty::IsType (inline) 442ms 2.21% 22.34% 2675ms 13.37% AbstractCellProperty::IsSame 2ms 0.01% 22.35% 2615ms 13.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.005% 22.36% 2325ms 11.62% MutableMesh::ReMesh 0 0% 22.36% 2265ms 11.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 290ms 1.45% 23.81% 2233ms 11.16% std::type_info::operator== (inline) 6ms 0.03% 23.84% 2215ms 11.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 23.84% 2089ms 10.44% AbstractCellPopulation::WriteResultsToFiles 2088ms 10.44% 34.28% 2088ms 10.44% __strcmp_avx2 863ms 4.31% 38.59% 1883ms 9.41% std::_Rb_tree::_M_lower_bound (inline) 173ms 0.86% 39.46% 1694ms 8.47% TetrahedralMesh::EdgeIterator::operator++ 63ms 0.31% 39.77% 1421ms 7.10% std::_Rb_tree::find (inline) 11ms 0.055% 39.83% 1185ms 5.92% TetrahedralMesh::ImportFromMesher 1ms 0.005% 39.83% 1179ms 5.89% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.045% 39.88% 1150ms 5.75% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 40ms 0.2% 40.08% 1102ms 5.51% operator new 252ms 1.26% 41.34% 1047ms 5.23% __GI___libc_malloc 16ms 0.08% 41.42% 1040ms 5.20% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.06% 41.48% 1016ms 5.08% std::set::insert (inline) 13ms 0.065% 41.54% 1004ms 5.02% std::_Rb_tree::_M_insert_unique 41ms 0.2% 41.75% 954ms 4.77% std::__new_allocator::allocate (inline) 0 0% 41.75% 947ms 4.73% std::allocator_traits::allocate (inline) 2ms 0.01% 41.76% 849ms 4.24% triangulate 0 0% 41.76% 840ms 4.20% std::set::count (inline) 2ms 0.01% 41.77% 778ms 3.89% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 41.77% 765ms 3.82% delaunay 3ms 0.015% 41.78% 764ms 3.82% divconqdelaunay 11ms 0.055% 41.84% 735ms 3.67% CellPropertyCollection::GetPropertiesType (inline) 67ms 0.33% 42.17% 729ms 3.64% std::map::operator[] (partial-inline) 248ms 1.24% 43.41% 724ms 3.62% __dynamic_cast 393ms 1.96% 45.38% 717ms 3.58% _int_malloc 716ms 3.58% 48.96% 716ms 3.58% WntCellCycleOdeSystem::CalculateStoppingEvent 714ms 3.57% 52.52% 714ms 3.57% std::_Rb_tree::_S_right (inline) 6ms 0.03% 52.55% 712ms 3.56% CellPopulationElementWriter::Visit 2ms 0.01% 52.56% 698ms 3.49% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.01% 52.57% 654ms 3.27% MeshBasedCellPopulation::AcceptCellWriter 0 0% 52.57% 627ms 3.13% std::_Rb_tree::_M_create_node (inline) 39ms 0.19% 52.77% 619ms 3.09% std::_Rb_tree::_M_insert_ (inline) 13ms 0.065% 52.83% 608ms 3.04% std::less::operator() (inline) 21ms 0.1% 52.94% 603ms 3.01% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.94% 596ms 2.98% std::_Rb_tree::_M_get_node (inline) 595ms 2.97% 55.91% 595ms 2.97% std::operator< (inline) 20ms 0.1% 56.01% 594ms 2.97% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 4ms 0.02% 56.03% 584ms 2.92% AbstractCellProperty::IsSubType (inline) 0 0% 56.03% 572ms 2.86% std::map::find (inline) 16ms 0.08% 56.11% 571ms 2.85% MutableMesh::ReIndex 0 0% 56.11% 566ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.035% 56.15% 565ms 2.82% Element::Element 0 0% 56.15% 553ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 56.15% 553ms 2.76% std::map::lower_bound (inline) 166ms 0.83% 56.98% 521ms 2.60% __GI___libc_free 11ms 0.055% 57.03% 504ms 2.52% Element::RegisterWithNodes (inline) 15ms 0.075% 57.11% 503ms 2.51% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.045% 57.15% 494ms 2.47% Node::AddElement 1ms 0.005% 57.16% 493ms 2.46% std::ostream::operator<< (inline) 66ms 0.33% 57.49% 490ms 2.45% std::ostream::_M_insert 10ms 0.05% 57.54% 473ms 2.36% Cylindrical2dMesh::ReconstructCylindricalMesh 297ms 1.48% 59.02% 450ms 2.25% AbstractCellMutationState::AbstractCellMutationState 130ms 0.65% 59.67% 449ms 2.24% std::_Rb_tree::_M_erase 27ms 0.13% 59.81% 413ms 2.06% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.045% 59.85% 406ms 2.03% std::__new_allocator::deallocate (inline) 0 0% 59.85% 404ms 2.02% std::allocator_traits::deallocate (inline) 6ms 0.03% 59.88% 395ms 1.97% Cell::GetMutationState 0 0% 59.88% 391ms 1.95% std::set::~set (inline) 1ms 0.005% 59.89% 385ms 1.92% std::set::erase (inline) 8ms 0.04% 59.93% 384ms 1.92% std::_Rb_tree::erase 8ms 0.04% 59.97% 377ms 1.88% Node::RemoveElement 0 0% 59.97% 375ms 1.87% std::_Rb_tree::_M_drop_node (inline) 4ms 0.02% 59.99% 373ms 1.86% Cell::GetCellProliferativeType 133ms 0.66% 60.65% 372ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 371ms 1.85% 62.51% 371ms 1.85% [libchaste_cell_based.so] 11ms 0.055% 62.56% 357ms 1.78% divconqrecurse 290ms 1.45% 64.01% 354ms 1.77% _int_free 2ms 0.01% 64.02% 353ms 1.76% std::_Vector_base::_M_allocate (inline) 25ms 0.12% 64.15% 349ms 1.74% Element::ResetIndex 6ms 0.03% 64.18% 345ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.01% 64.19% 339ms 1.69% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.19% 339ms 1.69% std::_Rb_tree::_M_put_node (inline) 112ms 0.56% 64.75% 336ms 1.68% mergehulls 162ms 0.81% 65.56% 335ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 65.57% 325ms 1.62% LegacyCellProliferativeTypesWriter::VisitCell 40ms 0.2% 65.77% 314ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.005% 65.78% 312ms 1.56% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 65.79% 299ms 1.49% NodeLocationWriter::Visit 27ms 0.13% 65.92% 288ms 1.44% TetrahedralMesh::Clear 282ms 1.41% 67.33% 287ms 1.43% std::vector::operator[] (inline) 2ms 0.01% 67.34% 284ms 1.42% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 67.34% 284ms 1.42% MeshBasedCellPopulation::GetDampingConstant 17ms 0.085% 67.43% 283ms 1.41% std::_Rb_tree::_Rb_tree (partial-inline) 19ms 0.095% 67.52% 264ms 1.32% AbstractTetrahedralElement::CalculateJacobian 20ms 0.1% 67.62% 263ms 1.31% std::num_put::_M_insert_float 1ms 0.005% 67.63% 259ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.05% 67.68% 256ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.02% 67.70% 252ms 1.26% std::set::set (inline) 7ms 0.035% 67.73% 252ms 1.26% std::vector::push_back (inline) 1ms 0.005% 67.74% 251ms 1.25% alternateaxes 4ms 0.02% 67.76% 249ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 235ms 1.17% 68.93% 248ms 1.24% vertexmedian 93ms 0.46% 69.40% 240ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.075% 69.47% 239ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 27ms 0.13% 69.61% 236ms 1.18% std::_Rb_tree::_M_copy (inline) 1ms 0.005% 69.61% 234ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 75ms 0.37% 69.99% 234ms 1.17% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.035% 70.02% 233ms 1.16% std::vector::_M_realloc_insert 1ms 0.005% 70.03% 228ms 1.14% OffLatticeSimulation::ApplyBoundaries 49ms 0.24% 70.27% 220ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.045% 70.32% 215ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.005% 70.32% 215ms 1.07% CellPropertyCollection::HasProperty 7ms 0.035% 70.36% 215ms 1.07% std::__cxx11::collate::do_transform 0 0% 70.36% 211ms 1.05% Cell::HasCellProperty (inline) 12ms 0.06% 70.42% 208ms 1.04% Element::MarkAsDeleted 1ms 0.005% 70.42% 205ms 1.02% ___vsnprintf 0 0% 70.42% 204ms 1.02% __vsnprintf_internal (inline) 3ms 0.015% 70.44% 202ms 1.01% CellProliferativeTypesWriter::VisitCell 21ms 0.1% 70.54% 202ms 1.01% __printf_buffer 68ms 0.34% 70.88% 201ms 1.00% std::_Rb_tree::_M_clone_node (inline) 141ms 0.7% 71.59% 197ms 0.98% malloc_consolidate 132ms 0.66% 72.25% 195ms 0.97% AbstractElement::GetNodeGlobalIndex 22ms 0.11% 72.36% 193ms 0.96% AbstractTetrahedralElement::RefreshJacobian 8ms 0.04% 72.40% 186ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 174ms 0.87% 73.27% 174ms 0.87% unlink_chunk 8ms 0.04% 73.31% 172ms 0.86% Node::~Node 2ms 0.01% 73.32% 172ms 0.86% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 172ms 0.86% 74.18% 172ms 0.86% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 74.21% 169ms 0.84% __printf_fp_l_buffer 0 0% 74.21% 169ms 0.84% __printf_fp_spec (inline) 168ms 0.84% 75.05% 168ms 0.84% [libchaste_crypt.so] 168ms 0.84% 75.89% 168ms 0.84% std::vector::size (inline) 5ms 0.025% 75.91% 162ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 73ms 0.36% 76.28% 156ms 0.78% __printf_fp_buffer_1 2ms 0.01% 76.29% 154ms 0.77% boost::numeric::ublas::vector_assign (inline) 8ms 0.04% 76.33% 154ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 46ms 0.23% 76.56% 148ms 0.74% AbstractElement::GetNodeLocation 148ms 0.74% 77.30% 148ms 0.74% incircle 89ms 0.44% 77.74% 148ms 0.74% std::_Rb_tree::equal_range (inline) 148ms 0.74% 78.48% 148ms 0.74% std::type_info::name (inline) 139ms 0.69% 79.18% 148ms 0.74% vertexsort 45ms 0.22% 79.40% 147ms 0.73% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 146ms 0.73% 80.13% 146ms 0.73% Node::GetIndex 4ms 0.02% 80.15% 142ms 0.71% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.02% 80.17% 137ms 0.68% Cell::SetCellProliferativeType 80ms 0.4% 80.57% 137ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 46ms 0.23% 80.80% 136ms 0.68% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 26ms 0.13% 80.93% 133ms 0.66% TetrahedralMesh::EdgesEnd 131ms 0.65% 81.59% 131ms 0.65% std::_Rb_tree_increment 0 0% 81.59% 130ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.59% 130ms 0.65% OutputFileHandler::OpenOutputFile 13ms 0.065% 81.65% 130ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.04% 81.69% 130ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 81.69% 129ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 10ms 0.05% 81.74% 129ms 0.64% Cylindrical2dMesh::CreateMirrorNodes 5ms 0.025% 81.77% 128ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 46ms 0.23% 82.00% 125ms 0.62% boost::numeric::ublas::indexing_vector_assign 2ms 0.01% 82.01% 122ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.005% 82.01% 119ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 118ms 0.59% 82.60% 118ms 0.59% AbstractCellMutationState::~AbstractCellMutationState 40ms 0.2% 82.80% 110ms 0.55% std::__ostream_insert 4ms 0.02% 82.82% 109ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 21ms 0.1% 82.93% 109ms 0.54% std::num_put::_M_insert_int 1ms 0.005% 82.93% 108ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.005% 82.94% 108ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 12ms 0.06% 83.00% 108ms 0.54% boost::detail::shared_count::~shared_count (inline) 0 0% 83.00% 108ms 0.54% boost::shared_ptr::~shared_ptr (inline) 104ms 0.52% 83.52% 104ms 0.52% TetrahedralMesh::EdgeIterator::operator!= 66ms 0.33% 83.85% 103ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 61ms 0.3% 84.15% 103ms 0.51% boost::numeric::ublas::c_matrix::operator() 103ms 0.51% 84.67% 103ms 0.51% boost::shared_ptr::operator-> (inline) 1ms 0.005% 84.67% 101ms 0.5% std::vector::resize (inline)