File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16228ms, 84.00% of 19320ms total Dropped 807 nodes (cum <= 96.60ms) flat flat% sum% cum cum% 0 0% 0% 19273ms 99.76% __libc_start_call_main 0 0% 0% 19273ms 99.76% __libc_start_main_impl 0 0% 0% 19273ms 99.76% _start 0 0% 0% 19250ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19250ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19250ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19250ms 99.64% main 0 0% 0% 19209ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19209ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19209ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19182ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 14712ms 76.15% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9373ms 48.51% AbstractCellBasedSimulation::DoCellBirth 6ms 0.031% 0.041% 9278ms 48.02% Cell::ReadyToDivide 4ms 0.021% 0.062% 9189ms 47.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.021% 0.083% 9020ms 46.69% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.078% 0.16% 9013ms 46.65% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.17% 8992ms 46.54% CellCycleModelOdeHandler::SolveOdeToTime 69ms 0.36% 0.53% 8807ms 45.58% AbstractOneStepIvpOdeSolver::InternalSolve 987ms 5.11% 5.64% 7875ms 40.76% RungeKutta4IvpOdeSolver::CalculateNextYValue 2735ms 14.16% 19.79% 6705ms 34.70% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.79% 5216ms 27.00% MeshBasedCellPopulation::Update 7ms 0.036% 19.83% 4039ms 20.91% Cylindrical2dMesh::ReMesh 66ms 0.34% 20.17% 3982ms 20.61% AbstractCellProperty::IsType (inline) 358ms 1.85% 22.02% 2602ms 13.47% AbstractCellProperty::IsSame 2ms 0.01% 22.03% 2453ms 12.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.03% 2258ms 11.69% MutableMesh::ReMesh 227ms 1.17% 23.21% 2244ms 11.61% std::type_info::operator== (inline) 0 0% 23.21% 2134ms 11.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 2134ms 11.05% 34.25% 2134ms 11.05% __strcmp_avx2 9ms 0.047% 34.30% 2086ms 10.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0052% 34.31% 2009ms 10.40% AbstractCellPopulation::WriteResultsToFiles 891ms 4.61% 38.92% 1730ms 8.95% std::_Rb_tree::_M_lower_bound (inline) 181ms 0.94% 39.86% 1597ms 8.27% TetrahedralMesh::EdgeIterator::operator++ 70ms 0.36% 40.22% 1302ms 6.74% std::_Rb_tree::find (partial-inline) 14ms 0.072% 40.29% 1137ms 5.89% TetrahedralMesh::ImportFromMesher 2ms 0.01% 40.30% 1133ms 5.86% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.031% 40.33% 1103ms 5.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 45ms 0.23% 40.56% 1032ms 5.34% operator new 12ms 0.062% 40.63% 1005ms 5.20% MeshBasedCellPopulation::SpringIterator::operator++ 252ms 1.30% 41.93% 971ms 5.03% __GI___libc_malloc 11ms 0.057% 41.99% 963ms 4.98% std::set::insert (inline) 16ms 0.083% 42.07% 952ms 4.93% std::_Rb_tree::_M_insert_unique 28ms 0.14% 42.22% 884ms 4.58% std::__new_allocator::allocate (inline) 0 0% 42.22% 882ms 4.57% std::allocator_traits::allocate (inline) 1ms 0.0052% 42.22% 863ms 4.47% triangulate 1ms 0.0052% 42.23% 783ms 4.05% delaunay 0 0% 42.23% 783ms 4.05% std::set::count (inline) 3ms 0.016% 42.24% 782ms 4.05% divconqdelaunay 759ms 3.93% 46.17% 759ms 3.93% WntCellCycleOdeSystem::CalculateStoppingEvent 6ms 0.031% 46.20% 705ms 3.65% CellPopulationElementWriter::Visit 4ms 0.021% 46.22% 705ms 3.65% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 68ms 0.35% 46.57% 685ms 3.55% std::map::operator[] (partial-inline) 3ms 0.016% 46.59% 660ms 3.42% AbstractTwoBodyInteractionForce::AddForceContribution 365ms 1.89% 48.48% 634ms 3.28% _int_malloc 171ms 0.89% 49.36% 611ms 3.16% __dynamic_cast 25ms 0.13% 49.49% 603ms 3.12% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.057% 49.55% 597ms 3.09% CellPropertyCollection::GetPropertiesType (inline) 0 0% 49.55% 591ms 3.06% std::_Rb_tree::_M_create_node (inline) 9ms 0.047% 49.60% 577ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 19ms 0.098% 49.69% 571ms 2.96% std::less::operator() (inline) 41ms 0.21% 49.91% 562ms 2.91% std::_Rb_tree::_M_insert_ (inline) 27ms 0.14% 50.05% 561ms 2.90% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 50.05% 559ms 2.89% std::_Rb_tree::_M_get_node (inline) 551ms 2.85% 52.90% 552ms 2.86% std::operator< (inline) 5ms 0.026% 52.92% 544ms 2.82% Element::Element 0 0% 52.92% 538ms 2.78% std::_Rb_tree::_Alloc_node::operator() (inline) 534ms 2.76% 55.69% 534ms 2.76% std::_Rb_tree::_S_right (inline) 0 0% 55.69% 523ms 2.71% std::_Rb_tree::lower_bound (inline) 0 0% 55.69% 523ms 2.71% std::map::lower_bound (inline) 0 0% 55.69% 512ms 2.65% std::map::find (inline) 9ms 0.047% 55.73% 500ms 2.59% MutableMesh::ReIndex 15ms 0.078% 55.81% 485ms 2.51% Cylindrical2dMesh::CorrectNonPeriodicMesh 159ms 0.82% 56.64% 480ms 2.48% __GI___libc_free 11ms 0.057% 56.69% 477ms 2.47% Element::RegisterWithNodes (inline) 10ms 0.052% 56.74% 476ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0052% 56.75% 470ms 2.43% AbstractCellProperty::IsSubType (inline) 14ms 0.072% 56.82% 465ms 2.41% Node::AddElement 58ms 0.3% 57.12% 462ms 2.39% std::ostream::_M_insert 0 0% 57.12% 462ms 2.39% std::ostream::operator<< (inline) 284ms 1.47% 58.59% 426ms 2.20% AbstractCellMutationState::AbstractCellMutationState 104ms 0.54% 59.13% 411ms 2.13% std::_Rb_tree::_M_erase 6ms 0.031% 59.16% 411ms 2.13% std::_Rb_tree::erase 1ms 0.0052% 59.17% 410ms 2.12% std::set::erase (inline) 18ms 0.093% 59.26% 402ms 2.08% Node::RemoveElement 20ms 0.1% 59.36% 398ms 2.06% std::__new_allocator::deallocate (inline) 0 0% 59.36% 392ms 2.03% std::allocator_traits::deallocate (inline) 0 0% 59.36% 381ms 1.97% std::_Rb_tree::_M_drop_node (inline) 23ms 0.12% 59.48% 381ms 1.97% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.052% 59.53% 374ms 1.94% divconqrecurse 158ms 0.82% 60.35% 374ms 1.94% std::_Rb_tree::_M_get_insert_unique_pos 367ms 1.90% 62.25% 367ms 1.90% [libchaste_cell_based.so] 113ms 0.58% 62.84% 357ms 1.85% mergehulls 0 0% 62.84% 356ms 1.84% std::set::~set (inline) 21ms 0.11% 62.95% 349ms 1.81% Element::ResetIndex 0 0% 62.95% 331ms 1.71% std::_Rb_tree::_M_put_node (inline) 5ms 0.026% 62.97% 325ms 1.68% Cell::GetMutationState 0 0% 62.97% 323ms 1.67% std::_Vector_base::_M_allocate (inline) 4ms 0.021% 62.99% 322ms 1.67% Cell::GetCellProliferativeType 165ms 0.85% 63.85% 322ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 260ms 1.35% 65.19% 320ms 1.66% _int_free 13ms 0.067% 65.26% 308ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.026% 65.28% 305ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.026% 65.31% 293ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.31% 287ms 1.49% NodeLocationWriter::Visit 14ms 0.072% 65.38% 284ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 275ms 1.42% 66.81% 276ms 1.43% std::vector::operator[] (inline) 15ms 0.078% 66.88% 268ms 1.39% std::_Rb_tree::_M_erase_aux (inline) 24ms 0.12% 67.01% 267ms 1.38% std::num_put::_M_insert_float 3ms 0.016% 67.02% 264ms 1.37% alternateaxes 246ms 1.27% 68.30% 260ms 1.35% vertexmedian 35ms 0.18% 68.48% 259ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.48% 257ms 1.33% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.016% 68.49% 252ms 1.30% std::set::set (inline) 59ms 0.31% 68.80% 249ms 1.29% ApcOneHitCellMutationState::ApcOneHitCellMutationState 15ms 0.078% 68.88% 248ms 1.28% AbstractTetrahedralElement::CalculateJacobian 8ms 0.041% 68.92% 246ms 1.27% std::vector::push_back (inline) 19ms 0.098% 69.02% 237ms 1.23% TetrahedralMesh::Clear 101ms 0.52% 69.54% 231ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 25ms 0.13% 69.67% 229ms 1.19% std::_Rb_tree::_M_copy (inline) 10ms 0.052% 69.72% 228ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.072% 69.79% 228ms 1.18% Element::MarkAsDeleted 84ms 0.43% 70.23% 227ms 1.17% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.078% 70.31% 225ms 1.16% std::vector::_M_realloc_insert 2ms 0.01% 70.32% 219ms 1.13% MeshBasedCellPopulation::GetDampingConstant 3ms 0.016% 70.33% 217ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.34% 212ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.036% 70.38% 212ms 1.10% std::__cxx11::collate::do_transform 5ms 0.026% 70.40% 211ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 70.41% 201ms 1.04% ___vsnprintf 0 0% 70.41% 199ms 1.03% __vsnprintf_internal (inline) 51ms 0.26% 70.68% 199ms 1.03% std::_Rb_tree::_M_clone_node (inline) 14ms 0.072% 70.75% 194ms 1.00% __printf_buffer 18ms 0.093% 70.84% 193ms 1% AbstractTetrahedralElement::RefreshJacobian 0 0% 70.84% 191ms 0.99% OffLatticeSimulation::ApplyBoundaries 3ms 0.016% 70.86% 188ms 0.97% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 70.87% 183ms 0.95% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 11ms 0.057% 70.93% 182ms 0.94% AbstractTetrahedralElement::CalculateInverseJacobian 124ms 0.64% 71.57% 179ms 0.93% AbstractElement::GetNodeGlobalIndex 3ms 0.016% 71.58% 175ms 0.91% CellPropertyCollection::HasProperty 0 0% 71.58% 173ms 0.9% Cell::HasCellProperty (inline) 2ms 0.01% 71.59% 169ms 0.87% __printf_fp_l_buffer 0 0% 71.59% 169ms 0.87% __printf_fp_spec (inline) 123ms 0.64% 72.23% 168ms 0.87% malloc_consolidate 166ms 0.86% 73.09% 166ms 0.86% [libchaste_crypt.so] 7ms 0.036% 73.13% 165ms 0.85% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 74ms 0.38% 73.51% 165ms 0.85% __printf_fp_buffer_1 2ms 0.01% 73.52% 161ms 0.83% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 72ms 0.37% 73.89% 157ms 0.81% AbstractElement::GetNodeLocation 40ms 0.21% 74.10% 157ms 0.81% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.026% 74.13% 155ms 0.8% boost::numeric::ublas::vector_assign (inline) 154ms 0.8% 74.92% 154ms 0.8% std::vector::size (inline) 1ms 0.0052% 74.93% 152ms 0.79% CellProliferativeTypesWriter::VisitCell 26ms 0.13% 75.06% 151ms 0.78% TetrahedralMesh::EdgesEnd (partial-inline) 149ms 0.77% 75.83% 149ms 0.77% incircle 12ms 0.062% 75.90% 146ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 94ms 0.49% 76.38% 146ms 0.76% std::_Rb_tree::equal_range 44ms 0.23% 76.61% 145ms 0.75% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 145ms 0.75% 77.36% 145ms 0.75% std::_Rb_tree_insert_and_rebalance 10ms 0.052% 77.41% 143ms 0.74% Node::~Node 142ms 0.73% 78.15% 142ms 0.73% Node::GetIndex 21ms 0.11% 78.26% 141ms 0.73% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.031% 78.29% 141ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.052% 78.34% 140ms 0.72% boost::numeric::ublas::c_vector::c_vector (inline) 137ms 0.71% 79.05% 137ms 0.71% unlink_chunk 87ms 0.45% 79.50% 134ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0052% 79.50% 133ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.016% 79.52% 133ms 0.69% Cell::SetCellProliferativeType 0 0% 79.52% 130ms 0.67% OutputFileHandler::OpenOutputFile 128ms 0.66% 80.18% 128ms 0.66% std::type_info::name (inline) 119ms 0.62% 80.80% 127ms 0.66% vertexsort 0 0% 80.80% 123ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 31ms 0.16% 80.96% 123ms 0.64% boost::numeric::ublas::indexing_vector_assign 122ms 0.63% 81.59% 122ms 0.63% AbstractCellMutationState::~AbstractCellMutationState 122ms 0.63% 82.22% 122ms 0.63% std::_Rb_tree_increment 16ms 0.083% 82.30% 120ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 82.30% 120ms 0.62% boost::shared_ptr::~shared_ptr (inline) 5ms 0.026% 82.33% 120ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 40ms 0.21% 82.54% 120ms 0.62% std::__ostream_insert 1ms 0.0052% 82.54% 117ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 113ms 0.58% 83.13% 113ms 0.58% std::_Rb_tree_rebalance_for_erase 72ms 0.37% 83.50% 112ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 2ms 0.01% 83.51% 110ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0052% 83.51% 109ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 52ms 0.27% 83.78% 104ms 0.54% boost::shared_ptr::shared_ptr (inline) 20ms 0.1% 83.89% 101ms 0.52% std::num_put::_M_insert_int 17ms 0.088% 83.98% 99ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.021% 84.00% 97ms 0.5% Cylindrical2dMesh::CreateMirrorNodes