File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16777ms, 84.36% of 19888ms total Dropped 787 nodes (cum <= 99.44ms) flat flat% sum% cum cum% 0 0% 0% 19840ms 99.76% __libc_start_call_main 0 0% 0% 19840ms 99.76% __libc_start_main_impl 0 0% 0% 19840ms 99.76% _start 0 0% 0% 19820ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19820ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19820ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19820ms 99.66% main 0 0% 0% 19778ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19778ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19778ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 19751ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0.005% 15273ms 76.80% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.01% 9939ms 49.97% AbstractCellBasedSimulation::DoCellBirth 7ms 0.035% 0.045% 9846ms 49.51% Cell::ReadyToDivide 1ms 0.005% 0.05% 9771ms 49.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.05% 9633ms 48.44% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.065% 0.12% 9623ms 48.39% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9607ms 48.31% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.4% 0.52% 9445ms 47.49% AbstractOneStepIvpOdeSolver::InternalSolve 904ms 4.55% 5.07% 8632ms 43.40% RungeKutta4IvpOdeSolver::CalculateNextYValue 3604ms 18.12% 23.19% 7516ms 37.79% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.19% 5203ms 26.16% MeshBasedCellPopulation::Update 5ms 0.025% 23.22% 4027ms 20.25% Cylindrical2dMesh::ReMesh 102ms 0.51% 23.73% 3969ms 19.96% AbstractCellProperty::IsType (inline) 558ms 2.81% 26.53% 2732ms 13.74% AbstractCellProperty::IsSame 1ms 0.005% 26.54% 2478ms 12.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 26.54% 2217ms 11.15% MutableMesh::ReMesh 2ms 0.01% 26.55% 2178ms 10.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 431ms 2.17% 28.72% 2174ms 10.93% std::type_info::operator== (inline) 11ms 0.055% 28.77% 2125ms 10.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 28.78% 1991ms 10.01% AbstractCellPopulation::WriteResultsToFiles 808ms 4.06% 32.84% 1860ms 9.35% std::_Rb_tree::_M_lower_bound (inline) 181ms 0.91% 33.75% 1706ms 8.58% TetrahedralMesh::EdgeIterator::operator++ 1666ms 8.38% 42.13% 1666ms 8.38% __strcmp_avx2 61ms 0.31% 42.43% 1393ms 7.00% std::_Rb_tree::find (inline) 3ms 0.015% 42.45% 1145ms 5.76% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 42.47% 1117ms 5.62% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.075% 42.55% 1100ms 5.53% TetrahedralMesh::ImportFromMesher 39ms 0.2% 42.74% 1100ms 5.53% operator new 247ms 1.24% 43.99% 1050ms 5.28% __GI___libc_malloc 7ms 0.035% 44.02% 1018ms 5.12% MeshBasedCellPopulation::SpringIterator::operator++ 44ms 0.22% 44.24% 977ms 4.91% std::__new_allocator::allocate (inline) 0 0% 44.24% 972ms 4.89% std::allocator_traits::allocate (inline) 14ms 0.07% 44.31% 963ms 4.84% std::set::insert (inline) 15ms 0.075% 44.39% 949ms 4.77% std::_Rb_tree::_M_insert_unique 0 0% 44.39% 857ms 4.31% std::set::count (inline) 0 0% 44.39% 838ms 4.21% triangulate 0 0% 44.39% 748ms 3.76% delaunay 3ms 0.015% 44.40% 747ms 3.76% divconqdelaunay 399ms 2.01% 46.41% 725ms 3.65% _int_malloc 3ms 0.015% 46.42% 719ms 3.62% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 46.44% 714ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.04% 46.48% 697ms 3.50% CellPopulationElementWriter::Visit 35ms 0.18% 46.65% 684ms 3.44% std::map::operator[] (partial-inline) 662ms 3.33% 49.98% 662ms 3.33% std::_Rb_tree::_S_right (inline) 27ms 0.14% 50.12% 655ms 3.29% std::less::operator() (inline) 26ms 0.13% 50.25% 632ms 3.18% std::_Rb_tree::_M_insert_ (inline) 628ms 3.16% 53.40% 628ms 3.16% std::operator< (inline) 0 0% 53.40% 624ms 3.14% std::_Rb_tree::_M_create_node (inline) 608ms 3.06% 56.46% 616ms 3.10% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 56.46% 604ms 3.04% std::_Rb_tree::_M_get_node (inline) 182ms 0.92% 57.38% 595ms 2.99% __dynamic_cast 21ms 0.11% 57.48% 594ms 2.99% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 20ms 0.1% 57.58% 581ms 2.92% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 57.60% 571ms 2.87% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.60% 563ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 57.60% 555ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 57.60% 555ms 2.79% std::map::lower_bound (inline) 4ms 0.02% 57.62% 552ms 2.78% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.005% 57.63% 550ms 2.77% Element::Element 0 0% 57.63% 532ms 2.67% std::map::find (inline) 7ms 0.035% 57.66% 507ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.01% 57.67% 505ms 2.54% std::ostream::operator<< (inline) 62ms 0.31% 57.98% 503ms 2.53% std::ostream::_M_insert 10ms 0.05% 58.03% 500ms 2.51% MutableMesh::ReIndex 354ms 1.78% 59.81% 498ms 2.50% AbstractCellMutationState::AbstractCellMutationState 7ms 0.035% 59.85% 482ms 2.42% Element::RegisterWithNodes (inline) 15ms 0.075% 59.93% 474ms 2.38% Node::AddElement 12ms 0.06% 59.99% 465ms 2.34% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.02% 60.01% 438ms 2.20% AbstractCellProperty::IsSubType (inline) 146ms 0.73% 60.74% 431ms 2.17% __GI___libc_free 21ms 0.11% 60.85% 390ms 1.96% divconqrecurse 11ms 0.055% 60.90% 371ms 1.87% Node::RemoveElement 1ms 0.005% 60.91% 369ms 1.86% std::_Vector_base::_M_allocate (inline) 7ms 0.035% 60.94% 367ms 1.85% std::_Rb_tree::erase 108ms 0.54% 61.48% 366ms 1.84% mergehulls 1ms 0.005% 61.49% 366ms 1.84% std::set::erase (inline) 118ms 0.59% 62.08% 363ms 1.83% std::_Rb_tree::_M_erase 343ms 1.72% 63.81% 343ms 1.72% std::type_info::name (inline) 12ms 0.06% 63.87% 337ms 1.69% std::__new_allocator::deallocate (inline) 0 0% 63.87% 335ms 1.68% std::allocator_traits::deallocate (inline) 28ms 0.14% 64.01% 330ms 1.66% Element::ResetIndex 26ms 0.13% 64.14% 325ms 1.63% std::_Rb_tree::~_Rb_tree (inline) 147ms 0.74% 64.88% 318ms 1.60% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 64.90% 305ms 1.53% LegacyCellProliferativeTypesWriter::VisitCell 107ms 0.54% 65.44% 302ms 1.52% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.035% 65.47% 301ms 1.51% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.47% 301ms 1.51% std::set::~set (inline) 2ms 0.01% 65.48% 297ms 1.49% NodeLocationWriter::Visit 0 0% 65.48% 296ms 1.49% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 65.49% 295ms 1.48% Cell::GetCellProliferativeType 3ms 0.015% 65.51% 291ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 65.52% 284ms 1.43% Cell::GetMutationState 226ms 1.14% 66.65% 284ms 1.43% _int_free 0 0% 66.65% 277ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.15% 66.80% 276ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 10ms 0.05% 66.85% 274ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 14ms 0.07% 66.92% 273ms 1.37% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.92% 265ms 1.33% std::_Rb_tree::_M_put_node (inline) 14ms 0.07% 67.00% 259ms 1.30% std::num_put::_M_insert_float 2ms 0.01% 67.01% 258ms 1.30% std::set::set (inline) 0 0% 67.01% 256ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 253ms 1.27% 68.28% 255ms 1.28% std::vector::operator[] (inline) 64ms 0.32% 68.60% 249ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 14ms 0.07% 68.67% 246ms 1.24% std::vector::push_back (inline) 52ms 0.26% 68.93% 240ms 1.21% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 11ms 0.055% 68.99% 234ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.03% 69.02% 226ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 69.03% 222ms 1.12% alternateaxes 165ms 0.83% 69.86% 222ms 1.12% malloc_consolidate 11ms 0.055% 69.91% 221ms 1.11% std::vector::_M_realloc_insert 27ms 0.14% 70.05% 220ms 1.11% std::_Rb_tree::_M_copy (inline) 199ms 1.00% 71.05% 219ms 1.10% vertexmedian 10ms 0.05% 71.10% 218ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 31ms 0.16% 71.25% 217ms 1.09% AbstractTetrahedralElement::RefreshJacobian 1ms 0.005% 71.26% 212ms 1.07% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.02% 71.28% 212ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 71.29% 202ms 1.02% std::__cxx11::collate::do_transform 19ms 0.096% 71.38% 201ms 1.01% Element::MarkAsDeleted 2ms 0.01% 71.39% 194ms 0.98% ___vsnprintf 39ms 0.2% 71.59% 192ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 71.59% 192ms 0.97% OffLatticeSimulation::ApplyBoundaries 0 0% 71.59% 192ms 0.97% __vsnprintf_internal (inline) 65ms 0.33% 71.92% 192ms 0.97% std::_Rb_tree::_M_clone_node (inline) 1ms 0.005% 71.92% 191ms 0.96% MeshBasedCellPopulation::GetDampingConstant 0 0% 71.92% 190ms 0.96% AbstractCentreBasedCellPopulation::GetDampingConstant 17ms 0.085% 72.01% 190ms 0.96% __printf_buffer 11ms 0.055% 72.06% 184ms 0.93% TetrahedralMesh::Clear 183ms 0.92% 72.98% 183ms 0.92% Node::GetIndex 181ms 0.91% 73.89% 181ms 0.91% [libchaste_cell_based.so] 142ms 0.71% 74.61% 180ms 0.91% AbstractElement::GetNodeGlobalIndex 180ms 0.91% 75.51% 180ms 0.91% std::_Rb_tree_insert_and_rebalance 82ms 0.41% 75.93% 170ms 0.85% AbstractElement::GetNodeLocation 169ms 0.85% 76.77% 169ms 0.85% unlink_chunk 3ms 0.015% 76.79% 167ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.03% 76.82% 157ms 0.79% __printf_fp_l_buffer 0 0% 76.82% 157ms 0.79% __printf_fp_spec (inline) 5ms 0.025% 76.85% 155ms 0.78% CellPropertyCollection::HasProperty 0 0% 76.85% 154ms 0.77% Cell::HasCellProperty (inline) 154ms 0.77% 77.62% 154ms 0.77% incircle 2ms 0.01% 77.63% 152ms 0.76% boost::numeric::ublas::vector_assign (inline) 3ms 0.015% 77.64% 150ms 0.75% CellProliferativeTypesWriter::VisitCell 94ms 0.47% 78.12% 146ms 0.73% std::_Rb_tree::equal_range (inline) 63ms 0.32% 78.43% 145ms 0.73% __printf_fp_buffer_1 6ms 0.03% 78.46% 142ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.045% 78.51% 141ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 135ms 0.68% 79.19% 135ms 0.68% AbstractCellProperty::~AbstractCellProperty 0 0% 79.19% 132ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 22ms 0.11% 79.30% 132ms 0.66% std::num_put::_M_insert_int 10ms 0.05% 79.35% 131ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 79.35% 130ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 34ms 0.17% 79.52% 130ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 31ms 0.16% 79.68% 130ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 68ms 0.34% 80.02% 128ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.02% 127ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 40ms 0.2% 80.22% 125ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 80.22% 125ms 0.63% OutputFileHandler::OpenOutputFile 2ms 0.01% 80.23% 125ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 109ms 0.55% 80.78% 125ms 0.63% vertexsort 2ms 0.01% 80.79% 124ms 0.62% std::vector::resize (inline) 1ms 0.005% 80.79% 122ms 0.61% std::vector::_M_default_append 40ms 0.2% 80.99% 120ms 0.6% boost::numeric::ublas::indexing_vector_assign 13ms 0.065% 81.06% 119ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 119ms 0.6% 81.66% 119ms 0.6% std::_Rb_tree_increment 119ms 0.6% 82.26% 119ms 0.6% std::vector::size (inline) 2ms 0.01% 82.27% 118ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 116ms 0.58% 82.85% 116ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 47ms 0.24% 83.09% 116ms 0.58% std::__ostream_insert 2ms 0.01% 83.10% 113ms 0.57% Cell::SetCellProliferativeType 0 0% 83.10% 112ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 34ms 0.17% 83.27% 112ms 0.56% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 83.27% 112ms 0.56% NodeMap::NodeMap 1ms 0.005% 83.27% 108ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 104ms 0.52% 83.79% 104ms 0.52% AbstractElement::IsDeleted 104ms 0.52% 84.32% 104ms 0.52% std::_Rb_tree_rebalance_for_erase 8ms 0.04% 84.36% 103ms 0.52% Node::~Node