File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17216ms, 85.00% of 20254ms total Dropped 783 nodes (cum <= 101.27ms) flat flat% sum% cum cum% 0 0% 0% 20208ms 99.77% __libc_start_call_main 0 0% 0% 20208ms 99.77% __libc_start_main_impl 0 0% 0% 20208ms 99.77% _start 0 0% 0% 20188ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20188ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20188ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20188ms 99.67% main 0 0% 0% 20147ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20147ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20147ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20122ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15518ms 76.62% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.0049% 10025ms 49.50% AbstractCellBasedSimulation::DoCellBirth 15ms 0.074% 0.079% 9915ms 48.95% Cell::ReadyToDivide 9ms 0.044% 0.12% 9809ms 48.43% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0099% 0.13% 9651ms 47.65% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.064% 0.2% 9644ms 47.62% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.22% 9630ms 47.55% CellCycleModelOdeHandler::SolveOdeToTime 73ms 0.36% 0.58% 9452ms 46.67% AbstractOneStepIvpOdeSolver::InternalSolve 928ms 4.58% 5.16% 8626ms 42.59% RungeKutta4IvpOdeSolver::CalculateNextYValue 3579ms 17.67% 22.83% 7484ms 36.95% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 22.83% 5376ms 26.54% MeshBasedCellPopulation::Update 8ms 0.039% 22.87% 4197ms 20.72% Cylindrical2dMesh::ReMesh 87ms 0.43% 23.30% 3973ms 19.62% AbstractCellProperty::IsType (inline) 539ms 2.66% 25.97% 2765ms 13.65% AbstractCellProperty::IsSame 0 0% 25.97% 2537ms 12.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.97% 2318ms 11.44% MutableMesh::ReMesh 401ms 1.98% 27.95% 2226ms 10.99% std::type_info::operator== (inline) 0 0% 27.95% 2205ms 10.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.035% 27.98% 2153ms 10.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 27.98% 2057ms 10.16% AbstractCellPopulation::WriteResultsToFiles 846ms 4.18% 32.16% 1928ms 9.52% std::_Rb_tree::_M_lower_bound (inline) 1759ms 8.68% 40.84% 1759ms 8.68% __strcmp_avx2 153ms 0.76% 41.60% 1721ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 55ms 0.27% 41.87% 1448ms 7.15% std::_Rb_tree::find (inline) 17ms 0.084% 41.95% 1207ms 5.96% TetrahedralMesh::ImportFromMesher 0 0% 41.95% 1143ms 5.64% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 41.98% 1135ms 5.60% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 48ms 0.24% 42.21% 1071ms 5.29% operator new 9ms 0.044% 42.26% 1025ms 5.06% MeshBasedCellPopulation::SpringIterator::operator++ 198ms 0.98% 43.24% 1009ms 4.98% __GI___libc_malloc 14ms 0.069% 43.31% 971ms 4.79% std::set::insert (inline) 19ms 0.094% 43.40% 957ms 4.72% std::_Rb_tree::_M_insert_unique 32ms 0.16% 43.56% 944ms 4.66% std::__new_allocator::allocate (inline) 0 0% 43.56% 937ms 4.63% std::allocator_traits::allocate (inline) 0 0% 43.56% 906ms 4.47% std::set::count (inline) 1ms 0.0049% 43.56% 803ms 3.96% triangulate 62ms 0.31% 43.87% 738ms 3.64% std::map::operator[] (partial-inline) 0 0% 43.87% 732ms 3.61% delaunay 3ms 0.015% 43.88% 731ms 3.61% divconqdelaunay 409ms 2.02% 45.90% 727ms 3.59% _int_malloc 3ms 0.015% 45.92% 726ms 3.58% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 696ms 3.44% 49.35% 696ms 3.44% std::_Rb_tree::_S_right (inline) 1ms 0.0049% 49.36% 682ms 3.37% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.044% 49.40% 678ms 3.35% CellPopulationElementWriter::Visit 653ms 3.22% 52.63% 659ms 3.25% WntCellCycleOdeSystem::CalculateStoppingEvent 17ms 0.084% 52.71% 656ms 3.24% std::less::operator() (inline) 639ms 3.15% 55.87% 639ms 3.15% std::operator< (inline) 7ms 0.035% 55.90% 623ms 3.08% CellPropertyCollection::GetPropertiesType (inline) 31ms 0.15% 56.05% 614ms 3.03% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.05% 611ms 3.02% std::_Rb_tree::_M_create_node (inline) 30ms 0.15% 56.20% 610ms 3.01% AbstractCellPopulation::GetCellUsingLocationIndex 209ms 1.03% 57.23% 593ms 2.93% __dynamic_cast 0 0% 57.23% 589ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.23% 580ms 2.86% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 57.34% 577ms 2.85% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.34% 566ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 57.34% 566ms 2.79% std::map::lower_bound (inline) 6ms 0.03% 57.37% 553ms 2.73% Element::Element 5ms 0.025% 57.40% 549ms 2.71% std::ostream::operator<< (inline) 8ms 0.039% 57.44% 548ms 2.71% MutableMesh::ReIndex 74ms 0.37% 57.80% 544ms 2.69% std::ostream::_M_insert 0 0% 57.80% 539ms 2.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 57.80% 533ms 2.63% std::map::find (inline) 18ms 0.089% 57.89% 492ms 2.43% Cylindrical2dMesh::CorrectNonPeriodicMesh 186ms 0.92% 58.81% 490ms 2.42% __GI___libc_free 9ms 0.044% 58.85% 485ms 2.39% Element::RegisterWithNodes (inline) 6ms 0.03% 58.88% 476ms 2.35% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 58.90% 473ms 2.34% AbstractCellProperty::IsSubType (inline) 5ms 0.025% 58.92% 472ms 2.33% Node::AddElement 323ms 1.59% 60.52% 467ms 2.31% AbstractCellMutationState::AbstractCellMutationState 149ms 0.74% 61.25% 402ms 1.98% std::_Rb_tree::_M_erase 3ms 0.015% 61.27% 382ms 1.89% std::_Rb_tree::erase 2ms 0.0099% 61.28% 381ms 1.88% std::set::erase (inline) 11ms 0.054% 61.33% 373ms 1.84% Node::RemoveElement 25ms 0.12% 61.45% 372ms 1.84% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0099% 61.46% 369ms 1.82% NodeLocationWriter::Visit 25ms 0.12% 61.59% 364ms 1.80% Element::ResetIndex 6ms 0.03% 61.62% 363ms 1.79% std::_Vector_base::_M_allocate (inline) 20ms 0.099% 61.72% 352ms 1.74% divconqrecurse 10ms 0.049% 61.77% 352ms 1.74% std::__new_allocator::deallocate (inline) 0 0% 61.77% 346ms 1.71% std::allocator_traits::deallocate (inline) 0 0% 61.77% 342ms 1.69% std::set::~set (inline) 3ms 0.015% 61.78% 331ms 1.63% Cell::GetCellProliferativeType 1ms 0.0049% 61.79% 330ms 1.63% Cell::GetMutationState 97ms 0.48% 62.26% 329ms 1.62% mergehulls 133ms 0.66% 62.92% 324ms 1.60% std::_Rb_tree::_M_get_insert_unique_pos 22ms 0.11% 63.03% 321ms 1.58% std::num_put::_M_insert_float 8ms 0.039% 63.07% 317ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.079% 63.15% 314ms 1.55% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 63.15% 308ms 1.52% std::_Rb_tree::_M_drop_node (inline) 307ms 1.52% 64.66% 307ms 1.52% std::type_info::name (inline) 232ms 1.15% 65.81% 303ms 1.50% _int_free 1ms 0.0049% 65.81% 294ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 41ms 0.2% 66.02% 292ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 8ms 0.039% 66.06% 288ms 1.42% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.06% 278ms 1.37% std::_Rb_tree::_M_put_node (inline) 145ms 0.72% 66.77% 276ms 1.36% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.064% 66.84% 273ms 1.35% AbstractTetrahedralElement::CalculateJacobian 33ms 0.16% 67.00% 273ms 1.35% TetrahedralMesh::Clear 10ms 0.049% 67.05% 261ms 1.29% std::vector::push_back (inline) 1ms 0.0049% 67.05% 254ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 249ms 1.23% 68.28% 250ms 1.23% std::vector::operator[] (inline) 7ms 0.035% 68.32% 246ms 1.21% alternateaxes 12ms 0.059% 68.38% 246ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.0099% 68.39% 243ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 63ms 0.31% 68.70% 243ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 68.70% 243ms 1.20% MeshBasedCellPopulation::GetDampingConstant 8ms 0.039% 68.74% 241ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 17ms 0.084% 68.82% 241ms 1.19% std::vector::_M_realloc_insert 8ms 0.039% 68.86% 239ms 1.18% std::__cxx11::collate::do_transform 217ms 1.07% 69.93% 237ms 1.17% vertexmedian 8ms 0.039% 69.97% 230ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 70.00% 223ms 1.10% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.0099% 70.01% 223ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 70.03% 222ms 1.10% ___vsnprintf 0 0% 70.03% 218ms 1.08% __vsnprintf_internal (inline) 24ms 0.12% 70.15% 214ms 1.06% __printf_buffer 20ms 0.099% 70.25% 213ms 1.05% std::_Rb_tree::_M_copy (inline) 1ms 0.0049% 70.25% 213ms 1.05% std::set::set (inline) 21ms 0.1% 70.36% 209ms 1.03% AbstractTetrahedralElement::RefreshJacobian 160ms 0.79% 71.15% 208ms 1.03% malloc_consolidate 203ms 1.00% 72.15% 203ms 1.00% [libchaste_cell_based.so] 6ms 0.03% 72.18% 201ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 201ms 0.99% 73.17% 201ms 0.99% std::_Rb_tree_insert_and_rebalance 1ms 0.0049% 73.18% 198ms 0.98% CellProliferativeTypesWriter::VisitCell 35ms 0.17% 73.35% 197ms 0.97% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 42ms 0.21% 73.56% 197ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 73.56% 194ms 0.96% OffLatticeSimulation::ApplyBoundaries 62ms 0.31% 73.86% 191ms 0.94% std::_Rb_tree::_M_clone_node (inline) 9ms 0.044% 73.91% 184ms 0.91% Element::MarkAsDeleted 4ms 0.02% 73.93% 183ms 0.9% AbstractTetrahedralElement::AbstractTetrahedralElement 134ms 0.66% 74.59% 182ms 0.9% AbstractElement::GetNodeGlobalIndex 5ms 0.025% 74.61% 177ms 0.87% CellPropertyCollection::HasProperty 7ms 0.035% 74.65% 177ms 0.87% __printf_fp_l_buffer 0 0% 74.65% 177ms 0.87% __printf_fp_spec (inline) 175ms 0.86% 75.51% 175ms 0.86% Node::GetIndex 79ms 0.39% 75.90% 171ms 0.84% AbstractElement::GetNodeLocation 0 0% 75.90% 171ms 0.84% Cell::HasCellProperty (inline) 166ms 0.82% 76.72% 166ms 0.82% std::vector::size (inline) 83ms 0.41% 77.13% 161ms 0.79% __printf_fp_buffer_1 13ms 0.064% 77.19% 156ms 0.77% Node::~Node 92ms 0.45% 77.65% 156ms 0.77% std::_Rb_tree::equal_range (inline) 155ms 0.77% 78.41% 155ms 0.77% unlink_chunk 7ms 0.035% 78.45% 154ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.025% 78.47% 145ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.0099% 78.48% 143ms 0.71% boost::numeric::ublas::vector_assign (inline) 142ms 0.7% 79.18% 142ms 0.7% std::_Rb_tree_increment 83ms 0.41% 79.59% 137ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.039% 79.63% 137ms 0.68% std::_Rb_tree_const_iterator::operator++ (inline) 135ms 0.67% 80.30% 135ms 0.67% incircle 48ms 0.24% 80.54% 131ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 10ms 0.049% 80.59% 130ms 0.64% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.59% 124ms 0.61% Cell::SetCellProliferativeType 10ms 0.049% 80.64% 122ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 116ms 0.57% 81.21% 122ms 0.6% vertexsort 118ms 0.58% 81.79% 118ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 0 0% 81.79% 116ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 39ms 0.19% 81.98% 115ms 0.57% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 43ms 0.21% 82.20% 113ms 0.56% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0049% 82.20% 113ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.18% 82.38% 113ms 0.56% boost::numeric::ublas::indexing_vector_assign 49ms 0.24% 82.63% 113ms 0.56% std::__ostream_insert 0 0% 82.63% 110ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 110ms 0.54% 83.17% 110ms 0.54% AbstractElement::IsDeleted 3ms 0.015% 83.18% 110ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 107ms 0.53% 83.71% 107ms 0.53% AbstractCellProperty::~AbstractCellProperty 1ms 0.0049% 83.72% 106ms 0.52% MeshBasedCellPopulation::SpringsEnd (inline) 25ms 0.12% 83.84% 106ms 0.52% TetrahedralMesh::EdgesEnd 23ms 0.11% 83.95% 106ms 0.52% std::num_put::_M_insert_int 0 0% 83.95% 105ms 0.52% OutputFileHandler::OpenOutputFile 2ms 0.0099% 83.96% 105ms 0.52% std::vector::_M_default_append 0 0% 83.96% 105ms 0.52% std::vector::resize (inline) 103ms 0.51% 84.47% 103ms 0.51% boost::shared_ptr::operator-> (inline) 5ms 0.025% 84.50% 102ms 0.5% Cylindrical2dMesh::CreateMirrorNodes 102ms 0.5% 85.00% 102ms 0.5% std::_Rb_tree_rebalance_for_erase