File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17077ms, 84.51% of 20206ms total Dropped 823 nodes (cum <= 101.03ms) flat flat% sum% cum cum% 0 0% 0% 20159ms 99.77% __libc_start_call_main 0 0% 0% 20159ms 99.77% __libc_start_main_impl 0 0% 0% 20159ms 99.77% _start 0 0% 0% 20139ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20139ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20139ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20139ms 99.67% main 0 0% 0% 20101ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20101ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20101ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20074ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15545ms 76.93% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10229ms 50.62% AbstractCellBasedSimulation::DoCellBirth 8ms 0.04% 0.04% 10145ms 50.21% Cell::ReadyToDivide 6ms 0.03% 0.069% 10037ms 49.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0099% 0.079% 9898ms 48.99% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.079% 0.16% 9888ms 48.94% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0099% 0.17% 9871ms 48.85% CellCycleModelOdeHandler::SolveOdeToTime 77ms 0.38% 0.55% 9702ms 48.02% AbstractOneStepIvpOdeSolver::InternalSolve 840ms 4.16% 4.71% 8871ms 43.90% RungeKutta4IvpOdeSolver::CalculateNextYValue 3693ms 18.28% 22.98% 7832ms 38.76% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 22.99% 5205ms 25.76% MeshBasedCellPopulation::Update 83ms 0.41% 23.40% 4223ms 20.90% AbstractCellProperty::IsType (inline) 3ms 0.015% 23.41% 4030ms 19.94% Cylindrical2dMesh::ReMesh 789ms 3.90% 27.32% 2986ms 14.78% AbstractCellProperty::IsSame 1ms 0.0049% 27.32% 2487ms 12.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 406ms 2.01% 29.33% 2197ms 10.87% std::type_info::operator== (inline) 1ms 0.0049% 29.34% 2195ms 10.86% MutableMesh::ReMesh 0 0% 29.34% 2152ms 10.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.035% 29.37% 2122ms 10.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.37% 2034ms 10.07% AbstractCellPopulation::WriteResultsToFiles 765ms 3.79% 33.16% 1810ms 8.96% std::_Rb_tree::_M_lower_bound (inline) 1742ms 8.62% 41.78% 1742ms 8.62% __strcmp_avx2 169ms 0.84% 42.62% 1696ms 8.39% TetrahedralMesh::EdgeIterator::operator++ 74ms 0.37% 42.98% 1392ms 6.89% std::_Rb_tree::find (inline) 0 0% 42.98% 1142ms 5.65% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 43.00% 1128ms 5.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.049% 43.05% 1102ms 5.45% TetrahedralMesh::ImportFromMesher 46ms 0.23% 43.28% 1096ms 5.42% operator new 229ms 1.13% 44.41% 1039ms 5.14% __GI___libc_malloc 8ms 0.04% 44.45% 1023ms 5.06% MeshBasedCellPopulation::SpringIterator::operator++ 14ms 0.069% 44.52% 946ms 4.68% std::set::insert (inline) 30ms 0.15% 44.67% 942ms 4.66% std::__new_allocator::allocate (inline) 0 0% 44.67% 936ms 4.63% std::allocator_traits::allocate (inline) 12ms 0.059% 44.73% 932ms 4.61% std::_Rb_tree::_M_insert_unique 0 0% 44.73% 863ms 4.27% std::set::count (inline) 2ms 0.0099% 44.74% 819ms 4.05% triangulate 5ms 0.025% 44.76% 773ms 3.83% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.76% 737ms 3.65% delaunay 6ms 0.03% 44.79% 737ms 3.65% divconqdelaunay 409ms 2.02% 46.82% 718ms 3.55% _int_malloc 1ms 0.0049% 46.82% 696ms 3.44% AbstractTwoBodyInteractionForce::AddForceContribution 54ms 0.27% 47.09% 692ms 3.42% std::map::operator[] (partial-inline) 3ms 0.015% 47.10% 680ms 3.37% CellPopulationElementWriter::Visit 679ms 3.36% 50.47% 679ms 3.36% std::_Rb_tree::_S_right (inline) 12ms 0.059% 50.52% 643ms 3.18% std::less::operator() (inline) 2ms 0.0099% 50.53% 632ms 3.13% MeshBasedCellPopulation::AcceptCellWriter 631ms 3.12% 53.66% 631ms 3.12% std::operator< (inline) 610ms 3.02% 56.68% 624ms 3.09% WntCellCycleOdeSystem::CalculateStoppingEvent 181ms 0.9% 57.57% 623ms 3.08% __dynamic_cast 27ms 0.13% 57.71% 594ms 2.94% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.71% 591ms 2.92% std::_Rb_tree::_M_create_node (inline) 7ms 0.035% 57.74% 587ms 2.91% CellPropertyCollection::GetPropertiesType (inline) 25ms 0.12% 57.86% 572ms 2.83% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.86% 569ms 2.82% std::_Rb_tree::_M_get_node (inline) 8ms 0.04% 57.90% 567ms 2.81% Element::Element 25ms 0.12% 58.03% 552ms 2.73% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.03% 534ms 2.64% std::_Rb_tree::lower_bound (inline) 0 0% 58.03% 534ms 2.64% std::map::lower_bound (inline) 0 0% 58.03% 528ms 2.61% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.03% 525ms 2.60% std::map::find (inline) 6ms 0.03% 58.06% 519ms 2.57% MutableMesh::ReIndex 15ms 0.074% 58.13% 503ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.0049% 58.14% 499ms 2.47% std::ostream::operator<< (inline) 57ms 0.28% 58.42% 498ms 2.46% std::ostream::_M_insert 11ms 0.054% 58.47% 486ms 2.41% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.069% 58.54% 485ms 2.40% Element::RegisterWithNodes (inline) 326ms 1.61% 60.16% 483ms 2.39% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 60.18% 483ms 2.39% AbstractCellProperty::IsSubType (inline) 7ms 0.035% 60.21% 471ms 2.33% Node::AddElement 142ms 0.7% 60.91% 429ms 2.12% __GI___libc_free 17ms 0.084% 61.00% 396ms 1.96% Node::RemoveElement 7ms 0.035% 61.03% 395ms 1.95% std::_Rb_tree::erase 3ms 0.015% 61.05% 395ms 1.95% std::set::erase (inline) 16ms 0.079% 61.13% 370ms 1.83% divconqrecurse 1ms 0.0049% 61.13% 368ms 1.82% std::_Vector_base::_M_allocate (inline) 104ms 0.51% 61.65% 356ms 1.76% std::_Rb_tree::_M_erase 97ms 0.48% 62.13% 348ms 1.72% mergehulls 34ms 0.17% 62.29% 345ms 1.71% Element::ResetIndex 11ms 0.054% 62.35% 340ms 1.68% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 62.36% 338ms 1.67% LegacyCellProliferativeTypesWriter::VisitCell 19ms 0.094% 62.46% 337ms 1.67% std::_Rb_tree::~_Rb_tree (inline) 8ms 0.04% 62.50% 333ms 1.65% std::__new_allocator::deallocate (inline) 328ms 1.62% 64.12% 328ms 1.62% std::type_info::name (inline) 0 0% 64.12% 327ms 1.62% std::allocator_traits::deallocate (inline) 125ms 0.62% 64.74% 326ms 1.61% std::_Rb_tree::_M_get_insert_unique_pos 158ms 0.78% 65.52% 322ms 1.59% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.52% 321ms 1.59% std::_Rb_tree::_M_drop_node (inline) 4ms 0.02% 65.54% 318ms 1.57% Cell::GetCellProliferativeType 4ms 0.02% 65.56% 311ms 1.54% Cell::GetMutationState 0 0% 65.56% 306ms 1.51% std::set::~set (inline) 3ms 0.015% 65.57% 294ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.57% 292ms 1.45% NodeLocationWriter::Visit 36ms 0.18% 65.75% 290ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 250ms 1.24% 66.99% 285ms 1.41% _int_free 12ms 0.059% 67.05% 284ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.089% 67.14% 280ms 1.39% std::num_put::_M_insert_float 0 0% 67.14% 272ms 1.35% std::_Rb_tree::_M_put_node (inline) 16ms 0.079% 67.22% 259ms 1.28% AbstractTetrahedralElement::CalculateJacobian 257ms 1.27% 68.49% 259ms 1.28% std::vector::operator[] (inline) 7ms 0.035% 68.52% 254ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0049% 68.53% 251ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.054% 68.58% 250ms 1.24% std::vector::push_back (inline) 16ms 0.079% 68.66% 245ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.045% 68.71% 242ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 68ms 0.34% 69.04% 234ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 18ms 0.089% 69.13% 230ms 1.14% std::vector::_M_realloc_insert 43ms 0.21% 69.35% 229ms 1.13% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.04% 69.39% 227ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0099% 69.40% 226ms 1.12% std::set::set (inline) 10ms 0.049% 69.44% 223ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.035% 69.48% 221ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 216ms 1.07% 70.55% 216ms 1.07% [libchaste_cell_based.so] 1ms 0.0049% 70.55% 215ms 1.06% alternateaxes 2ms 0.0099% 70.56% 215ms 1.06% std::__cxx11::collate::do_transform 198ms 0.98% 71.54% 213ms 1.05% vertexmedian 17ms 0.084% 71.63% 212ms 1.05% Element::MarkAsDeleted 1ms 0.0049% 71.63% 209ms 1.03% ___vsnprintf 0 0% 71.63% 208ms 1.03% __vsnprintf_internal (inline) 0 0% 71.63% 207ms 1.02% OffLatticeSimulation::ApplyBoundaries 46ms 0.23% 71.86% 206ms 1.02% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 163ms 0.81% 72.67% 205ms 1.01% AbstractElement::GetNodeGlobalIndex 18ms 0.089% 72.76% 203ms 1.00% std::_Rb_tree::_M_copy (inline) 154ms 0.76% 73.52% 202ms 1% malloc_consolidate 24ms 0.12% 73.64% 201ms 0.99% __printf_buffer 0 0% 73.64% 196ms 0.97% MeshBasedCellPopulation::GetDampingConstant 2ms 0.0099% 73.65% 195ms 0.97% AbstractCentreBasedCellPopulation::GetDampingConstant 17ms 0.084% 73.73% 193ms 0.96% TetrahedralMesh::Clear 7ms 0.035% 73.77% 191ms 0.95% CellPropertyCollection::HasProperty 0 0% 73.77% 189ms 0.94% Cell::HasCellProperty (inline) 18ms 0.089% 73.85% 187ms 0.93% AbstractTetrahedralElement::RefreshJacobian 61ms 0.3% 74.16% 184ms 0.91% std::_Rb_tree::_M_clone_node (inline) 183ms 0.91% 75.06% 183ms 0.91% std::_Rb_tree_insert_and_rebalance 9ms 0.045% 75.11% 178ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.025% 75.13% 171ms 0.85% CellProliferativeTypesWriter::VisitCell 169ms 0.84% 75.97% 169ms 0.84% Node::GetIndex 60ms 0.3% 76.26% 157ms 0.78% AbstractElement::GetNodeLocation 4ms 0.02% 76.28% 156ms 0.77% __printf_fp_l_buffer 0 0% 76.28% 156ms 0.77% __printf_fp_spec (inline) 154ms 0.76% 77.05% 154ms 0.76% incircle 92ms 0.46% 77.50% 152ms 0.75% std::_Rb_tree::equal_range (inline) 147ms 0.73% 78.23% 147ms 0.73% unlink_chunk 68ms 0.34% 78.57% 146ms 0.72% __printf_fp_buffer_1 34ms 0.17% 78.73% 141ms 0.7% TetrahedralMesh::EdgesEnd 3ms 0.015% 78.75% 139ms 0.69% boost::numeric::ublas::vector_assign (inline) 48ms 0.24% 78.99% 138ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 6ms 0.03% 79.02% 137ms 0.68% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 79.02% 135ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 135ms 0.67% 79.68% 135ms 0.67% std::vector::size (inline) 0 0% 79.68% 134ms 0.66% OutputFileHandler::OpenOutputFile 33ms 0.16% 79.85% 133ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 122ms 0.6% 80.45% 132ms 0.65% vertexsort 2ms 0.0099% 80.46% 130ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.049% 80.51% 129ms 0.64% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 2ms 0.0099% 80.52% 126ms 0.62% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 82ms 0.41% 80.93% 125ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 123ms 0.61% 81.54% 123ms 0.61% AbstractElement::IsDeleted 0 0% 81.54% 121ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 10ms 0.049% 81.58% 117ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 81.58% 117ms 0.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.58% 114ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 33ms 0.16% 81.75% 114ms 0.56% std::num_put::_M_insert_int 6ms 0.03% 81.78% 112ms 0.55% Node::~Node 0 0% 81.78% 111ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 110ms 0.54% 82.32% 110ms 0.54% AbstractCellMutationState::~AbstractCellMutationState 109ms 0.54% 82.86% 109ms 0.54% AbstractCellProperty::~AbstractCellProperty 38ms 0.19% 83.05% 108ms 0.53% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.02% 83.07% 108ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 108ms 0.53% 83.60% 108ms 0.53% std::_Rb_tree_rebalance_for_erase 0 0% 83.60% 107ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 105ms 0.52% 84.12% 106ms 0.52% boost::detail::sp_counted_base::release 36ms 0.18% 84.30% 105ms 0.52% boost::numeric::ublas::indexing_vector_assign 2ms 0.0099% 84.31% 104ms 0.51% Cell::SetCellProliferativeType 2ms 0.0099% 84.32% 104ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 39ms 0.19% 84.51% 104ms 0.51% std::__ostream_insert 0 0% 84.51% 102ms 0.5% std::vector::vector (inline)