File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16773ms, 84.19% of 19922ms total Dropped 772 nodes (cum <= 99.61ms) flat flat% sum% cum cum% 0 0% 0% 19877ms 99.77% __libc_start_call_main 0 0% 0% 19877ms 99.77% __libc_start_main_impl 0 0% 0% 19877ms 99.77% _start 0 0% 0% 19858ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19858ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19858ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19858ms 99.68% main 0 0% 0% 19823ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19823ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19823ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19795ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15381ms 77.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10196ms 51.18% AbstractCellBasedSimulation::DoCellBirth 7ms 0.035% 0.04% 10100ms 50.70% Cell::ReadyToDivide 1ms 0.005% 0.045% 10033ms 50.36% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.05% 9896ms 49.67% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.04% 0.09% 9890ms 49.64% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.09% 9879ms 49.59% CellCycleModelOdeHandler::SolveOdeToTime 82ms 0.41% 0.5% 9724ms 48.81% AbstractOneStepIvpOdeSolver::InternalSolve 869ms 4.36% 4.86% 8872ms 44.53% RungeKutta4IvpOdeSolver::CalculateNextYValue 3654ms 18.34% 23.21% 7786ms 39.08% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.22% 5071ms 25.45% MeshBasedCellPopulation::Update 184ms 0.92% 24.14% 4171ms 20.94% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.16% 3908ms 19.62% Cylindrical2dMesh::ReMesh 586ms 2.94% 27.10% 2902ms 14.57% AbstractCellProperty::IsSame 0 0% 27.10% 2459ms 12.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 401ms 2.01% 29.11% 2316ms 11.63% std::type_info::operator== (inline) 1ms 0.005% 29.12% 2142ms 10.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.12% 2107ms 10.58% MutableMesh::ReMesh 12ms 0.06% 29.18% 2105ms 10.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.18% 1950ms 9.79% AbstractCellPopulation::WriteResultsToFiles 811ms 4.07% 33.25% 1889ms 9.48% std::_Rb_tree::_M_lower_bound (inline) 1852ms 9.30% 42.55% 1852ms 9.30% __strcmp_avx2 178ms 0.89% 43.44% 1706ms 8.56% TetrahedralMesh::EdgeIterator::operator++ 40ms 0.2% 43.64% 1400ms 7.03% std::_Rb_tree::find (inline) 1ms 0.005% 43.65% 1141ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.04% 43.69% 1130ms 5.67% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.09% 43.78% 1061ms 5.33% TetrahedralMesh::ImportFromMesher 43ms 0.22% 43.99% 1015ms 5.09% operator new 8ms 0.04% 44.03% 1012ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.055% 44.09% 980ms 4.92% std::set::insert (inline) 22ms 0.11% 44.20% 969ms 4.86% std::_Rb_tree::_M_insert_unique 222ms 1.11% 45.31% 957ms 4.80% __GI___libc_malloc 37ms 0.19% 45.50% 889ms 4.46% std::__new_allocator::allocate (inline) 0 0% 45.50% 880ms 4.42% std::allocator_traits::allocate (inline) 0 0% 45.50% 862ms 4.33% std::set::count (inline) 2ms 0.01% 45.51% 797ms 4.00% triangulate 6ms 0.03% 45.54% 738ms 3.70% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.54% 718ms 3.60% delaunay 1ms 0.005% 45.54% 718ms 3.60% divconqdelaunay 714ms 3.58% 49.13% 714ms 3.58% std::_Rb_tree::_S_right (inline) 1ms 0.005% 49.13% 692ms 3.47% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.015% 49.15% 689ms 3.46% CellPopulationElementWriter::Visit 373ms 1.87% 51.02% 664ms 3.33% _int_malloc 46ms 0.23% 51.25% 662ms 3.32% std::map::operator[] (partial-inline) 14ms 0.07% 51.32% 661ms 3.32% std::less::operator() (inline) 647ms 3.25% 54.57% 647ms 3.25% std::operator< (inline) 626ms 3.14% 57.71% 640ms 3.21% WntCellCycleOdeSystem::CalculateStoppingEvent 166ms 0.83% 58.54% 607ms 3.05% __dynamic_cast 19ms 0.095% 58.64% 604ms 3.03% std::_Rb_tree::_M_insert_ (inline) 3ms 0.015% 58.65% 602ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.11% 58.76% 582ms 2.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.76% 570ms 2.86% std::_Rb_tree::_M_create_node (inline) 6ms 0.03% 58.79% 558ms 2.80% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.095% 58.89% 551ms 2.77% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.89% 550ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 58.89% 550ms 2.76% std::map::lower_bound (inline) 0 0% 58.89% 547ms 2.75% std::_Rb_tree::_M_get_node (inline) 9ms 0.045% 58.93% 534ms 2.68% MutableMesh::ReIndex 0 0% 58.93% 532ms 2.67% std::map::find (inline) 4ms 0.02% 58.95% 530ms 2.66% Element::Element 0 0% 58.95% 525ms 2.64% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.04% 59.00% 496ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 59.01% 493ms 2.47% std::ostream::operator<< (inline) 60ms 0.3% 59.31% 489ms 2.45% std::ostream::_M_insert 8ms 0.04% 59.35% 486ms 2.44% Cylindrical2dMesh::ReconstructCylindricalMesh 323ms 1.62% 60.97% 485ms 2.43% AbstractCellMutationState::AbstractCellMutationState 8ms 0.04% 61.01% 468ms 2.35% Element::RegisterWithNodes (inline) 7ms 0.035% 61.05% 458ms 2.30% Node::AddElement 1ms 0.005% 61.05% 449ms 2.25% AbstractCellProperty::IsSubType (inline) 161ms 0.81% 61.86% 426ms 2.14% __GI___libc_free 116ms 0.58% 62.44% 387ms 1.94% std::_Rb_tree::_M_erase 19ms 0.095% 62.54% 368ms 1.85% divconqrecurse 17ms 0.085% 62.62% 359ms 1.80% std::__new_allocator::deallocate (inline) 14ms 0.07% 62.69% 358ms 1.80% Node::RemoveElement 0 0% 62.69% 354ms 1.78% std::allocator_traits::deallocate (inline) 6ms 0.03% 62.72% 352ms 1.77% std::_Rb_tree::erase 1ms 0.005% 62.73% 352ms 1.77% std::set::erase (inline) 27ms 0.14% 62.87% 350ms 1.76% std::_Rb_tree::~_Rb_tree (inline) 32ms 0.16% 63.03% 348ms 1.75% Element::ResetIndex 108ms 0.54% 63.57% 343ms 1.72% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.065% 63.63% 342ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 103ms 0.52% 64.15% 338ms 1.70% mergehulls 2ms 0.01% 64.16% 335ms 1.68% std::_Vector_base::_M_allocate (inline) 152ms 0.76% 64.92% 328ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.92% 328ms 1.65% std::set::~set (inline) 318ms 1.60% 66.52% 318ms 1.60% std::type_info::name (inline) 0 0% 66.52% 311ms 1.56% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 66.53% 305ms 1.53% Cell::GetCellProliferativeType 2ms 0.01% 66.54% 300ms 1.51% NodeLocationWriter::Visit 3ms 0.015% 66.55% 297ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.005% 66.56% 294ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 66.57% 293ms 1.47% Cell::GetMutationState 30ms 0.15% 66.73% 287ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.73% 287ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.73% 277ms 1.39% std::_Rb_tree::_M_put_node (inline) 268ms 1.35% 68.07% 269ms 1.35% std::vector::operator[] (inline) 22ms 0.11% 68.18% 266ms 1.34% AbstractTetrahedralElement::CalculateJacobian 219ms 1.10% 69.28% 265ms 1.33% _int_free 14ms 0.07% 69.35% 260ms 1.31% std::num_put::_M_insert_float 11ms 0.055% 69.41% 257ms 1.29% std::vector::push_back (inline) 253ms 1.27% 70.68% 253ms 1.27% [libchaste_cell_based.so] 9ms 0.045% 70.72% 246ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 80ms 0.4% 71.12% 241ms 1.21% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.08% 71.20% 240ms 1.20% std::vector::_M_realloc_insert 15ms 0.075% 71.28% 237ms 1.19% std::_Rb_tree::_Rb_tree (partial-inline) 62ms 0.31% 71.59% 234ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.005% 71.59% 227ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.055% 71.65% 224ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.03% 71.68% 220ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 71.68% 212ms 1.06% std::__cxx11::collate::do_transform 8ms 0.04% 71.72% 211ms 1.06% alternateaxes 1ms 0.005% 71.73% 211ms 1.06% std::set::set (inline) 46ms 0.23% 71.96% 207ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 28ms 0.14% 72.10% 205ms 1.03% AbstractTetrahedralElement::RefreshJacobian 1ms 0.005% 72.11% 205ms 1.03% ___vsnprintf 6ms 0.03% 72.14% 205ms 1.03% std::_Rb_tree::_M_erase_aux (inline) 0 0% 72.14% 204ms 1.02% __vsnprintf_internal (inline) 192ms 0.96% 73.10% 203ms 1.02% vertexmedian 0 0% 73.10% 200ms 1.00% OffLatticeSimulation::ApplyBoundaries 21ms 0.11% 73.21% 200ms 1.00% std::_Rb_tree::_M_copy (inline) 31ms 0.16% 73.36% 198ms 0.99% __printf_buffer 15ms 0.075% 73.44% 197ms 0.99% Element::MarkAsDeleted 137ms 0.69% 74.12% 196ms 0.98% malloc_consolidate 12ms 0.06% 74.18% 189ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 131ms 0.66% 74.84% 186ms 0.93% AbstractElement::GetNodeGlobalIndex 184ms 0.92% 75.77% 184ms 0.92% std::_Rb_tree_insert_and_rebalance 7ms 0.035% 75.80% 182ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.005% 75.81% 182ms 0.91% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.81% 181ms 0.91% AbstractCentreBasedCellPopulation::GetDampingConstant 181ms 0.91% 76.71% 181ms 0.91% Node::GetIndex 2ms 0.01% 76.72% 178ms 0.89% CellProliferativeTypesWriter::VisitCell 57ms 0.29% 77.01% 177ms 0.89% std::_Rb_tree::_M_clone_node (inline) 17ms 0.085% 77.10% 165ms 0.83% TetrahedralMesh::Clear 3ms 0.015% 77.11% 160ms 0.8% __printf_fp_l_buffer 0 0% 77.11% 160ms 0.8% __printf_fp_spec (inline) 78ms 0.39% 77.50% 159ms 0.8% AbstractElement::GetNodeLocation 5ms 0.025% 77.53% 159ms 0.8% CellPropertyCollection::HasProperty 0 0% 77.53% 153ms 0.77% Cell::HasCellProperty (inline) 149ms 0.75% 78.28% 149ms 0.75% unlink_chunk 82ms 0.41% 78.69% 148ms 0.74% std::_Rb_tree::equal_range (inline) 69ms 0.35% 79.03% 147ms 0.74% __printf_fp_buffer_1 4ms 0.02% 79.05% 145ms 0.73% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 79.08% 139ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 139ms 0.7% 79.78% 139ms 0.7% incircle 77ms 0.39% 80.16% 132ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.16% 130ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 124ms 0.62% 80.79% 130ms 0.65% vertexsort 14ms 0.07% 80.86% 129ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 123ms 0.62% 81.47% 123ms 0.62% std::vector::size (inline) 21ms 0.11% 81.58% 120ms 0.6% std::num_put::_M_insert_int 45ms 0.23% 81.80% 116ms 0.58% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 9ms 0.045% 81.85% 116ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.005% 81.85% 116ms 0.58% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 49ms 0.25% 82.10% 115ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 2ms 0.01% 82.11% 115ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 82.11% 112ms 0.56% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.11% 111ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 111ms 0.56% 82.67% 111ms 0.56% AbstractElement::IsDeleted 0 0% 82.67% 111ms 0.56% OutputFileHandler::OpenOutputFile 0 0% 82.67% 110ms 0.55% Cell::SetCellProliferativeType 110ms 0.55% 83.22% 110ms 0.55% boost::shared_ptr::operator-> (inline) 22ms 0.11% 83.33% 109ms 0.55% boost::numeric::ublas::indexing_vector_assign 108ms 0.54% 83.87% 108ms 0.54% std::_Rb_tree_increment 3ms 0.015% 83.89% 107ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 13ms 0.065% 83.95% 107ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 46ms 0.23% 84.18% 104ms 0.52% std::__ostream_insert 0 0% 84.18% 102ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 84.19% 102ms 0.51% MeshBasedCellPopulation::SpringsEnd (inline)