File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16730ms, 83.92% of 19935ms total Dropped 752 nodes (cum <= 99.67ms) flat flat% sum% cum cum% 0 0% 0% 19891ms 99.78% __libc_start_call_main 0 0% 0% 19891ms 99.78% __libc_start_main_impl 0 0% 0% 19891ms 99.78% _start 0 0% 0% 19872ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19872ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19872ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19872ms 99.68% main 0 0% 0% 19840ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19840ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19840ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19814ms 99.39% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15343ms 76.97% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.005% 10113ms 50.73% AbstractCellBasedSimulation::DoCellBirth 1ms 0.005% 0.01% 10008ms 50.20% Cell::ReadyToDivide 2ms 0.01% 0.02% 9960ms 49.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.02% 9834ms 49.33% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.08% 0.1% 9826ms 49.29% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.1% 9803ms 49.17% CellCycleModelOdeHandler::SolveOdeToTime 63ms 0.32% 0.42% 9640ms 48.36% AbstractOneStepIvpOdeSolver::InternalSolve 906ms 4.54% 4.96% 8823ms 44.26% RungeKutta4IvpOdeSolver::CalculateNextYValue 3589ms 18.00% 22.96% 7705ms 38.65% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 22.97% 5114ms 25.65% MeshBasedCellPopulation::Update 182ms 0.91% 23.89% 4131ms 20.72% AbstractCellProperty::IsType (inline) 3ms 0.015% 23.90% 3903ms 19.58% Cylindrical2dMesh::ReMesh 571ms 2.86% 26.77% 2880ms 14.45% AbstractCellProperty::IsSame 1ms 0.005% 26.77% 2491ms 12.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 414ms 2.08% 28.85% 2309ms 11.58% std::type_info::operator== (inline) 1ms 0.005% 28.85% 2187ms 10.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.06% 28.91% 2155ms 10.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 28.92% 2125ms 10.66% MutableMesh::ReMesh 0 0% 28.92% 1976ms 9.91% AbstractCellPopulation::WriteResultsToFiles 792ms 3.97% 32.89% 1891ms 9.49% std::_Rb_tree::_M_lower_bound (inline) 1881ms 9.44% 42.33% 1881ms 9.44% __strcmp_avx2 161ms 0.81% 43.14% 1685ms 8.45% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.33% 43.46% 1424ms 7.14% std::_Rb_tree::find (inline) 1ms 0.005% 43.47% 1170ms 5.87% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.49% 1134ms 5.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 61ms 0.31% 43.80% 1057ms 5.30% operator new 17ms 0.085% 43.88% 1052ms 5.28% TetrahedralMesh::ImportFromMesher 19ms 0.095% 43.98% 1036ms 5.20% MeshBasedCellPopulation::SpringIterator::operator++ 233ms 1.17% 45.15% 986ms 4.95% __GI___libc_malloc 9ms 0.045% 45.19% 953ms 4.78% std::set::insert (inline) 12ms 0.06% 45.25% 944ms 4.74% std::_Rb_tree::_M_insert_unique 30ms 0.15% 45.40% 925ms 4.64% std::__new_allocator::allocate (inline) 0 0% 45.40% 918ms 4.60% std::allocator_traits::allocate (inline) 0 0% 45.40% 867ms 4.35% std::set::count (inline) 1ms 0.005% 45.41% 814ms 4.08% triangulate 0 0% 45.41% 732ms 3.67% delaunay 7ms 0.035% 45.44% 732ms 3.67% divconqdelaunay 2ms 0.01% 45.45% 726ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 67ms 0.34% 45.79% 719ms 3.61% std::map::operator[] (partial-inline) 10ms 0.05% 45.84% 706ms 3.54% CellPopulationElementWriter::Visit 703ms 3.53% 49.37% 703ms 3.53% std::_Rb_tree::_S_right (inline) 4ms 0.02% 49.39% 697ms 3.50% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 382ms 1.92% 51.30% 679ms 3.41% _int_malloc 16ms 0.08% 51.38% 658ms 3.30% std::less::operator() (inline) 642ms 3.22% 54.60% 642ms 3.22% std::operator< (inline) 620ms 3.11% 57.71% 629ms 3.16% WntCellCycleOdeSystem::CalculateStoppingEvent 179ms 0.9% 58.61% 626ms 3.14% __dynamic_cast 22ms 0.11% 58.72% 615ms 3.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.72% 607ms 3.04% std::_Rb_tree::_M_create_node (inline) 28ms 0.14% 58.86% 598ms 3.00% std::_Rb_tree::_M_insert_ (inline) 22ms 0.11% 58.97% 588ms 2.95% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.97% 575ms 2.88% std::_Rb_tree::_M_get_node (inline) 0 0% 58.97% 572ms 2.87% std::_Rb_tree::lower_bound (inline) 0 0% 58.97% 572ms 2.87% std::map::lower_bound (inline) 0 0% 58.97% 561ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.97% 554ms 2.78% std::map::find (inline) 6ms 0.03% 59.00% 553ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.015% 59.02% 548ms 2.75% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.02% 59.04% 534ms 2.68% Element::Element 11ms 0.055% 59.09% 518ms 2.60% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.055% 59.15% 495ms 2.48% MutableMesh::ReIndex 328ms 1.65% 60.79% 486ms 2.44% AbstractCellMutationState::AbstractCellMutationState 11ms 0.055% 60.85% 472ms 2.37% Element::RegisterWithNodes (inline) 1ms 0.005% 60.85% 472ms 2.37% std::ostream::operator<< (inline) 64ms 0.32% 61.17% 471ms 2.36% std::ostream::_M_insert 7ms 0.035% 61.21% 459ms 2.30% Node::AddElement 16ms 0.08% 61.29% 458ms 2.30% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 61.30% 450ms 2.26% AbstractCellProperty::IsSubType (inline) 142ms 0.71% 62.02% 416ms 2.09% __GI___libc_free 10ms 0.05% 62.07% 375ms 1.88% divconqrecurse 103ms 0.52% 62.58% 355ms 1.78% mergehulls 6ms 0.03% 62.61% 353ms 1.77% std::_Rb_tree::erase 0 0% 62.61% 351ms 1.76% std::set::erase (inline) 11ms 0.055% 62.67% 349ms 1.75% Node::RemoveElement 2ms 0.01% 62.68% 345ms 1.73% std::_Vector_base::_M_allocate (inline) 13ms 0.065% 62.74% 339ms 1.70% std::__new_allocator::deallocate (inline) 111ms 0.56% 63.30% 337ms 1.69% std::_Rb_tree::_M_erase 130ms 0.65% 63.95% 334ms 1.68% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 63.95% 334ms 1.68% std::allocator_traits::deallocate (inline) 25ms 0.13% 64.08% 322ms 1.62% Element::ResetIndex 6ms 0.03% 64.11% 321ms 1.61% Cell::GetMutationState 149ms 0.75% 64.86% 321ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 64.87% 320ms 1.61% NodeLocationWriter::Visit 4ms 0.02% 64.89% 319ms 1.60% AbstractCellPopulation::GetLocationIndexUsingCell 28ms 0.14% 65.03% 319ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.045% 65.07% 314ms 1.58% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.01% 65.08% 313ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 27ms 0.14% 65.22% 308ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.22% 294ms 1.47% std::set::~set (inline) 0 0% 65.22% 288ms 1.44% std::_Rb_tree::_M_drop_node (inline) 5ms 0.025% 65.24% 287ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 15ms 0.075% 65.32% 285ms 1.43% AbstractTetrahedralElement::CalculateJacobian 285ms 1.43% 66.75% 285ms 1.43% std::type_info::name (inline) 18ms 0.09% 66.84% 276ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 223ms 1.12% 67.96% 274ms 1.37% _int_free 6ms 0.03% 67.99% 272ms 1.36% Cell::GetCellProliferativeType 5ms 0.025% 68.01% 266ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 23ms 0.12% 68.13% 266ms 1.33% std::num_put::_M_insert_float 0 0% 68.13% 261ms 1.31% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 68.14% 260ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.005% 68.15% 249ms 1.25% std::set::set (inline) 4ms 0.02% 68.17% 248ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 248ms 1.24% 69.41% 248ms 1.24% [libchaste_cell_based.so] 245ms 1.23% 70.64% 245ms 1.23% std::vector::operator[] (inline) 9ms 0.045% 70.68% 240ms 1.20% std::vector::push_back (inline) 21ms 0.11% 70.79% 238ms 1.19% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 70.82% 236ms 1.18% alternateaxes 0 0% 70.82% 235ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 52ms 0.26% 71.08% 232ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 215ms 1.08% 72.15% 231ms 1.16% vertexmedian 86ms 0.43% 72.59% 226ms 1.13% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.055% 72.64% 224ms 1.12% std::vector::_M_realloc_insert 21ms 0.11% 72.75% 222ms 1.11% AbstractTetrahedralElement::RefreshJacobian 74ms 0.37% 73.12% 214ms 1.07% std::_Rb_tree::_M_clone_node (inline) 5ms 0.025% 73.14% 209ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.07% 73.21% 208ms 1.04% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 73.22% 208ms 1.04% std::__cxx11::collate::do_transform 0 0% 73.22% 201ms 1.01% OffLatticeSimulation::ApplyBoundaries 38ms 0.19% 73.41% 200ms 1.00% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 14ms 0.07% 73.48% 200ms 1.00% Element::MarkAsDeleted 3ms 0.015% 73.50% 200ms 1.00% ___vsnprintf 22ms 0.11% 73.61% 198ms 0.99% __printf_buffer 0 0% 73.61% 197ms 0.99% __vsnprintf_internal (inline) 1ms 0.005% 73.61% 194ms 0.97% MeshBasedCellPopulation::GetDampingConstant 0 0% 73.61% 193ms 0.97% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 73.62% 186ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 136ms 0.68% 74.31% 185ms 0.93% malloc_consolidate 137ms 0.69% 74.99% 179ms 0.9% AbstractElement::GetNodeGlobalIndex 88ms 0.44% 75.44% 177ms 0.89% AbstractElement::GetNodeLocation 174ms 0.87% 76.31% 174ms 0.87% Node::GetIndex 14ms 0.07% 76.38% 171ms 0.86% TetrahedralMesh::Clear 166ms 0.83% 77.21% 166ms 0.83% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 77.24% 161ms 0.81% CellProliferativeTypesWriter::VisitCell 5ms 0.025% 77.27% 161ms 0.81% __printf_fp_l_buffer 0 0% 77.27% 161ms 0.81% __printf_fp_spec (inline) 159ms 0.8% 78.06% 159ms 0.8% incircle 36ms 0.18% 78.24% 155ms 0.78% TetrahedralMesh::EdgesEnd (partial-inline) 70ms 0.35% 78.60% 149ms 0.75% __printf_fp_buffer_1 93ms 0.47% 79.06% 147ms 0.74% std::_Rb_tree::equal_range (inline) 147ms 0.74% 79.80% 147ms 0.74% unlink_chunk 7ms 0.035% 79.83% 146ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.025% 79.86% 143ms 0.72% boost::numeric::ublas::vector_assign (inline) 7ms 0.035% 79.89% 142ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 46ms 0.23% 80.13% 141ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 133ms 0.67% 80.79% 133ms 0.67% std::vector::size (inline) 70ms 0.35% 81.14% 129ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.04% 81.18% 126ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 7ms 0.035% 81.22% 125ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.015% 81.23% 121ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.23% 120ms 0.6% AbstractCellBasedWriter::OpenOutputFileForAppend 44ms 0.22% 81.45% 119ms 0.6% std::__ostream_insert 0 0% 81.45% 118ms 0.59% OutputFileHandler::OpenOutputFile 1ms 0.005% 81.46% 118ms 0.59% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 3ms 0.015% 81.47% 117ms 0.59% CellPropertyCollection::HasProperty 0 0% 81.47% 114ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 113ms 0.57% 82.04% 113ms 0.57% AbstractCellProperty::~AbstractCellProperty 113ms 0.57% 82.61% 113ms 0.57% AbstractElement::IsDeleted 34ms 0.17% 82.78% 113ms 0.57% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 82.78% 113ms 0.57% Cell::HasCellProperty (inline) 33ms 0.17% 82.94% 111ms 0.56% boost::numeric::ublas::indexing_vector_assign 1ms 0.005% 82.95% 107ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.015% 82.96% 106ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 10ms 0.05% 83.01% 105ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 83.01% 105ms 0.53% boost::shared_ptr::~shared_ptr (inline) 101ms 0.51% 83.52% 105ms 0.53% vertexsort 76ms 0.38% 83.90% 104ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.005% 83.91% 102ms 0.51% Cell::SetCellProliferativeType 3ms 0.015% 83.92% 100ms 0.5% std::operator<< (inline)