File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16373ms, 83.47% of 19616ms total Dropped 799 nodes (cum <= 98.08ms) flat flat% sum% cum cum% 0 0% 0% 19567ms 99.75% __libc_start_call_main 0 0% 0% 19567ms 99.75% __libc_start_main_impl 0 0% 0% 19567ms 99.75% _start 0 0% 0% 19546ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19546ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19546ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19546ms 99.64% main 0 0% 0% 19505ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19505ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19505ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19477ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 14865ms 75.78% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9323ms 47.53% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.036% 9209ms 46.95% Cell::ReadyToDivide 5ms 0.025% 0.061% 9127ms 46.53% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.076% 8969ms 45.72% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.056% 0.13% 8955ms 45.65% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.14% 8940ms 45.58% CellCycleModelOdeHandler::SolveOdeToTime 68ms 0.35% 0.48% 8766ms 44.69% AbstractOneStepIvpOdeSolver::InternalSolve 956ms 4.87% 5.36% 7919ms 40.37% RungeKutta4IvpOdeSolver::CalculateNextYValue 2817ms 14.36% 19.72% 6785ms 34.59% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.72% 5404ms 27.55% MeshBasedCellPopulation::Update 5ms 0.025% 19.74% 4182ms 21.32% Cylindrical2dMesh::ReMesh 60ms 0.31% 20.05% 4014ms 20.46% AbstractCellProperty::IsType (inline) 348ms 1.77% 21.82% 2615ms 13.33% AbstractCellProperty::IsSame 0 0% 21.82% 2594ms 13.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.82% 2298ms 11.71% MutableMesh::ReMesh 223ms 1.14% 22.96% 2267ms 11.56% std::type_info::operator== (inline) 0 0% 22.96% 2259ms 11.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.031% 22.99% 2212ms 11.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 2156ms 10.99% 33.98% 2156ms 10.99% __strcmp_avx2 0 0% 33.98% 2011ms 10.25% AbstractCellPopulation::WriteResultsToFiles 807ms 4.11% 38.10% 1887ms 9.62% std::_Rb_tree::_M_lower_bound (inline) 151ms 0.77% 38.87% 1697ms 8.65% TetrahedralMesh::EdgeIterator::operator++ 91ms 0.46% 39.33% 1422ms 7.25% std::_Rb_tree::find (inline) 0 0% 39.33% 1182ms 6.03% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.01% 39.34% 1164ms 5.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.061% 39.40% 1156ms 5.89% TetrahedralMesh::ImportFromMesher 35ms 0.18% 39.58% 1106ms 5.64% operator new 248ms 1.26% 40.84% 1048ms 5.34% __GI___libc_malloc 15ms 0.076% 40.92% 1045ms 5.33% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.061% 40.98% 1003ms 5.11% std::set::insert (inline) 15ms 0.076% 41.06% 991ms 5.05% std::_Rb_tree::_M_insert_unique 38ms 0.19% 41.25% 973ms 4.96% std::__new_allocator::allocate (inline) 0 0% 41.25% 963ms 4.91% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.26% 873ms 4.45% triangulate 0 0% 41.26% 829ms 4.23% std::set::count (inline) 0 0% 41.26% 794ms 4.05% delaunay 7ms 0.036% 41.29% 794ms 4.05% divconqdelaunay 742ms 3.78% 45.08% 742ms 3.78% std::_Rb_tree::_S_right (inline) 2ms 0.01% 45.09% 729ms 3.72% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 72ms 0.37% 45.45% 729ms 3.72% std::map::operator[] (partial-inline) 7ms 0.036% 45.49% 705ms 3.59% CellPopulationElementWriter::Visit 388ms 1.98% 47.47% 698ms 3.56% _int_malloc 0 0% 47.47% 691ms 3.52% AbstractTwoBodyInteractionForce::AddForceContribution 656ms 3.34% 50.81% 656ms 3.34% WntCellCycleOdeSystem::CalculateStoppingEvent 192ms 0.98% 51.79% 656ms 3.34% __dynamic_cast 7ms 0.036% 51.83% 629ms 3.21% CellPropertyCollection::GetPropertiesType (inline) 0 0% 51.83% 616ms 3.14% std::_Rb_tree::_M_create_node (inline) 11ms 0.056% 51.88% 611ms 3.11% std::less::operator() (inline) 15ms 0.076% 51.96% 610ms 3.11% AbstractCellPopulation::GetCellUsingLocationIndex 600ms 3.06% 55.02% 600ms 3.06% std::operator< (inline) 3ms 0.015% 55.03% 599ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 16ms 0.082% 55.11% 595ms 3.03% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 36ms 0.18% 55.30% 592ms 3.02% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.30% 589ms 3.00% std::map::find (inline) 0 0% 55.30% 584ms 2.98% std::_Rb_tree::_M_get_node (inline) 0 0% 55.30% 579ms 2.95% std::_Rb_tree::lower_bound (inline) 0 0% 55.30% 579ms 2.95% std::map::lower_bound (inline) 0 0% 55.30% 566ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.036% 55.33% 547ms 2.79% MutableMesh::ReIndex 3ms 0.015% 55.35% 541ms 2.76% Element::Element 2ms 0.01% 55.36% 507ms 2.58% AbstractCellProperty::IsSubType (inline) 6ms 0.031% 55.39% 503ms 2.56% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.0051% 55.39% 488ms 2.49% std::ostream::operator<< (inline) 62ms 0.32% 55.71% 487ms 2.48% std::ostream::_M_insert 9ms 0.046% 55.76% 478ms 2.44% Element::RegisterWithNodes (inline) 13ms 0.066% 55.82% 475ms 2.42% Cylindrical2dMesh::ReconstructCylindricalMesh 16ms 0.082% 55.90% 474ms 2.42% Node::AddElement 123ms 0.63% 56.53% 461ms 2.35% __GI___libc_free 286ms 1.46% 57.99% 430ms 2.19% AbstractCellMutationState::AbstractCellMutationState 130ms 0.66% 58.65% 399ms 2.03% std::_Rb_tree::_M_erase 14ms 0.071% 58.72% 393ms 2.00% divconqrecurse 160ms 0.82% 59.54% 385ms 1.96% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.02% 59.56% 383ms 1.95% std::_Vector_base::_M_allocate (inline) 10ms 0.051% 59.61% 372ms 1.90% std::_Rb_tree::erase 0 0% 59.61% 369ms 1.88% std::set::erase (inline) 12ms 0.061% 59.67% 367ms 1.87% Node::RemoveElement 112ms 0.57% 60.24% 366ms 1.87% mergehulls 11ms 0.056% 60.30% 365ms 1.86% std::__new_allocator::deallocate (inline) 22ms 0.11% 60.41% 364ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 60.41% 359ms 1.83% std::allocator_traits::deallocate (inline) 0 0% 60.41% 355ms 1.81% Cell::GetMutationState 25ms 0.13% 60.54% 354ms 1.80% Element::ResetIndex 171ms 0.87% 61.41% 346ms 1.76% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.41% 340ms 1.73% std::set::~set (inline) 272ms 1.39% 62.80% 338ms 1.72% _int_free 4ms 0.02% 62.82% 330ms 1.68% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 62.82% 328ms 1.67% std::_Rb_tree::_M_drop_node (inline) 6ms 0.031% 62.85% 326ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.036% 62.88% 318ms 1.62% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.087% 62.97% 316ms 1.61% std::_Rb_tree::_Rb_tree (partial-inline) 315ms 1.61% 64.57% 315ms 1.61% [libchaste_cell_based.so] 0 0% 64.57% 311ms 1.59% NodeLocationWriter::Visit 0 0% 64.57% 307ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 64.59% 305ms 1.55% Cell::GetCellProliferativeType 42ms 0.21% 64.80% 304ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 64.80% 294ms 1.50% std::_Rb_tree::_M_put_node (inline) 16ms 0.082% 64.88% 283ms 1.44% std::num_put::_M_insert_float 9ms 0.046% 64.93% 282ms 1.44% std::vector::push_back (inline) 2ms 0.01% 64.94% 279ms 1.42% std::set::set (inline) 272ms 1.39% 66.32% 274ms 1.40% std::vector::operator[] (inline) 2ms 0.01% 66.33% 271ms 1.38% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 66.34% 267ms 1.36% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.041% 66.38% 265ms 1.35% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.1% 66.49% 262ms 1.34% AbstractTetrahedralElement::CalculateJacobian 3ms 0.015% 66.50% 262ms 1.34% alternateaxes 22ms 0.11% 66.61% 262ms 1.34% std::vector::_M_realloc_insert 246ms 1.25% 67.87% 259ms 1.32% vertexmedian 31ms 0.16% 68.03% 258ms 1.32% std::_Rb_tree::_M_copy (inline) 94ms 0.48% 68.51% 244ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 19ms 0.097% 68.60% 243ms 1.24% TetrahedralMesh::Clear 0 0% 68.60% 241ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 68.61% 236ms 1.20% std::__cxx11::collate::do_transform 10ms 0.051% 68.66% 234ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 55ms 0.28% 68.94% 230ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0051% 68.95% 228ms 1.16% ___vsnprintf 1ms 0.0051% 68.95% 227ms 1.16% __vsnprintf_internal (inline) 4ms 0.02% 68.97% 226ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 94ms 0.48% 69.45% 225ms 1.15% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.071% 69.52% 224ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 12ms 0.061% 69.59% 223ms 1.14% __printf_buffer 64ms 0.33% 69.91% 221ms 1.13% std::_Rb_tree::_M_clone_node (inline) 11ms 0.056% 69.97% 218ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 69.97% 202ms 1.03% OffLatticeSimulation::ApplyBoundaries 31ms 0.16% 70.13% 199ms 1.01% AbstractTetrahedralElement::RefreshJacobian 8ms 0.041% 70.17% 197ms 1.00% __printf_fp_l_buffer 0 0% 70.17% 197ms 1.00% __printf_fp_spec (inline) 139ms 0.71% 70.88% 189ms 0.96% AbstractElement::GetNodeGlobalIndex 141ms 0.72% 71.59% 189ms 0.96% malloc_consolidate 2ms 0.01% 71.60% 187ms 0.95% CellPropertyCollection::HasProperty 5ms 0.025% 71.63% 185ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 85ms 0.43% 72.06% 184ms 0.94% __printf_fp_buffer_1 0 0% 72.06% 183ms 0.93% Cell::HasCellProperty (inline) 12ms 0.061% 72.12% 182ms 0.93% Element::MarkAsDeleted 182ms 0.93% 73.05% 182ms 0.93% [libchaste_crypt.so] 166ms 0.85% 73.90% 166ms 0.85% incircle 161ms 0.82% 74.72% 161ms 0.82% Node::GetIndex 159ms 0.81% 75.53% 159ms 0.81% unlink_chunk 8ms 0.041% 75.57% 158ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 7ms 0.036% 75.61% 158ms 0.81% Node::~Node 58ms 0.3% 75.90% 157ms 0.8% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0051% 75.91% 156ms 0.8% boost::numeric::ublas::vector_assign (inline) 25ms 0.13% 76.03% 154ms 0.79% TetrahedralMesh::EdgesEnd (partial-inline) 154ms 0.79% 76.82% 154ms 0.79% std::_Rb_tree_insert_and_rebalance 153ms 0.78% 77.60% 153ms 0.78% AbstractCellMutationState::~AbstractCellMutationState 61ms 0.31% 77.91% 151ms 0.77% AbstractElement::GetNodeLocation 6ms 0.031% 77.94% 148ms 0.75% MeshBasedCellPopulation::SpringsEnd (inline) 148ms 0.75% 78.70% 148ms 0.75% std::vector::size (inline) 3ms 0.015% 78.71% 147ms 0.75% CellProliferativeTypesWriter::VisitCell 6ms 0.031% 78.74% 147ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 88ms 0.45% 79.19% 143ms 0.73% std::_Rb_tree::equal_range (inline) 143ms 0.73% 79.92% 143ms 0.73% std::type_info::name (inline) 6ms 0.031% 79.95% 141ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 44ms 0.22% 80.17% 138ms 0.7% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 12ms 0.061% 80.24% 137ms 0.7% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0051% 80.24% 134ms 0.68% AbstractCellBasedSimulation::DoCellRemoval (inline) 48ms 0.24% 80.49% 133ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 78ms 0.4% 80.88% 133ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 24ms 0.12% 81.01% 130ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 81.01% 130ms 0.66% boost::shared_ptr::~shared_ptr (inline) 120ms 0.61% 81.62% 130ms 0.66% vertexsort 6ms 0.031% 81.65% 125ms 0.64% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 87ms 0.44% 82.09% 124ms 0.63% TetrahedralMesh::EdgeIterator::EdgeIterator 3ms 0.015% 82.11% 122ms 0.62% Cell::SetCellProliferativeType 35ms 0.18% 82.28% 122ms 0.62% std::__ostream_insert 36ms 0.18% 82.47% 121ms 0.62% boost::numeric::ublas::indexing_vector_assign 16ms 0.082% 82.55% 118ms 0.6% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 82.55% 117ms 0.6% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.55% 117ms 0.6% OutputFileHandler::OpenOutputFile 5ms 0.025% 82.58% 113ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 13ms 0.066% 82.64% 108ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.64% 103ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 63ms 0.32% 82.96% 99ms 0.5% TimeStepper::AdvanceOneTimeStep 99ms 0.5% 83.47% 99ms 0.5% std::_Rb_tree_rebalance_for_erase 0 0% 83.47% 99ms 0.5% std::vector::vector (inline)