File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16573ms, 84.78% of 19548ms total Dropped 760 nodes (cum <= 97.74ms) flat flat% sum% cum cum% 0 0% 0% 19501ms 99.76% __libc_start_call_main 0 0% 0% 19501ms 99.76% __libc_start_main_impl 0 0% 0% 19501ms 99.76% _start 0 0% 0% 19478ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19478ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19478ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19478ms 99.64% main 0 0% 0% 19433ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19433ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19433ms 99.41% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.01% 0.01% 19407ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0.01% 14826ms 75.84% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.01% 9353ms 47.85% AbstractCellBasedSimulation::DoCellBirth 7ms 0.036% 0.046% 9260ms 47.37% Cell::ReadyToDivide 6ms 0.031% 0.077% 9180ms 46.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.087% 9038ms 46.23% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.067% 0.15% 9028ms 46.18% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.15% 9009ms 46.09% CellCycleModelOdeHandler::SolveOdeToTime 71ms 0.36% 0.52% 8839ms 45.22% AbstractOneStepIvpOdeSolver::InternalSolve 1025ms 5.24% 5.76% 7962ms 40.73% RungeKutta4IvpOdeSolver::CalculateNextYValue 2753ms 14.08% 19.84% 6744ms 34.50% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 19.85% 5341ms 27.32% MeshBasedCellPopulation::Update 3ms 0.015% 19.87% 4099ms 20.97% Cylindrical2dMesh::ReMesh 50ms 0.26% 20.12% 3999ms 20.46% AbstractCellProperty::IsType (inline) 331ms 1.69% 21.82% 2536ms 12.97% AbstractCellProperty::IsSame 0 0% 21.82% 2535ms 12.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.82% 2242ms 11.47% MutableMesh::ReMesh 0 0% 21.82% 2228ms 11.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 253ms 1.29% 23.11% 2205ms 11.28% std::type_info::operator== (inline) 12ms 0.061% 23.17% 2184ms 11.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 2073ms 10.60% 33.78% 2073ms 10.60% __strcmp_avx2 0 0% 33.78% 2040ms 10.44% AbstractCellPopulation::WriteResultsToFiles 805ms 4.12% 37.90% 1895ms 9.69% std::_Rb_tree::_M_lower_bound (inline) 157ms 0.8% 38.70% 1704ms 8.72% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.32% 39.02% 1428ms 7.31% std::_Rb_tree::find (inline) 1ms 0.0051% 39.02% 1199ms 6.13% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.031% 39.05% 1170ms 5.99% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.092% 39.14% 1128ms 5.77% TetrahedralMesh::ImportFromMesher 12ms 0.061% 39.21% 1046ms 5.35% MeshBasedCellPopulation::SpringIterator::operator++ 50ms 0.26% 39.46% 1043ms 5.34% operator new 7ms 0.036% 39.50% 1025ms 5.24% std::set::insert (inline) 11ms 0.056% 39.55% 1018ms 5.21% std::_Rb_tree::_M_insert_unique 248ms 1.27% 40.82% 983ms 5.03% __GI___libc_malloc 33ms 0.17% 40.99% 902ms 4.61% std::__new_allocator::allocate (inline) 0 0% 40.99% 895ms 4.58% std::allocator_traits::allocate (inline) 0 0% 40.99% 893ms 4.57% triangulate 0 0% 40.99% 849ms 4.34% std::set::count (inline) 1ms 0.0051% 41.00% 826ms 4.23% delaunay 7ms 0.036% 41.03% 824ms 4.22% divconqdelaunay 5ms 0.026% 41.06% 767ms 3.92% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 724ms 3.70% 44.76% 724ms 3.70% std::_Rb_tree::_S_right (inline) 7ms 0.036% 44.80% 713ms 3.65% CellPopulationElementWriter::Visit 50ms 0.26% 45.05% 705ms 3.61% std::map::operator[] (partial-inline) 0 0% 45.05% 687ms 3.51% AbstractTwoBodyInteractionForce::AddForceContribution 687ms 3.51% 48.57% 687ms 3.51% WntCellCycleOdeSystem::CalculateStoppingEvent 22ms 0.11% 48.68% 668ms 3.42% std::less::operator() (inline) 210ms 1.07% 49.75% 657ms 3.36% __dynamic_cast 385ms 1.97% 51.72% 656ms 3.36% _int_malloc 646ms 3.30% 55.03% 646ms 3.30% std::operator< (inline) 0 0% 55.03% 625ms 3.20% std::_Rb_tree::_M_create_node (inline) 5ms 0.026% 55.05% 618ms 3.16% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.01% 55.06% 617ms 3.16% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.14% 55.20% 611ms 3.13% std::_Rb_tree::_M_insert_ (inline) 29ms 0.15% 55.35% 602ms 3.08% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.082% 55.43% 587ms 3.00% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.43% 586ms 3.00% std::_Rb_tree::_M_get_node (inline) 5ms 0.026% 55.46% 583ms 2.98% Element::Element 0 0% 55.46% 575ms 2.94% std::map::find (inline) 0 0% 55.46% 571ms 2.92% std::_Rb_tree::_Alloc_node::operator() (inline) 16ms 0.082% 55.54% 558ms 2.85% MutableMesh::ReIndex 0 0% 55.54% 557ms 2.85% std::_Rb_tree::lower_bound (inline) 0 0% 55.54% 557ms 2.85% std::map::lower_bound (inline) 12ms 0.061% 55.60% 531ms 2.72% Element::RegisterWithNodes (inline) 3ms 0.015% 55.62% 521ms 2.67% AbstractCellProperty::IsSubType (inline) 8ms 0.041% 55.66% 517ms 2.64% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.077% 55.73% 512ms 2.62% Node::AddElement 13ms 0.067% 55.80% 492ms 2.52% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 55.81% 488ms 2.50% std::ostream::operator<< (inline) 66ms 0.34% 56.14% 487ms 2.49% std::ostream::_M_insert 135ms 0.69% 56.83% 461ms 2.36% __GI___libc_free 300ms 1.53% 58.37% 457ms 2.34% AbstractCellMutationState::AbstractCellMutationState 402ms 2.06% 60.43% 402ms 2.06% [libchaste_cell_based.so] 154ms 0.79% 61.21% 396ms 2.03% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 61.32% 387ms 1.98% Node::RemoveElement 8ms 0.041% 61.36% 381ms 1.95% std::_Rb_tree::erase 1ms 0.0051% 61.36% 381ms 1.95% std::set::erase (inline) 18ms 0.092% 61.45% 375ms 1.92% divconqrecurse 13ms 0.067% 61.52% 356ms 1.82% std::__new_allocator::deallocate (inline) 104ms 0.53% 62.05% 352ms 1.80% std::_Rb_tree::_M_erase 0 0% 62.05% 350ms 1.79% std::allocator_traits::deallocate (inline) 99ms 0.51% 62.56% 349ms 1.79% mergehulls 35ms 0.18% 62.74% 348ms 1.78% Element::ResetIndex 10ms 0.051% 62.79% 339ms 1.73% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 33ms 0.17% 62.96% 334ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 253ms 1.29% 64.25% 326ms 1.67% _int_free 3ms 0.015% 64.27% 323ms 1.65% Cell::GetMutationState 4ms 0.02% 64.29% 321ms 1.64% Cell::GetCellProliferativeType 1ms 0.0051% 64.29% 320ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 149ms 0.76% 65.06% 320ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.06% 316ms 1.62% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.06% 313ms 1.60% std::set::~set (inline) 1ms 0.0051% 65.06% 310ms 1.59% std::_Vector_base::_M_allocate (inline) 6ms 0.031% 65.09% 300ms 1.53% alternateaxes 275ms 1.41% 66.50% 292ms 1.49% vertexmedian 5ms 0.026% 66.52% 289ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.52% 284ms 1.45% std::_Rb_tree::_M_put_node (inline) 280ms 1.43% 67.96% 282ms 1.44% std::vector::operator[] (inline) 0 0% 67.96% 280ms 1.43% NodeLocationWriter::Visit 1ms 0.0051% 67.96% 277ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 34ms 0.17% 68.13% 273ms 1.40% AbstractCellPopulation::Iterator::IsRealCell 21ms 0.11% 68.24% 271ms 1.39% std::_Rb_tree::_Rb_tree (partial-inline) 101ms 0.52% 68.76% 262ms 1.34% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 7ms 0.036% 68.79% 258ms 1.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 107ms 0.55% 69.34% 253ms 1.29% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 55ms 0.28% 69.62% 245ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 8ms 0.041% 69.66% 244ms 1.25% std::vector::push_back (inline) 6ms 0.031% 69.70% 240ms 1.23% std::set::set (inline) 16ms 0.082% 69.78% 236ms 1.21% std::num_put::_M_insert_float 18ms 0.092% 69.87% 229ms 1.17% std::vector::_M_realloc_insert 1ms 0.0051% 69.87% 227ms 1.16% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.87% 227ms 1.16% MeshBasedCellPopulation::GetDampingConstant 10ms 0.051% 69.93% 225ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.11% 70.03% 220ms 1.13% std::_Rb_tree::_M_copy (inline) 14ms 0.072% 70.10% 214ms 1.09% AbstractTetrahedralElement::CalculateJacobian 10ms 0.051% 70.16% 211ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 149ms 0.76% 70.92% 208ms 1.06% AbstractElement::GetNodeGlobalIndex 10ms 0.051% 70.97% 206ms 1.05% Element::MarkAsDeleted 56ms 0.29% 71.26% 196ms 1.00% std::_Rb_tree::_M_clone_node (inline) 15ms 0.077% 71.33% 194ms 0.99% TetrahedralMesh::Clear 2ms 0.01% 71.34% 193ms 0.99% std::__cxx11::collate::do_transform 0 0% 71.34% 192ms 0.98% TetrahedralMesh::RefreshJacobianCachedData 192ms 0.98% 72.32% 192ms 0.98% [libchaste_crypt.so] 1ms 0.0051% 72.33% 191ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.33% 186ms 0.95% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 72.34% 185ms 0.95% ___vsnprintf 0 0% 72.34% 183ms 0.94% __vsnprintf_internal (inline) 21ms 0.11% 72.45% 180ms 0.92% __printf_buffer 6ms 0.031% 72.48% 178ms 0.91% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 178ms 0.91% 73.39% 178ms 0.91% Node::GetIndex 25ms 0.13% 73.52% 174ms 0.89% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.02% 73.54% 173ms 0.89% CellPropertyCollection::HasProperty 16ms 0.082% 73.62% 172ms 0.88% AbstractTetrahedralElement::CalculateInverseJacobian 27ms 0.14% 73.76% 172ms 0.88% AbstractTetrahedralElement::RefreshJacobian 17ms 0.087% 73.84% 172ms 0.88% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 73.84% 171ms 0.87% Cell::HasCellProperty (inline) 5ms 0.026% 73.87% 169ms 0.86% CellProliferativeTypesWriter::VisitCell 163ms 0.83% 74.70% 163ms 0.83% incircle 57ms 0.29% 74.99% 162ms 0.83% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 160ms 0.82% 75.81% 160ms 0.82% std::_Rb_tree_insert_and_rebalance 104ms 0.53% 76.35% 159ms 0.81% malloc_consolidate 5ms 0.026% 76.37% 158ms 0.81% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.031% 76.40% 155ms 0.79% MeshBasedCellPopulation::SpringsEnd (inline) 96ms 0.49% 76.89% 152ms 0.78% std::_Rb_tree::equal_range (inline) 152ms 0.78% 77.67% 152ms 0.78% unlink_chunk 2ms 0.01% 77.68% 150ms 0.77% boost::numeric::ublas::vector_assign (inline) 149ms 0.76% 78.44% 149ms 0.76% std::type_info::name (inline) 4ms 0.02% 78.46% 148ms 0.76% __printf_fp_l_buffer 0 0% 78.46% 148ms 0.76% __printf_fp_spec (inline) 145ms 0.74% 79.21% 146ms 0.75% std::vector::size (inline) 46ms 0.24% 79.44% 139ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 8ms 0.041% 79.48% 138ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 87ms 0.45% 79.93% 137ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 95ms 0.49% 80.41% 137ms 0.7% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 80.41% 136ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 58ms 0.3% 80.71% 136ms 0.7% __printf_fp_buffer_1 0 0% 80.71% 135ms 0.69% OutputFileHandler::OpenOutputFile 123ms 0.63% 81.34% 134ms 0.69% vertexsort 59ms 0.3% 81.64% 132ms 0.68% AbstractElement::GetNodeLocation 0 0% 81.64% 131ms 0.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.64% 131ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 3ms 0.015% 81.66% 125ms 0.64% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.15% 81.81% 125ms 0.64% std::num_put::_M_insert_int 6ms 0.031% 81.84% 121ms 0.62% Node::~Node 4ms 0.02% 81.86% 120ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.86% 117ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 81.87% 115ms 0.59% Cell::SetCellProliferativeType 24ms 0.12% 81.99% 110ms 0.56% boost::numeric::ublas::indexing_vector_assign 47ms 0.24% 82.23% 109ms 0.56% std::__ostream_insert 12ms 0.061% 82.29% 108ms 0.55% boost::detail::shared_count::~shared_count (inline) 108ms 0.55% 82.85% 108ms 0.55% boost::shared_ptr::operator-> (inline) 0 0% 82.85% 108ms 0.55% boost::shared_ptr::~shared_ptr (inline) 107ms 0.55% 83.39% 107ms 0.55% AbstractCellMutationState::~AbstractCellMutationState 7ms 0.036% 83.43% 107ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 107ms 0.55% 83.98% 107ms 0.55% std::_Rb_tree_increment 12ms 0.061% 84.04% 102ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 39ms 0.2% 84.24% 100ms 0.51% boost::shared_ptr::shared_ptr (inline) 8ms 0.041% 84.28% 99ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 98ms 0.5% 84.78% 98ms 0.5% AbstractCellProperty::AbstractCellProperty