File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16888ms, 84.41% of 20007ms total Dropped 766 nodes (cum <= 100.03ms) flat flat% sum% cum cum% 0 0% 0% 19958ms 99.76% __libc_start_call_main 0 0% 0% 19958ms 99.76% __libc_start_main_impl 0 0% 0% 19958ms 99.76% _start 0 0% 0% 19938ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19938ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19938ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19938ms 99.66% main 0 0% 0% 19904ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19904ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19904ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19879ms 99.36% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15362ms 76.78% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.005% 10018ms 50.07% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 9942ms 49.69% Cell::ReadyToDivide 2ms 0.01% 0.03% 9866ms 49.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.03% 9698ms 48.47% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.04% 0.07% 9687ms 48.42% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.09% 9677ms 48.37% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.31% 0.4% 9516ms 47.56% AbstractOneStepIvpOdeSolver::InternalSolve 902ms 4.51% 4.91% 8700ms 43.48% RungeKutta4IvpOdeSolver::CalculateNextYValue 3670ms 18.34% 23.25% 7562ms 37.80% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.26% 5225ms 26.12% MeshBasedCellPopulation::Update 4ms 0.02% 23.28% 4042ms 20.20% Cylindrical2dMesh::ReMesh 76ms 0.38% 23.66% 3969ms 19.84% AbstractCellProperty::IsType (inline) 550ms 2.75% 26.41% 2793ms 13.96% AbstractCellProperty::IsSame 0 0% 26.41% 2479ms 12.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 391ms 1.95% 28.36% 2243ms 11.21% std::type_info::operator== (inline) 0 0% 28.36% 2196ms 10.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.36% 2177ms 10.88% MutableMesh::ReMesh 6ms 0.03% 28.39% 2139ms 10.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.39% 2032ms 10.16% AbstractCellPopulation::WriteResultsToFiles 879ms 4.39% 32.78% 1901ms 9.50% std::_Rb_tree::_M_lower_bound (inline) 1795ms 8.97% 41.76% 1795ms 8.97% __strcmp_avx2 157ms 0.78% 42.54% 1735ms 8.67% TetrahedralMesh::EdgeIterator::operator++ 68ms 0.34% 42.88% 1409ms 7.04% std::_Rb_tree::find (inline) 0 0% 42.88% 1146ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 42.90% 1143ms 5.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.075% 42.98% 1119ms 5.59% TetrahedralMesh::ImportFromMesher 38ms 0.19% 43.17% 1086ms 5.43% operator new 9ms 0.045% 43.21% 1043ms 5.21% MeshBasedCellPopulation::SpringIterator::operator++ 229ms 1.14% 44.36% 1040ms 5.20% __GI___libc_malloc 5ms 0.025% 44.38% 1011ms 5.05% std::set::insert (inline) 12ms 0.06% 44.44% 1005ms 5.02% std::_Rb_tree::_M_insert_unique 43ms 0.21% 44.66% 946ms 4.73% std::__new_allocator::allocate (inline) 0 0% 44.66% 943ms 4.71% std::allocator_traits::allocate (inline) 0 0% 44.66% 886ms 4.43% std::set::count (inline) 0 0% 44.66% 794ms 3.97% triangulate 10ms 0.05% 44.71% 742ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 429ms 2.14% 46.85% 735ms 3.67% _int_malloc 0 0% 46.85% 721ms 3.60% delaunay 2ms 0.01% 46.86% 720ms 3.60% divconqdelaunay 61ms 0.3% 47.17% 715ms 3.57% std::map::operator[] (partial-inline) 2ms 0.01% 47.18% 703ms 3.51% CellPopulationElementWriter::Visit 3ms 0.015% 47.19% 679ms 3.39% AbstractTwoBodyInteractionForce::AddForceContribution 672ms 3.36% 50.55% 672ms 3.36% std::_Rb_tree::_S_right (inline) 17ms 0.085% 50.64% 649ms 3.24% std::less::operator() (inline) 27ms 0.13% 50.77% 634ms 3.17% std::_Rb_tree::_M_insert_ (inline) 622ms 3.11% 53.88% 632ms 3.16% WntCellCycleOdeSystem::CalculateStoppingEvent 632ms 3.16% 57.04% 632ms 3.16% std::operator< (inline) 0 0% 57.04% 625ms 3.12% std::_Rb_tree::_M_create_node (inline) 187ms 0.93% 57.97% 616ms 3.08% __dynamic_cast 1ms 0.005% 57.98% 604ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.98% 594ms 2.97% std::_Rb_tree::_M_get_node (inline) 10ms 0.05% 58.03% 588ms 2.94% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.03% 586ms 2.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.03% 584ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 58.03% 584ms 2.92% std::map::lower_bound (inline) 33ms 0.16% 58.19% 568ms 2.84% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.055% 58.25% 568ms 2.84% Element::Element 16ms 0.08% 58.33% 553ms 2.76% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 58.35% 543ms 2.71% MutableMesh::ReIndex 0 0% 58.35% 517ms 2.58% std::map::find (inline) 16ms 0.08% 58.43% 516ms 2.58% Element::RegisterWithNodes (inline) 0 0% 58.43% 512ms 2.56% std::ostream::operator<< (inline) 55ms 0.27% 58.71% 511ms 2.55% std::ostream::_M_insert 10ms 0.05% 58.76% 503ms 2.51% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.065% 58.82% 496ms 2.48% Node::AddElement 11ms 0.055% 58.88% 493ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 58.89% 474ms 2.37% AbstractCellProperty::IsSubType (inline) 311ms 1.55% 60.45% 440ms 2.20% AbstractCellMutationState::AbstractCellMutationState 141ms 0.7% 61.15% 423ms 2.11% __GI___libc_free 12ms 0.06% 61.21% 385ms 1.92% Node::RemoveElement 9ms 0.045% 61.26% 385ms 1.92% std::_Rb_tree::erase 1ms 0.005% 61.26% 383ms 1.91% std::set::erase (inline) 115ms 0.57% 61.84% 374ms 1.87% std::_Rb_tree::_M_erase 33ms 0.16% 62.00% 362ms 1.81% Element::ResetIndex 28ms 0.14% 62.14% 362ms 1.81% std::_Rb_tree::~_Rb_tree (inline) 139ms 0.69% 62.84% 360ms 1.80% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.07% 62.91% 359ms 1.79% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 62.92% 352ms 1.76% std::_Vector_base::_M_allocate (inline) 13ms 0.065% 62.99% 352ms 1.76% std::__new_allocator::deallocate (inline) 16ms 0.08% 63.07% 349ms 1.74% divconqrecurse 0 0% 63.07% 348ms 1.74% std::allocator_traits::deallocate (inline) 1ms 0.005% 63.07% 341ms 1.70% Cell::GetCellProliferativeType 165ms 0.82% 63.90% 339ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.90% 337ms 1.68% std::set::~set (inline) 2ms 0.01% 63.91% 334ms 1.67% NodeLocationWriter::Visit 99ms 0.49% 64.40% 326ms 1.63% mergehulls 0 0% 64.40% 321ms 1.60% std::_Rb_tree::_M_drop_node (inline) 319ms 1.59% 66.00% 319ms 1.59% std::type_info::name (inline) 2ms 0.01% 66.01% 302ms 1.51% Cell::GetMutationState 10ms 0.05% 66.06% 302ms 1.51% LegacyCellProliferativeTypesWriter::VisitCell 30ms 0.15% 66.21% 300ms 1.50% std::num_put::_M_insert_float 225ms 1.12% 67.33% 282ms 1.41% _int_free 0 0% 67.33% 279ms 1.39% std::_Rb_tree::_M_put_node (inline) 271ms 1.35% 68.69% 273ms 1.36% std::vector::operator[] (inline) 22ms 0.11% 68.80% 270ms 1.35% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 68.81% 269ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.015% 68.82% 262ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 39ms 0.19% 69.02% 257ms 1.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.02% 256ms 1.28% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.08% 69.10% 247ms 1.23% std::_Rb_tree::_Rb_tree (partial-inline) 10ms 0.05% 69.15% 246ms 1.23% std::vector::push_back (inline) 1ms 0.005% 69.15% 240ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 69.16% 233ms 1.16% alternateaxes 11ms 0.055% 69.22% 232ms 1.16% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 69.25% 232ms 1.16% std::__cxx11::collate::do_transform 216ms 1.08% 70.33% 230ms 1.15% vertexmedian 0 0% 70.33% 225ms 1.12% std::set::set (inline) 8ms 0.04% 70.37% 224ms 1.12% std::vector::_M_realloc_insert 60ms 0.3% 70.67% 221ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.005% 70.67% 220ms 1.10% MeshBasedCellPopulation::GetDampingConstant 0 0% 70.67% 218ms 1.09% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.035% 70.71% 213ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.065% 70.77% 210ms 1.05% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.005% 70.78% 205ms 1.02% ___vsnprintf 0 0% 70.78% 204ms 1.02% __vsnprintf_internal (inline) 27ms 0.13% 70.91% 202ms 1.01% std::_Rb_tree::_M_copy (inline) 16ms 0.08% 70.99% 201ms 1.00% __printf_buffer 164ms 0.82% 71.81% 200ms 1% AbstractElement::GetNodeGlobalIndex 20ms 0.1% 71.91% 198ms 0.99% AbstractTetrahedralElement::RefreshJacobian 13ms 0.065% 71.97% 197ms 0.98% Element::MarkAsDeleted 29ms 0.14% 72.12% 197ms 0.98% TetrahedralMesh::Clear 41ms 0.2% 72.32% 196ms 0.98% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.02% 72.34% 196ms 0.98% CellProliferativeTypesWriter::VisitCell 42ms 0.21% 72.55% 195ms 0.97% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.01% 72.56% 192ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 182ms 0.91% 73.47% 182ms 0.91% [libchaste_cell_based.so] 1ms 0.005% 73.48% 181ms 0.9% OffLatticeSimulation::ApplyBoundaries 179ms 0.89% 74.37% 179ms 0.89% Node::GetIndex 2ms 0.01% 74.38% 174ms 0.87% CellPropertyCollection::HasProperty 0 0% 74.38% 173ms 0.86% Cell::HasCellProperty (inline) 120ms 0.6% 74.98% 173ms 0.86% malloc_consolidate 53ms 0.26% 75.25% 172ms 0.86% std::_Rb_tree::_M_clone_node (inline) 170ms 0.85% 76.10% 170ms 0.85% unlink_chunk 1ms 0.005% 76.10% 165ms 0.82% __printf_fp_spec (inline) 5ms 0.025% 76.13% 164ms 0.82% __printf_fp_l_buffer 74ms 0.37% 76.50% 161ms 0.8% AbstractElement::GetNodeLocation 0 0% 76.50% 159ms 0.79% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.02% 76.52% 158ms 0.79% AbstractTetrahedralElement::AbstractTetrahedralElement 87ms 0.43% 76.95% 158ms 0.79% std::_Rb_tree::equal_range (inline) 77ms 0.38% 77.34% 154ms 0.77% __printf_fp_buffer_1 151ms 0.75% 78.09% 151ms 0.75% std::_Rb_tree_insert_and_rebalance 7ms 0.035% 78.13% 146ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 145ms 0.72% 78.85% 145ms 0.72% incircle 46ms 0.23% 79.08% 140ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 51ms 0.25% 79.34% 139ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 17ms 0.085% 79.42% 135ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.015% 79.44% 134ms 0.67% Cell::SetCellProliferativeType 6ms 0.03% 79.47% 134ms 0.67% boost::numeric::ublas::vector_assign (inline) 129ms 0.64% 80.11% 129ms 0.64% AbstractCellProperty::~AbstractCellProperty 126ms 0.63% 80.74% 126ms 0.63% std::vector::size (inline) 112ms 0.56% 81.30% 125ms 0.62% vertexsort 10ms 0.05% 81.35% 122ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 82ms 0.41% 81.76% 119ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.005% 81.77% 117ms 0.58% AbstractCellBasedSimulation::DoCellRemoval (inline) 25ms 0.12% 81.89% 117ms 0.58% std::num_put::_M_insert_int 22ms 0.11% 82.00% 116ms 0.58% TetrahedralMesh::EdgesEnd 113ms 0.56% 82.57% 113ms 0.56% AbstractCellMutationState::~AbstractCellMutationState 112ms 0.56% 83.13% 112ms 0.56% AbstractElement::IsDeleted 3ms 0.015% 83.14% 108ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.14% 107ms 0.53% AbstractCellBasedWriter::OpenOutputFileForAppend 7ms 0.035% 83.18% 107ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.04% 83.22% 104ms 0.52% Node::~Node 0 0% 83.22% 104ms 0.52% OutputFileHandler::OpenOutputFile 11ms 0.055% 83.27% 102ms 0.51% boost::detail::shared_count::~shared_count (inline) 25ms 0.12% 83.40% 102ms 0.51% boost::numeric::ublas::indexing_vector_assign 0 0% 83.40% 102ms 0.51% boost::shared_ptr::~shared_ptr (inline) 102ms 0.51% 83.91% 102ms 0.51% std::_Rb_tree_rebalance_for_erase 101ms 0.5% 84.41% 101ms 0.5% std::_Rb_tree_increment