File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16906ms, 85.04% of 19879ms total Dropped 751 nodes (cum <= 99.39ms) flat flat% sum% cum cum% 0 0% 0% 19836ms 99.78% __libc_start_call_main 0 0% 0% 19836ms 99.78% __libc_start_main_impl 0 0% 0% 19836ms 99.78% _start 0 0% 0% 19817ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19817ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19817ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19817ms 99.69% main 0 0% 0% 19780ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19780ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19780ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19753ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 15335ms 77.14% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10153ms 51.07% AbstractCellBasedSimulation::DoCellBirth 9ms 0.045% 0.05% 10056ms 50.59% Cell::ReadyToDivide 7ms 0.035% 0.086% 9983ms 50.22% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.1% 9838ms 49.49% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.16% 9829ms 49.44% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.17% 9815ms 49.37% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.36% 0.53% 9675ms 48.67% AbstractOneStepIvpOdeSolver::InternalSolve 873ms 4.39% 4.92% 8807ms 44.30% RungeKutta4IvpOdeSolver::CalculateNextYValue 3636ms 18.29% 23.22% 7706ms 38.76% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.23% 5068ms 25.49% MeshBasedCellPopulation::Update 182ms 0.92% 24.14% 4107ms 20.66% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.16% 3879ms 19.51% Cylindrical2dMesh::ReMesh 568ms 2.86% 27.02% 2896ms 14.57% AbstractCellProperty::IsSame 1ms 0.005% 27.02% 2456ms 12.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 447ms 2.25% 29.27% 2328ms 11.71% std::type_info::operator== (inline) 0 0% 29.27% 2156ms 10.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.27% 2112ms 10.62% MutableMesh::ReMesh 8ms 0.04% 29.31% 2111ms 10.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.31% 1957ms 9.84% AbstractCellPopulation::WriteResultsToFiles 792ms 3.98% 33.30% 1874ms 9.43% std::_Rb_tree::_M_lower_bound (inline) 1847ms 9.29% 42.59% 1847ms 9.29% __strcmp_avx2 146ms 0.73% 43.32% 1690ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 79ms 0.4% 43.72% 1419ms 7.14% std::_Rb_tree::find (inline) 0 0% 43.72% 1152ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.04% 43.76% 1129ms 5.68% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.05% 43.81% 1072ms 5.39% TetrahedralMesh::ImportFromMesher 9ms 0.045% 43.86% 1028ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.065% 43.92% 1016ms 5.11% std::set::insert (inline) 16ms 0.08% 44.00% 1003ms 5.05% std::_Rb_tree::_M_insert_unique 42ms 0.21% 44.21% 998ms 5.02% operator new 240ms 1.21% 45.42% 944ms 4.75% __GI___libc_malloc 43ms 0.22% 45.64% 889ms 4.47% std::__new_allocator::allocate (inline) 0 0% 45.64% 883ms 4.44% std::allocator_traits::allocate (inline) 0 0% 45.64% 845ms 4.25% std::set::count (inline) 0 0% 45.64% 822ms 4.14% triangulate 0 0% 45.64% 757ms 3.81% delaunay 2ms 0.01% 45.65% 757ms 3.81% divconqdelaunay 10ms 0.05% 45.70% 741ms 3.73% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 45.71% 717ms 3.61% AbstractTwoBodyInteractionForce::AddForceContribution 695ms 3.50% 49.20% 695ms 3.50% std::_Rb_tree::_S_right (inline) 60ms 0.3% 49.50% 689ms 3.47% std::map::operator[] (partial-inline) 5ms 0.025% 49.53% 672ms 3.38% CellPopulationElementWriter::Visit 652ms 3.28% 52.81% 670ms 3.37% WntCellCycleOdeSystem::CalculateStoppingEvent 22ms 0.11% 52.92% 662ms 3.33% std::less::operator() (inline) 640ms 3.22% 56.14% 640ms 3.22% std::operator< (inline) 23ms 0.12% 56.26% 619ms 3.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 357ms 1.80% 58.05% 619ms 3.11% _int_malloc 30ms 0.15% 58.20% 616ms 3.10% std::_Rb_tree::_M_insert_ (inline) 140ms 0.7% 58.91% 599ms 3.01% __dynamic_cast 0 0% 58.91% 597ms 3.00% std::_Rb_tree::_M_create_node (inline) 18ms 0.091% 59.00% 583ms 2.93% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 59.02% 581ms 2.92% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.04% 59.06% 572ms 2.88% Element::Element 0 0% 59.06% 572ms 2.88% std::map::find (inline) 0 0% 59.06% 568ms 2.86% std::_Rb_tree::_M_get_node (inline) 0 0% 59.06% 555ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 59.06% 555ms 2.79% std::map::lower_bound (inline) 0 0% 59.06% 552ms 2.78% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 59.08% 535ms 2.69% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.065% 59.14% 527ms 2.65% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.07% 59.21% 495ms 2.49% MutableMesh::ReIndex 11ms 0.055% 59.27% 474ms 2.38% Element::RegisterWithNodes (inline) 65ms 0.33% 59.60% 471ms 2.37% std::ostream::_M_insert 0 0% 59.60% 471ms 2.37% std::ostream::operator<< (inline) 11ms 0.055% 59.65% 464ms 2.33% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.035% 59.69% 464ms 2.33% Node::AddElement 301ms 1.51% 61.20% 455ms 2.29% AbstractCellMutationState::AbstractCellMutationState 148ms 0.74% 61.94% 445ms 2.24% __GI___libc_free 6ms 0.03% 61.97% 425ms 2.14% AbstractCellProperty::IsSubType (inline) 15ms 0.075% 62.05% 394ms 1.98% divconqrecurse 12ms 0.06% 62.11% 392ms 1.97% std::_Rb_tree::erase 2ms 0.01% 62.12% 392ms 1.97% std::set::erase (inline) 10ms 0.05% 62.17% 381ms 1.92% Node::RemoveElement 125ms 0.63% 62.80% 372ms 1.87% mergehulls 140ms 0.7% 63.50% 372ms 1.87% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.02% 63.52% 363ms 1.83% std::__new_allocator::deallocate (inline) 0 0% 63.52% 359ms 1.81% std::allocator_traits::deallocate (inline) 96ms 0.48% 64.01% 339ms 1.71% std::_Rb_tree::_M_erase 332ms 1.67% 65.68% 332ms 1.67% std::type_info::name (inline) 149ms 0.75% 66.43% 329ms 1.66% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.43% 329ms 1.66% std::_Rb_tree::_M_drop_node (inline) 23ms 0.12% 66.54% 327ms 1.64% Element::ResetIndex 11ms 0.055% 66.60% 317ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.03% 66.63% 316ms 1.59% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.005% 66.63% 316ms 1.59% std::_Vector_base::_M_allocate (inline) 2ms 0.01% 66.64% 312ms 1.57% Cell::GetCellProliferativeType 17ms 0.086% 66.73% 312ms 1.57% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.005% 66.73% 304ms 1.53% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 66.74% 303ms 1.52% NodeLocationWriter::Visit 231ms 1.16% 67.91% 297ms 1.49% _int_free 35ms 0.18% 68.08% 293ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.08% 293ms 1.47% std::_Rb_tree::_M_put_node (inline) 0 0% 68.08% 289ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.08% 287ms 1.44% std::set::~set (inline) 1ms 0.005% 68.09% 278ms 1.40% Cell::GetMutationState 278ms 1.40% 69.49% 278ms 1.40% std::vector::operator[] (inline) 16ms 0.08% 69.57% 261ms 1.31% AbstractTetrahedralElement::CalculateJacobian 13ms 0.065% 69.63% 261ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 10ms 0.05% 69.68% 259ms 1.30% std::num_put::_M_insert_float 13ms 0.065% 69.75% 249ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 69.76% 244ms 1.23% std::set::set (inline) 3ms 0.015% 69.78% 243ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.035% 69.81% 240ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 11ms 0.055% 69.87% 240ms 1.21% std::vector::push_back (inline) 2ms 0.01% 69.88% 237ms 1.19% alternateaxes 4ms 0.02% 69.90% 236ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 226ms 1.14% 71.03% 234ms 1.18% vertexmedian 230ms 1.16% 72.19% 230ms 1.16% [libchaste_cell_based.so] 11ms 0.055% 72.25% 220ms 1.11% std::vector::_M_realloc_insert 31ms 0.16% 72.40% 217ms 1.09% AbstractTetrahedralElement::RefreshJacobian 51ms 0.26% 72.66% 214ms 1.08% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 25ms 0.13% 72.79% 214ms 1.08% std::_Rb_tree::_M_copy (inline) 3ms 0.015% 72.80% 212ms 1.07% std::__cxx11::collate::do_transform 162ms 0.81% 73.62% 207ms 1.04% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 73.63% 207ms 1.04% ___vsnprintf 62ms 0.31% 73.94% 206ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 73.94% 205ms 1.03% __vsnprintf_internal (inline) 1ms 0.005% 73.94% 202ms 1.02% TetrahedralMesh::RefreshJacobianCachedData 23ms 0.12% 74.06% 201ms 1.01% __printf_buffer 0 0% 74.06% 195ms 0.98% OffLatticeSimulation::ApplyBoundaries 10ms 0.05% 74.11% 192ms 0.97% Element::MarkAsDeleted 2ms 0.01% 74.12% 186ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 36ms 0.18% 74.30% 186ms 0.94% ApcOneHitCellMutationState::ApcOneHitCellMutationState 49ms 0.25% 74.55% 183ms 0.92% std::_Rb_tree::_M_clone_node (inline) 179ms 0.9% 75.45% 179ms 0.9% std::_Rb_tree_insert_and_rebalance 5ms 0.025% 75.47% 175ms 0.88% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 75.48% 172ms 0.87% MeshBasedCellPopulation::GetDampingConstant 71ms 0.36% 75.84% 171ms 0.86% AbstractElement::GetNodeLocation 134ms 0.67% 76.51% 171ms 0.86% malloc_consolidate 1ms 0.005% 76.52% 170ms 0.86% AbstractCentreBasedCellPopulation::GetDampingConstant 168ms 0.85% 77.36% 168ms 0.85% Node::GetIndex 1ms 0.005% 77.37% 162ms 0.81% __printf_fp_spec (inline) 5ms 0.025% 77.39% 161ms 0.81% __printf_fp_l_buffer 161ms 0.81% 78.20% 161ms 0.81% std::vector::size (inline) 21ms 0.11% 78.31% 159ms 0.8% TetrahedralMesh::Clear 4ms 0.02% 78.33% 154ms 0.77% CellProliferativeTypesWriter::VisitCell 76ms 0.38% 78.71% 153ms 0.77% __printf_fp_buffer_1 23ms 0.12% 78.83% 152ms 0.76% TetrahedralMesh::EdgesEnd (partial-inline) 90ms 0.45% 79.28% 150ms 0.75% std::_Rb_tree::equal_range (inline) 149ms 0.75% 80.03% 149ms 0.75% incircle 12ms 0.06% 80.09% 146ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 57ms 0.29% 80.38% 143ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 80.38% 141ms 0.71% Cell::HasCellProperty (inline) 1ms 0.005% 80.38% 141ms 0.71% CellPropertyCollection::HasProperty 0 0% 80.38% 140ms 0.7% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 80.40% 139ms 0.7% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.005% 80.41% 132ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 15ms 0.075% 80.48% 129ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 83ms 0.42% 80.90% 128ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 127ms 0.64% 81.54% 127ms 0.64% unlink_chunk 13ms 0.065% 81.60% 123ms 0.62% boost::numeric::ublas::c_vector::c_vector (partial-inline) 112ms 0.56% 82.17% 119ms 0.6% vertexsort 5ms 0.025% 82.19% 118ms 0.59% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 82.19% 116ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 38ms 0.19% 82.38% 116ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 30ms 0.15% 82.53% 116ms 0.58% std::num_put::_M_insert_int 54ms 0.27% 82.81% 114ms 0.57% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 82.81% 113ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 82.81% 113ms 0.57% Cell::SetCellProliferativeType 0 0% 82.81% 113ms 0.57% OutputFileHandler::OpenOutputFile 36ms 0.18% 82.99% 111ms 0.56% boost::numeric::ublas::indexing_vector_assign 45ms 0.23% 83.21% 111ms 0.56% std::__ostream_insert 5ms 0.025% 83.24% 109ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.02% 83.26% 107ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 105ms 0.53% 83.79% 105ms 0.53% AbstractCellMutationState::~AbstractCellMutationState 102ms 0.51% 84.30% 102ms 0.51% AbstractElement::IsDeleted 0 0% 84.30% 101ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 48ms 0.24% 84.54% 100ms 0.5% boost::shared_ptr::shared_ptr (inline) 100ms 0.5% 85.04% 100ms 0.5% std::_Rb_tree_rebalance_for_erase