File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16762ms, 85.36% of 19636ms total Dropped 748 nodes (cum <= 98.18ms) flat flat% sum% cum cum% 0 0% 0% 19590ms 99.77% __libc_start_call_main 0 0% 0% 19590ms 99.77% __libc_start_main_impl 0 0% 0% 19590ms 99.77% _start 0 0% 0% 19570ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19570ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19570ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19570ms 99.66% main 0 0% 0% 19533ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19533ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19533ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19505ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15106ms 76.93% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.02% 0.02% 9916ms 50.50% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0051% 0.025% 9835ms 50.09% Cell::ReadyToDivide 5ms 0.025% 0.051% 9782ms 49.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.066% 9640ms 49.09% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.031% 0.097% 9630ms 49.04% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.11% 9624ms 49.01% CellCycleModelOdeHandler::SolveOdeToTime 85ms 0.43% 0.54% 9460ms 48.18% AbstractOneStepIvpOdeSolver::InternalSolve 873ms 4.45% 4.99% 8591ms 43.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 3599ms 18.33% 23.32% 7522ms 38.31% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.32% 5090ms 25.92% MeshBasedCellPopulation::Update 100ms 0.51% 23.83% 4000ms 20.37% AbstractCellProperty::IsType (inline) 5ms 0.025% 23.85% 3909ms 19.91% Cylindrical2dMesh::ReMesh 564ms 2.87% 26.73% 2757ms 14.04% AbstractCellProperty::IsSame 0 0% 26.73% 2438ms 12.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 407ms 2.07% 28.80% 2193ms 11.17% std::type_info::operator== (inline) 0 0% 28.80% 2131ms 10.85% MutableMesh::ReMesh 0 0% 28.80% 2130ms 10.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 28.85% 2080ms 10.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0051% 28.86% 1959ms 9.98% AbstractCellPopulation::WriteResultsToFiles 808ms 4.11% 32.97% 1843ms 9.39% std::_Rb_tree::_M_lower_bound (inline) 1706ms 8.69% 41.66% 1706ms 8.69% __strcmp_avx2 153ms 0.78% 42.44% 1704ms 8.68% TetrahedralMesh::EdgeIterator::operator++ 77ms 0.39% 42.83% 1381ms 7.03% std::_Rb_tree::find (inline) 0 0% 42.83% 1147ms 5.84% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 42.85% 1128ms 5.74% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 52ms 0.26% 43.12% 1078ms 5.49% operator new 12ms 0.061% 43.18% 1062ms 5.41% TetrahedralMesh::ImportFromMesher 10ms 0.051% 43.23% 1020ms 5.19% MeshBasedCellPopulation::SpringIterator::operator++ 220ms 1.12% 44.35% 1017ms 5.18% __GI___libc_malloc 5ms 0.025% 44.38% 1010ms 5.14% std::set::insert (inline) 20ms 0.1% 44.48% 1005ms 5.12% std::_Rb_tree::_M_insert_unique 42ms 0.21% 44.69% 923ms 4.70% std::__new_allocator::allocate (inline) 0 0% 44.69% 921ms 4.69% std::allocator_traits::allocate (inline) 0 0% 44.69% 852ms 4.34% std::set::count (inline) 0 0% 44.69% 836ms 4.26% triangulate 0 0% 44.69% 784ms 3.99% delaunay 4ms 0.02% 44.71% 782ms 3.98% divconqdelaunay 432ms 2.20% 46.91% 731ms 3.72% _int_malloc 9ms 0.046% 46.96% 721ms 3.67% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 50ms 0.25% 47.21% 698ms 3.55% std::map::operator[] (partial-inline) 681ms 3.47% 50.68% 681ms 3.47% std::_Rb_tree::_S_right (inline) 2ms 0.01% 50.69% 680ms 3.46% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.036% 50.73% 659ms 3.36% CellPopulationElementWriter::Visit 644ms 3.28% 54.01% 655ms 3.34% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 54.01% 636ms 3.24% std::_Rb_tree::_M_create_node (inline) 18ms 0.092% 54.10% 626ms 3.19% std::less::operator() (inline) 18ms 0.092% 54.19% 623ms 3.17% std::_Rb_tree::_M_insert_ (inline) 608ms 3.10% 57.29% 608ms 3.10% std::operator< (inline) 0 0% 57.29% 598ms 3.05% std::_Rb_tree::_M_get_node (inline) 183ms 0.93% 58.22% 595ms 3.03% __dynamic_cast 26ms 0.13% 58.35% 592ms 3.01% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.031% 58.38% 582ms 2.96% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.38% 581ms 2.96% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 58.40% 572ms 2.91% Element::Element 0 0% 58.40% 569ms 2.90% std::_Rb_tree::lower_bound (inline) 0 0% 58.40% 569ms 2.90% std::map::lower_bound (inline) 23ms 0.12% 58.52% 563ms 2.87% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 4ms 0.02% 58.54% 544ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.015% 58.56% 522ms 2.66% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 58.56% 520ms 2.65% std::map::find (inline) 13ms 0.066% 58.62% 508ms 2.59% Element::RegisterWithNodes (inline) 7ms 0.036% 58.66% 495ms 2.52% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.051% 58.71% 494ms 2.52% Node::AddElement 5ms 0.025% 58.73% 492ms 2.51% MutableMesh::ReIndex 2ms 0.01% 58.74% 474ms 2.41% std::ostream::operator<< (inline) 59ms 0.3% 59.04% 471ms 2.40% std::ostream::_M_insert 311ms 1.58% 60.63% 467ms 2.38% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 60.65% 458ms 2.33% AbstractCellProperty::IsSubType (inline) 143ms 0.73% 61.38% 424ms 2.16% __GI___libc_free 9ms 0.046% 61.42% 416ms 2.12% std::_Rb_tree::erase 1ms 0.0051% 61.43% 415ms 2.11% std::set::erase (inline) 9ms 0.046% 61.47% 412ms 2.10% Node::RemoveElement 20ms 0.1% 61.58% 411ms 2.09% divconqrecurse 114ms 0.58% 62.16% 386ms 1.97% mergehulls 153ms 0.78% 62.94% 363ms 1.85% std::_Rb_tree::_M_get_insert_unique_pos 16ms 0.081% 63.02% 360ms 1.83% std::__new_allocator::deallocate (inline) 15ms 0.076% 63.09% 352ms 1.79% Element::ResetIndex 0 0% 63.09% 352ms 1.79% std::allocator_traits::deallocate (inline) 349ms 1.78% 64.87% 349ms 1.78% std::type_info::name (inline) 101ms 0.51% 65.39% 341ms 1.74% std::_Rb_tree::_M_erase 1ms 0.0051% 65.39% 324ms 1.65% std::_Vector_base::_M_allocate (inline) 12ms 0.061% 65.45% 322ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.45% 314ms 1.60% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 65.46% 311ms 1.58% NodeLocationWriter::Visit 1ms 0.0051% 65.46% 309ms 1.57% Cell::GetCellProliferativeType 18ms 0.092% 65.55% 309ms 1.57% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0051% 65.56% 302ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 146ms 0.74% 66.30% 302ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0051% 66.31% 301ms 1.53% AbstractCellPopulation::GetLocationIndexUsingCell 235ms 1.20% 67.50% 279ms 1.42% _int_free 0 0% 67.50% 279ms 1.42% std::_Rb_tree::_M_put_node (inline) 0 0% 67.50% 277ms 1.41% std::set::~set (inline) 8ms 0.041% 67.54% 275ms 1.40% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.025% 67.57% 273ms 1.39% Cell::GetMutationState 23ms 0.12% 67.69% 271ms 1.38% std::num_put::_M_insert_float 23ms 0.12% 67.80% 253ms 1.29% AbstractTetrahedralElement::CalculateJacobian 0 0% 67.80% 252ms 1.28% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 67.81% 252ms 1.28% std::set::set (inline) 38ms 0.19% 68.01% 249ms 1.27% AbstractCellPopulation::Iterator::IsRealCell (inline) 66ms 0.34% 68.34% 247ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 6ms 0.031% 68.37% 245ms 1.25% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.046% 68.42% 244ms 1.24% std::vector::push_back (inline) 8ms 0.041% 68.46% 236ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 233ms 1.19% 69.65% 234ms 1.19% std::vector::operator[] (inline) 4ms 0.02% 69.67% 232ms 1.18% alternateaxes 24ms 0.12% 69.79% 232ms 1.18% std::_Rb_tree::_M_copy (inline) 219ms 1.12% 70.91% 228ms 1.16% vertexmedian 20ms 0.1% 71.01% 226ms 1.15% std::vector::_M_realloc_insert 15ms 0.076% 71.08% 217ms 1.11% Element::MarkAsDeleted 5ms 0.025% 71.11% 213ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 71.11% 210ms 1.07% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.031% 71.14% 210ms 1.07% std::__cxx11::collate::do_transform 209ms 1.06% 72.20% 209ms 1.06% [libchaste_cell_based.so] 45ms 0.23% 72.43% 208ms 1.06% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 59ms 0.3% 72.73% 203ms 1.03% std::_Rb_tree::_M_clone_node (inline) 145ms 0.74% 73.47% 198ms 1.01% AbstractElement::GetNodeGlobalIndex 34ms 0.17% 73.65% 196ms 1% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 22ms 0.11% 73.76% 195ms 0.99% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0051% 73.76% 195ms 0.99% ___vsnprintf 21ms 0.11% 73.87% 194ms 0.99% __printf_buffer 0 0% 73.87% 194ms 0.99% __vsnprintf_internal (inline) 0 0% 73.87% 192ms 0.98% OffLatticeSimulation::ApplyBoundaries 7ms 0.036% 73.91% 186ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 73.91% 182ms 0.93% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 73.91% 179ms 0.91% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.91% 179ms 0.91% MeshBasedCellPopulation::GetDampingConstant 124ms 0.63% 74.54% 178ms 0.91% malloc_consolidate 111ms 0.57% 75.11% 177ms 0.9% std::_Rb_tree::equal_range (inline) 177ms 0.9% 76.01% 177ms 0.9% std::_Rb_tree_insert_and_rebalance 167ms 0.85% 76.86% 167ms 0.85% Node::GetIndex 8ms 0.041% 76.90% 163ms 0.83% AbstractTetrahedralElement::AbstractTetrahedralElement 162ms 0.83% 77.72% 162ms 0.83% incircle 161ms 0.82% 78.54% 161ms 0.82% unlink_chunk 1ms 0.0051% 78.55% 160ms 0.81% CellProliferativeTypesWriter::VisitCell 1ms 0.0051% 78.55% 159ms 0.81% __printf_fp_spec (inline) 5ms 0.025% 78.58% 158ms 0.8% __printf_fp_l_buffer 74ms 0.38% 78.96% 149ms 0.76% AbstractElement::GetNodeLocation 64ms 0.33% 79.28% 146ms 0.74% __printf_fp_buffer_1 4ms 0.02% 79.30% 143ms 0.73% CellPropertyCollection::HasProperty 4ms 0.02% 79.32% 142ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 50ms 0.25% 79.58% 139ms 0.71% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 79.58% 138ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.58% 138ms 0.7% Cell::HasCellProperty (inline) 0 0% 79.58% 138ms 0.7% OutputFileHandler::OpenOutputFile 138ms 0.7% 80.28% 138ms 0.7% std::vector::size (inline) 16ms 0.081% 80.36% 135ms 0.69% TetrahedralMesh::Clear 26ms 0.13% 80.50% 131ms 0.67% TetrahedralMesh::EdgesEnd 1ms 0.0051% 80.50% 130ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 7ms 0.036% 80.54% 130ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 117ms 0.6% 81.13% 130ms 0.66% vertexsort 129ms 0.66% 81.79% 129ms 0.66% AbstractCellProperty::~AbstractCellProperty 2ms 0.01% 81.80% 129ms 0.66% boost::numeric::ublas::vector_assign (inline) 39ms 0.2% 82.00% 127ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 121ms 0.62% 82.61% 121ms 0.62% AbstractCellMutationState::~AbstractCellMutationState 11ms 0.056% 82.67% 118ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 82.67% 118ms 0.6% boost::shared_ptr::~shared_ptr (inline) 32ms 0.16% 82.83% 117ms 0.6% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.015% 82.85% 115ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.85% 113ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 113ms 0.58% 83.42% 113ms 0.58% AbstractElement::IsDeleted 0 0% 83.42% 110ms 0.56% Cell::SetCellProliferativeType 70ms 0.36% 83.78% 109ms 0.56% Cylindrical2dMesh::GetVectorFromAtoB 4ms 0.02% 83.80% 106ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 105ms 0.53% 84.33% 105ms 0.53% std::_Rb_tree_rebalance_for_erase 1ms 0.0051% 84.34% 104ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 102ms 0.52% 84.86% 102ms 0.52% counterclockwise 99ms 0.5% 85.36% 101ms 0.51% boost::detail::sp_counted_base::release 0 0% 85.36% 99ms 0.5% AbstractCellBasedSimulation::DoCellRemoval (inline)