File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16852ms, 84.71% of 19894ms total Dropped 767 nodes (cum <= 99.47ms) flat flat% sum% cum cum% 0 0% 0% 19848ms 99.77% __libc_start_call_main 0 0% 0% 19848ms 99.77% __libc_start_main_impl 0 0% 0% 19848ms 99.77% _start 0 0% 0% 19830ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19830ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19830ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19830ms 99.68% main 0 0% 0% 19794ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19794ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19794ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19767ms 99.36% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15365ms 77.23% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 10128ms 50.91% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.035% 10025ms 50.39% Cell::ReadyToDivide 3ms 0.015% 0.05% 9956ms 50.05% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.055% 9819ms 49.36% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.03% 0.085% 9812ms 49.32% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.09% 9804ms 49.28% CellCycleModelOdeHandler::SolveOdeToTime 80ms 0.4% 0.49% 9661ms 48.56% AbstractOneStepIvpOdeSolver::InternalSolve 885ms 4.45% 4.94% 8797ms 44.22% RungeKutta4IvpOdeSolver::CalculateNextYValue 3622ms 18.21% 23.15% 7721ms 38.81% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.15% 5125ms 25.76% MeshBasedCellPopulation::Update 202ms 1.02% 24.16% 4154ms 20.88% AbstractCellProperty::IsType (inline) 6ms 0.03% 24.19% 3932ms 19.76% Cylindrical2dMesh::ReMesh 558ms 2.80% 27.00% 2871ms 14.43% AbstractCellProperty::IsSame 2ms 0.01% 27.01% 2468ms 12.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 431ms 2.17% 29.17% 2313ms 11.63% std::type_info::operator== (inline) 0 0% 29.17% 2174ms 10.93% MutableMesh::ReMesh 0 0% 29.17% 2173ms 10.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.045% 29.22% 2116ms 10.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.22% 1930ms 9.70% AbstractCellPopulation::WriteResultsToFiles 1852ms 9.31% 38.53% 1852ms 9.31% __strcmp_avx2 784ms 3.94% 42.47% 1829ms 9.19% std::_Rb_tree::_M_lower_bound (inline) 157ms 0.79% 43.26% 1708ms 8.59% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.28% 43.54% 1377ms 6.92% std::_Rb_tree::find (inline) 2ms 0.01% 43.55% 1160ms 5.83% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.58% 1145ms 5.76% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.065% 43.64% 1086ms 5.46% TetrahedralMesh::ImportFromMesher 55ms 0.28% 43.92% 1053ms 5.29% operator new 8ms 0.04% 43.96% 1045ms 5.25% std::set::insert (inline) 21ms 0.11% 44.06% 1037ms 5.21% std::_Rb_tree::_M_insert_unique 16ms 0.08% 44.14% 1026ms 5.16% MeshBasedCellPopulation::SpringIterator::operator++ 262ms 1.32% 45.46% 996ms 5.01% __GI___libc_malloc 28ms 0.14% 45.60% 945ms 4.75% std::__new_allocator::allocate (inline) 0 0% 45.60% 940ms 4.73% std::allocator_traits::allocate (inline) 0 0% 45.60% 859ms 4.32% std::set::count (inline) 0 0% 45.60% 810ms 4.07% triangulate 0 0% 45.60% 736ms 3.70% delaunay 4ms 0.02% 45.62% 735ms 3.69% divconqdelaunay 5ms 0.025% 45.65% 710ms 3.57% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 45.66% 694ms 3.49% AbstractTwoBodyInteractionForce::AddForceContribution 23ms 0.12% 45.77% 674ms 3.39% std::less::operator() (inline) 51ms 0.26% 46.03% 666ms 3.35% std::map::operator[] (partial-inline) 654ms 3.29% 49.32% 665ms 3.34% WntCellCycleOdeSystem::CalculateStoppingEvent 660ms 3.32% 52.63% 660ms 3.32% std::_Rb_tree::_S_right (inline) 33ms 0.17% 52.80% 653ms 3.28% std::_Rb_tree::_M_insert_ (inline) 651ms 3.27% 56.07% 651ms 3.27% std::operator< (inline) 11ms 0.055% 56.13% 640ms 3.22% CellPopulationElementWriter::Visit 370ms 1.86% 57.99% 640ms 3.22% _int_malloc 176ms 0.88% 58.87% 634ms 3.19% __dynamic_cast 0 0% 58.87% 617ms 3.10% std::_Rb_tree::_M_create_node (inline) 0 0% 58.87% 597ms 3.00% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 58.98% 589ms 2.96% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.98% 573ms 2.88% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.015% 59.00% 565ms 2.84% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.035% 59.03% 556ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.02% 59.05% 544ms 2.73% Element::Element 0 0% 59.05% 542ms 2.72% std::_Rb_tree::lower_bound (inline) 0 0% 59.05% 542ms 2.72% std::map::lower_bound (inline) 22ms 0.11% 59.16% 531ms 2.67% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.04% 59.20% 523ms 2.63% MutableMesh::ReIndex 0 0% 59.20% 516ms 2.59% std::map::find (inline) 4ms 0.02% 59.22% 513ms 2.58% Element::RegisterWithNodes (inline) 4ms 0.02% 59.24% 507ms 2.55% Node::AddElement 11ms 0.055% 59.30% 497ms 2.50% Cylindrical2dMesh::ReconstructCylindricalMesh 57ms 0.29% 59.59% 490ms 2.46% std::ostream::_M_insert 0 0% 59.59% 490ms 2.46% std::ostream::operator<< (inline) 172ms 0.86% 60.45% 464ms 2.33% __GI___libc_free 7ms 0.035% 60.49% 459ms 2.31% Cylindrical2dMesh::CorrectNonPeriodicMesh 300ms 1.51% 61.99% 457ms 2.30% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 62.01% 448ms 2.25% AbstractCellProperty::IsSubType (inline) 12ms 0.06% 62.07% 386ms 1.94% std::__new_allocator::deallocate (inline) 0 0% 62.07% 379ms 1.91% std::allocator_traits::deallocate (inline) 17ms 0.085% 62.15% 373ms 1.87% divconqrecurse 5ms 0.025% 62.18% 366ms 1.84% std::_Rb_tree::erase 1ms 0.005% 62.18% 365ms 1.83% std::set::erase (inline) 134ms 0.67% 62.86% 364ms 1.83% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.055% 62.91% 363ms 1.82% Node::RemoveElement 104ms 0.52% 63.44% 347ms 1.74% mergehulls 1ms 0.005% 63.44% 344ms 1.73% std::_Vector_base::_M_allocate (inline) 93ms 0.47% 63.91% 342ms 1.72% std::_Rb_tree::_M_erase 17ms 0.085% 63.99% 337ms 1.69% Element::ResetIndex 157ms 0.79% 64.78% 337ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 64.80% 327ms 1.64% NodeLocationWriter::Visit 3ms 0.015% 64.81% 315ms 1.58% Cell::GetCellProliferativeType 11ms 0.055% 64.87% 313ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 16ms 0.08% 64.95% 310ms 1.56% std::_Rb_tree::~_Rb_tree (inline) 0 0% 64.95% 309ms 1.55% std::_Rb_tree::_M_drop_node (inline) 297ms 1.49% 66.44% 297ms 1.49% std::type_info::name (inline) 0 0% 66.44% 295ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.035% 66.48% 293ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 33ms 0.17% 66.64% 292ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 237ms 1.19% 67.83% 292ms 1.47% _int_free 8ms 0.04% 67.87% 288ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.085% 67.96% 288ms 1.45% std::num_put::_M_insert_float 0 0% 67.96% 286ms 1.44% std::set::~set (inline) 0 0% 67.96% 281ms 1.41% std::_Rb_tree::_M_put_node (inline) 280ms 1.41% 69.37% 280ms 1.41% [libchaste_cell_based.so] 2ms 0.01% 69.38% 276ms 1.39% Cell::GetMutationState 9ms 0.045% 69.42% 273ms 1.37% std::vector::push_back (inline) 4ms 0.02% 69.44% 257ms 1.29% std::vector::_M_realloc_insert 19ms 0.096% 69.54% 253ms 1.27% AbstractTetrahedralElement::CalculateJacobian 1ms 0.005% 69.54% 250ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.03% 69.57% 239ms 1.20% std::_Rb_tree::_Rb_tree 6ms 0.03% 69.60% 234ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 68ms 0.34% 69.95% 234ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.05% 70.00% 234ms 1.18% std::__cxx11::collate::do_transform 4ms 0.02% 70.02% 233ms 1.17% alternateaxes 214ms 1.08% 71.09% 229ms 1.15% vertexmedian 7ms 0.035% 71.13% 228ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.02% 71.15% 225ms 1.13% std::set::set (inline) 4ms 0.02% 71.17% 224ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 10ms 0.05% 71.22% 223ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 12ms 0.06% 71.28% 218ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 71.28% 217ms 1.09% ___vsnprintf 0 0% 71.28% 217ms 1.09% __vsnprintf_internal (inline) 18ms 0.09% 71.37% 215ms 1.08% __printf_buffer 206ms 1.04% 72.40% 206ms 1.04% std::vector::operator[] (inline) 25ms 0.13% 72.53% 203ms 1.02% std::_Rb_tree::_M_copy (inline) 16ms 0.08% 72.61% 202ms 1.02% Element::MarkAsDeleted 1ms 0.005% 72.61% 201ms 1.01% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 72.63% 199ms 1.00% AbstractCentreBasedCellPopulation::GetDampingConstant 36ms 0.18% 72.81% 199ms 1.00% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 72ms 0.36% 73.17% 198ms 1% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 73.17% 196ms 0.99% OffLatticeSimulation::ApplyBoundaries 23ms 0.12% 73.29% 195ms 0.98% TetrahedralMesh::Clear 9ms 0.045% 73.33% 188ms 0.95% __printf_fp_l_buffer 0 0% 73.33% 188ms 0.95% __printf_fp_spec (inline) 182ms 0.91% 74.25% 182ms 0.91% std::_Rb_tree_insert_and_rebalance 134ms 0.67% 74.92% 180ms 0.9% AbstractElement::GetNodeGlobalIndex 15ms 0.075% 75.00% 180ms 0.9% AbstractTetrahedralElement::RefreshJacobian 127ms 0.64% 75.64% 177ms 0.89% malloc_consolidate 53ms 0.27% 75.90% 176ms 0.88% std::_Rb_tree::_M_clone_node (inline) 91ms 0.46% 76.36% 172ms 0.86% __printf_fp_buffer_1 1ms 0.005% 76.36% 170ms 0.85% CellProliferativeTypesWriter::VisitCell 168ms 0.84% 77.21% 168ms 0.84% Node::GetIndex 3ms 0.015% 77.22% 160ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.075% 77.30% 151ms 0.76% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 151ms 0.76% 78.06% 151ms 0.76% incircle 58ms 0.29% 78.35% 149ms 0.75% AbstractElement::GetNodeLocation 2ms 0.01% 78.36% 148ms 0.74% boost::numeric::ublas::vector_assign (inline) 0 0% 78.36% 147ms 0.74% Cell::HasCellProperty (inline) 1ms 0.005% 78.37% 146ms 0.73% CellPropertyCollection::HasProperty 98ms 0.49% 78.86% 143ms 0.72% std::_Rb_tree::equal_range (inline) 7ms 0.035% 78.89% 139ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 32ms 0.16% 79.05% 138ms 0.69% TetrahedralMesh::EdgesEnd 47ms 0.24% 79.29% 135ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 134ms 0.67% 79.96% 134ms 0.67% std::vector::size (inline) 134ms 0.67% 80.64% 134ms 0.67% unlink_chunk 87ms 0.44% 81.07% 133ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.025% 81.10% 133ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.025% 81.12% 130ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 13ms 0.065% 81.19% 129ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.19% 126ms 0.63% AbstractCellBasedWriter::OpenOutputFileForAppend 45ms 0.23% 81.42% 123ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.42% 123ms 0.62% OutputFileHandler::OpenOutputFile 4ms 0.02% 81.44% 120ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 109ms 0.55% 81.98% 117ms 0.59% vertexsort 26ms 0.13% 82.12% 116ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 82.12% 111ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 82.13% 110ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 108ms 0.54% 82.67% 108ms 0.54% boost::shared_ptr::operator-> (inline) 0 0% 82.67% 106ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 82.68% 106ms 0.53% Cell::SetCellProliferativeType 0 0% 82.68% 106ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 105ms 0.53% 83.21% 105ms 0.53% AbstractElement::IsDeleted 8ms 0.04% 83.25% 105ms 0.53% std::_Vector_base::_M_deallocate (inline) 7ms 0.035% 83.29% 104ms 0.52% boost::detail::shared_count::~shared_count (inline) 0 0% 83.29% 104ms 0.52% boost::shared_ptr::~shared_ptr (inline) 103ms 0.52% 83.80% 103ms 0.52% AbstractCellProperty::~AbstractCellProperty 8ms 0.04% 83.84% 103ms 0.52% Node::~Node 46ms 0.23% 84.08% 103ms 0.52% std::__ostream_insert 100ms 0.5% 84.58% 100ms 0.5% std::_Rb_tree_rebalance_for_erase 26ms 0.13% 84.71% 100ms 0.5% std::num_put::_M_insert_int