File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 14356ms, 85.86% of 16721ms total Dropped 763 nodes (cum <= 83.61ms) flat flat% sum% cum cum% 0 0% 0% 16675ms 99.72% __libc_start_call_main 0 0% 0% 16675ms 99.72% __libc_start_main_impl 0 0% 0% 16675ms 99.72% _start 0 0% 0% 16657ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16657ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16657ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16657ms 99.62% main 0 0% 0% 16619ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16619ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16619ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16592ms 99.23% AbstractCellBasedSimulation::Solve 0 0% 0% 12253ms 73.28% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.018% 0.018% 7062ms 42.23% AbstractCellBasedSimulation::DoCellBirth 6ms 0.036% 0.054% 6980ms 41.74% Cell::ReadyToDivide 3ms 0.018% 0.072% 6915ms 41.36% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.072% 6745ms 40.34% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.096% 0.17% 6739ms 40.30% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.018% 0.19% 6722ms 40.20% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.42% 0.6% 6565ms 39.26% AbstractOneStepIvpOdeSolver::InternalSolve 892ms 5.33% 5.94% 5736ms 34.30% RungeKutta4IvpOdeSolver::CalculateNextYValue 0 0% 5.94% 5091ms 30.45% MeshBasedCellPopulation::Update 4210ms 25.18% 31.12% 4617ms 27.61% WntCellCycleOdeSystem::EvaluateYDerivatives 7ms 0.042% 31.16% 3916ms 23.42% Cylindrical2dMesh::ReMesh 0 0% 31.16% 2282ms 13.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.16% 2140ms 12.80% MutableMesh::ReMesh 0 0% 31.16% 2052ms 12.27% AbstractCellPopulation::WriteResultsToFiles 2ms 0.012% 31.17% 1999ms 11.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.042% 31.21% 1943ms 11.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 792ms 4.74% 35.95% 1795ms 10.74% std::_Rb_tree::_M_lower_bound (inline) 169ms 1.01% 36.96% 1731ms 10.35% TetrahedralMesh::EdgeIterator::operator++ 68ms 0.41% 37.37% 1351ms 8.08% std::_Rb_tree::find (inline) 0 0% 37.37% 1142ms 6.83% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.036% 37.40% 1119ms 6.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.072% 37.47% 1064ms 6.36% TetrahedralMesh::ImportFromMesher 12ms 0.072% 37.55% 1035ms 6.19% MeshBasedCellPopulation::SpringIterator::operator++ 57ms 0.34% 37.89% 1016ms 6.08% operator new 5ms 0.03% 37.92% 972ms 5.81% std::set::insert (inline) 14ms 0.084% 38.00% 967ms 5.78% std::_Rb_tree::_M_insert_unique 232ms 1.39% 39.39% 954ms 5.71% __GI___libc_malloc 41ms 0.25% 39.63% 889ms 5.32% std::__new_allocator::allocate (inline) 0 0% 39.63% 885ms 5.29% std::allocator_traits::allocate (inline) 0 0% 39.63% 855ms 5.11% std::set::count (inline) 1ms 0.006% 39.64% 820ms 4.90% triangulate 5ms 0.03% 39.67% 784ms 4.69% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 39.67% 733ms 4.38% delaunay 1ms 0.006% 39.67% 732ms 4.38% divconqdelaunay 1ms 0.006% 39.68% 709ms 4.24% CellPopulationElementWriter::Visit 53ms 0.32% 40.00% 676ms 4.04% std::map::operator[] (partial-inline) 4ms 0.024% 40.02% 667ms 3.99% CellPropertyCollection::GetPropertiesType (inline) 362ms 2.16% 42.19% 644ms 3.85% _int_malloc 623ms 3.73% 45.91% 634ms 3.79% WntCellCycleOdeSystem::CalculateStoppingEvent 633ms 3.79% 49.70% 633ms 3.79% std::_Rb_tree::_S_right (inline) 12ms 0.072% 49.77% 631ms 3.77% std::less::operator() (inline) 619ms 3.70% 53.47% 619ms 3.70% std::operator< (inline) 4ms 0.024% 53.50% 603ms 3.61% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.18% 53.68% 595ms 3.56% std::_Rb_tree::_M_insert_ (inline) 0 0% 53.68% 570ms 3.41% std::_Rb_tree::_M_create_node (inline) 32ms 0.19% 53.87% 559ms 3.34% AbstractCellPopulation::GetCellUsingLocationIndex 165ms 0.99% 54.85% 552ms 3.30% __dynamic_cast 3ms 0.018% 54.87% 550ms 3.29% AbstractCellProperty::IsSubType (inline) 1ms 0.006% 54.88% 545ms 3.26% Element::Element 0 0% 54.88% 545ms 3.26% std::_Rb_tree::lower_bound (inline) 0 0% 54.88% 545ms 3.26% std::map::lower_bound (inline) 0 0% 54.88% 543ms 3.25% std::_Rb_tree::_M_get_node (inline) 12ms 0.072% 54.95% 531ms 3.18% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.024% 54.97% 520ms 3.11% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 54.97% 520ms 3.11% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 54.97% 489ms 2.92% std::map::find (inline) 7ms 0.042% 55.01% 486ms 2.91% MutableMesh::ReIndex 1ms 0.006% 55.02% 466ms 2.79% std::ostream::operator<< (inline) 61ms 0.36% 55.39% 465ms 2.78% std::ostream::_M_insert 13ms 0.078% 55.46% 464ms 2.77% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.048% 55.51% 459ms 2.75% Element::RegisterWithNodes (inline) 155ms 0.93% 56.44% 456ms 2.73% __GI___libc_free 10ms 0.06% 56.50% 451ms 2.70% Node::AddElement 24ms 0.14% 56.64% 413ms 2.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.048% 56.69% 406ms 2.43% std::_Rb_tree::erase 0 0% 56.69% 406ms 2.43% std::set::erase (inline) 15ms 0.09% 56.78% 398ms 2.38% Node::RemoveElement 13ms 0.078% 56.86% 393ms 2.35% divconqrecurse 1ms 0.006% 56.86% 383ms 2.29% Cell::GetCellProliferativeType 118ms 0.71% 57.57% 377ms 2.25% std::_Rb_tree::_M_erase 7ms 0.042% 57.61% 371ms 2.22% std::__new_allocator::deallocate (inline) 104ms 0.62% 58.23% 368ms 2.20% mergehulls 0 0% 58.23% 365ms 2.18% std::allocator_traits::deallocate (inline) 150ms 0.9% 59.13% 359ms 2.15% std::_Rb_tree::_M_get_insert_unique_pos 61ms 0.36% 59.49% 355ms 2.12% AbstractCellProperty::IsType (inline) 4ms 0.024% 59.52% 346ms 2.07% std::_Vector_base::_M_allocate (inline) 1ms 0.006% 59.52% 342ms 2.05% Cell::GetMutationState 0 0% 59.52% 339ms 2.03% std::_Rb_tree::_M_drop_node (inline) 22ms 0.13% 59.66% 338ms 2.02% std::_Rb_tree::~_Rb_tree (inline) 28ms 0.17% 59.82% 326ms 1.95% Element::ResetIndex 8ms 0.048% 59.87% 318ms 1.90% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 59.87% 307ms 1.84% std::set::~set (inline) 233ms 1.39% 61.26% 300ms 1.79% _int_free 3ms 0.018% 61.28% 299ms 1.79% LegacyCellProliferativeTypesWriter::VisitCell 294ms 1.76% 63.04% 294ms 1.76% CellProperty::GetTypeId 0 0% 63.04% 294ms 1.76% std::_Rb_tree::_M_put_node (inline) 130ms 0.78% 63.82% 292ms 1.75% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.018% 63.84% 286ms 1.71% NodeLocationWriter::Visit 12ms 0.072% 63.91% 276ms 1.65% AbstractCellPopulation::IsCellAttachedToLocationIndex 271ms 1.62% 65.53% 271ms 1.62% std::vector::operator[] (inline) 259ms 1.55% 67.08% 259ms 1.55% __strcmp_avx2 17ms 0.1% 67.18% 258ms 1.54% AbstractTetrahedralElement::CalculateJacobian 6ms 0.036% 67.21% 254ms 1.52% std::vector::push_back (inline) 19ms 0.11% 67.33% 251ms 1.50% std::num_put::_M_insert_float 5ms 0.03% 67.36% 249ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.006% 67.36% 249ms 1.49% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.21% 67.57% 244ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.072% 67.65% 244ms 1.46% std::vector::_M_realloc_insert 11ms 0.066% 67.71% 235ms 1.41% std::_Rb_tree::_M_erase_aux (inline) 11ms 0.066% 67.78% 233ms 1.39% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.012% 67.79% 230ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.096% 67.88% 228ms 1.36% Element::MarkAsDeleted 0 0% 67.88% 227ms 1.36% alternateaxes 212ms 1.27% 69.15% 227ms 1.36% vertexmedian 152ms 0.91% 70.06% 211ms 1.26% AbstractElement::GetNodeGlobalIndex 1ms 0.006% 70.07% 210ms 1.26% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.07% 210ms 1.26% MeshBasedCellPopulation::GetDampingConstant 2ms 0.012% 70.08% 208ms 1.24% std::set::set (inline) 27ms 0.16% 70.24% 206ms 1.23% AbstractTetrahedralElement::RefreshJacobian 13ms 0.078% 70.32% 202ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.042% 70.36% 196ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.012% 70.37% 194ms 1.16% CellProliferativeTypesWriter::VisitCell 24ms 0.14% 70.52% 192ms 1.15% std::_Rb_tree::_M_copy (inline) 5ms 0.03% 70.55% 190ms 1.14% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.012% 70.56% 190ms 1.14% std::__cxx11::collate::do_transform 183ms 1.09% 71.65% 183ms 1.09% std::_Rb_tree_insert_and_rebalance 2ms 0.012% 71.66% 182ms 1.09% ___vsnprintf 0 0% 71.66% 180ms 1.08% __vsnprintf_internal (inline) 21ms 0.13% 71.79% 179ms 1.07% __printf_buffer 177ms 1.06% 72.85% 177ms 1.06% Node::GetIndex 1ms 0.006% 72.85% 176ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 119ms 0.71% 73.57% 176ms 1.05% std::_Rb_tree::equal_range (inline) 128ms 0.77% 74.33% 172ms 1.03% malloc_consolidate 46ms 0.28% 74.61% 166ms 0.99% std::_Rb_tree::_M_clone_node (inline) 26ms 0.16% 74.76% 164ms 0.98% TetrahedralMesh::Clear 0 0% 74.76% 163ms 0.97% OffLatticeSimulation::ApplyBoundaries 4ms 0.024% 74.79% 161ms 0.96% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 161ms 0.96% 75.75% 161ms 0.96% incircle 72ms 0.43% 76.18% 158ms 0.94% AbstractElement::GetNodeLocation 158ms 0.94% 77.12% 158ms 0.94% unlink_chunk 4ms 0.024% 77.15% 152ms 0.91% __printf_fp_l_buffer 0 0% 77.15% 152ms 0.91% __printf_fp_spec (inline) 84ms 0.5% 77.65% 148ms 0.89% __printf_fp_buffer_1 2ms 0.012% 77.66% 147ms 0.88% Cell::SetCellProliferativeType 3ms 0.018% 77.68% 141ms 0.84% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 141ms 0.84% 78.52% 141ms 0.84% std::vector::size (inline) 12ms 0.072% 78.60% 136ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.018% 78.61% 131ms 0.78% boost::numeric::ublas::vector_assign (inline) 1ms 0.006% 78.62% 128ms 0.77% AbstractCellBasedWriter::OpenOutputFileForAppend 126ms 0.75% 79.37% 126ms 0.75% AbstractElement::IsDeleted 0 0% 79.37% 124ms 0.74% OutputFileHandler::OpenOutputFile 11ms 0.066% 79.44% 118ms 0.71% boost::detail::shared_count::~shared_count (inline) 0 0% 79.44% 118ms 0.71% boost::shared_ptr::~shared_ptr (inline) 44ms 0.26% 79.70% 118ms 0.71% std::__ostream_insert 71ms 0.42% 80.13% 117ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.13% 116ms 0.69% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.03% 80.16% 115ms 0.69% CellPropertyCollection::HasProperty 8ms 0.048% 80.20% 115ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.012% 80.22% 114ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.22% 113ms 0.68% Cell::HasCellProperty (inline) 31ms 0.19% 80.40% 112ms 0.67% TetrahedralMesh::EdgesEnd 112ms 0.67% 81.07% 112ms 0.67% boost::shared_ptr::operator-> (inline) 105ms 0.63% 81.70% 106ms 0.63% boost::detail::sp_counted_base::release 13ms 0.078% 81.78% 106ms 0.63% std::_Rb_tree_const_iterator::operator++ (inline) 106ms 0.63% 82.41% 106ms 0.63% std::_Rb_tree_increment 16ms 0.096% 82.51% 102ms 0.61% boost::numeric::ublas::indexing_vector_assign 0 0% 82.51% 100ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 99ms 0.59% 83.10% 99ms 0.59% counterclockwise 90ms 0.54% 83.64% 99ms 0.59% vertexsort 19ms 0.11% 83.75% 98ms 0.59% std::num_put::_M_insert_int 1ms 0.006% 83.76% 94ms 0.56% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 94ms 0.56% 84.32% 94ms 0.56% std::_Rb_tree_rebalance_for_erase 10ms 0.06% 84.38% 92ms 0.55% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 0 0% 84.38% 92ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 84.38% 91ms 0.54% std::vector::vector (inline) 3ms 0.018% 84.40% 89ms 0.53% std::operator<< (inline) 1ms 0.006% 84.40% 85ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 31ms 0.19% 84.59% 85ms 0.51% boost::shared_ptr::shared_ptr (inline) 54ms 0.32% 84.91% 85ms 0.51% std::basic_filebuf::xsputn 61ms 0.36% 85.28% 84ms 0.5% TimeStepper::AdvanceOneTimeStep 84ms 0.5% 85.78% 84ms 0.5% [libchaste_mesh.so] 13ms 0.078% 85.86% 84ms 0.5% std::_Vector_base::_M_deallocate (inline)