File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16496ms, 84.68% of 19481ms total Dropped 825 nodes (cum <= 97.41ms) flat flat% sum% cum cum% 0 0% 0% 19436ms 99.77% __libc_start_call_main 0 0% 0% 19436ms 99.77% __libc_start_main_impl 0 0% 0% 19436ms 99.77% _start 0 0% 0% 19415ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19415ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19415ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19415ms 99.66% main 0 0% 0% 19374ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19374ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19373ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19346ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14718ms 75.55% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9265ms 47.56% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.036% 9164ms 47.04% Cell::ReadyToDivide 4ms 0.021% 0.056% 9090ms 46.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.067% 8950ms 45.94% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.1% 8943ms 45.91% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.11% 8929ms 45.83% CellCycleModelOdeHandler::SolveOdeToTime 66ms 0.34% 0.45% 8770ms 45.02% AbstractOneStepIvpOdeSolver::InternalSolve 1043ms 5.35% 5.81% 7886ms 40.48% RungeKutta4IvpOdeSolver::CalculateNextYValue 2739ms 14.06% 19.87% 6656ms 34.17% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.87% 5340ms 27.41% MeshBasedCellPopulation::Update 4ms 0.021% 19.89% 4107ms 21.08% Cylindrical2dMesh::ReMesh 58ms 0.3% 20.19% 3926ms 20.15% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.19% 2594ms 13.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 306ms 1.57% 21.76% 2483ms 12.75% AbstractCellProperty::IsSame 0 0% 21.76% 2279ms 11.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 21.76% 2266ms 11.63% MutableMesh::ReMesh 11ms 0.056% 21.82% 2221ms 11.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 1.09% 22.91% 2177ms 11.17% std::type_info::operator== (inline) 2107ms 10.82% 33.73% 2107ms 10.82% __strcmp_avx2 0 0% 33.73% 2030ms 10.42% AbstractCellPopulation::WriteResultsToFiles 784ms 4.02% 37.75% 1889ms 9.70% std::_Rb_tree::_M_lower_bound (inline) 159ms 0.82% 38.57% 1729ms 8.88% TetrahedralMesh::EdgeIterator::operator++ 82ms 0.42% 38.99% 1453ms 7.46% std::_Rb_tree::find (inline) 1ms 0.0051% 39.00% 1201ms 6.16% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 39.02% 1164ms 5.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 5ms 0.026% 39.04% 1133ms 5.82% TetrahedralMesh::ImportFromMesher 40ms 0.21% 39.25% 1100ms 5.65% operator new 12ms 0.062% 39.31% 1063ms 5.46% MeshBasedCellPopulation::SpringIterator::operator++ 246ms 1.26% 40.57% 1045ms 5.36% __GI___libc_malloc 12ms 0.062% 40.63% 1017ms 5.22% std::set::insert (inline) 13ms 0.067% 40.70% 1005ms 5.16% std::_Rb_tree::_M_insert_unique 39ms 0.2% 40.90% 943ms 4.84% std::__new_allocator::allocate (inline) 0 0% 40.90% 941ms 4.83% std::allocator_traits::allocate (inline) 0 0% 40.90% 895ms 4.59% std::set::count (inline) 0 0% 40.90% 879ms 4.51% triangulate 0 0% 40.90% 812ms 4.17% delaunay 6ms 0.031% 40.93% 812ms 4.17% divconqdelaunay 0 0% 40.93% 745ms 3.82% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.015% 40.95% 742ms 3.81% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 399ms 2.05% 43.00% 709ms 3.64% _int_malloc 701ms 3.60% 46.59% 701ms 3.60% WntCellCycleOdeSystem::CalculateStoppingEvent 69ms 0.35% 46.95% 696ms 3.57% std::map::operator[] (partial-inline) 691ms 3.55% 50.50% 691ms 3.55% std::_Rb_tree::_S_right (inline) 13ms 0.067% 50.56% 688ms 3.53% std::less::operator() (inline) 13ms 0.067% 50.63% 685ms 3.52% CellPopulationElementWriter::Visit 675ms 3.46% 54.09% 675ms 3.46% std::operator< (inline) 9ms 0.046% 54.14% 649ms 3.33% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 181ms 0.93% 55.07% 636ms 3.26% __dynamic_cast 0 0% 55.07% 629ms 3.23% std::_Rb_tree::_M_create_node (inline) 26ms 0.13% 55.20% 616ms 3.16% std::_Rb_tree::_M_insert_ (inline) 23ms 0.12% 55.32% 607ms 3.12% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.046% 55.37% 606ms 3.11% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.37% 600ms 3.08% std::_Rb_tree::_M_get_node (inline) 0 0% 55.37% 581ms 2.98% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.041% 55.41% 579ms 2.97% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.036% 55.44% 568ms 2.92% Element::Element 0 0% 55.44% 553ms 2.84% std::map::find (inline) 0 0% 55.44% 545ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 55.44% 545ms 2.80% std::map::lower_bound (inline) 7ms 0.036% 55.48% 517ms 2.65% MutableMesh::ReIndex 11ms 0.056% 55.54% 512ms 2.63% Element::RegisterWithNodes (inline) 18ms 0.092% 55.63% 510ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 19ms 0.098% 55.73% 494ms 2.54% Node::AddElement 13ms 0.067% 55.79% 476ms 2.44% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 55.81% 472ms 2.42% AbstractCellProperty::IsSubType (inline) 4ms 0.021% 55.83% 472ms 2.42% std::ostream::operator<< (inline) 71ms 0.36% 56.19% 468ms 2.40% std::ostream::_M_insert 286ms 1.47% 57.66% 460ms 2.36% AbstractCellMutationState::AbstractCellMutationState 122ms 0.63% 58.29% 431ms 2.21% __GI___libc_free 4ms 0.021% 58.31% 412ms 2.11% std::set::erase (inline) 14ms 0.072% 58.38% 411ms 2.11% Node::RemoveElement 9ms 0.046% 58.43% 411ms 2.11% std::_Rb_tree::erase 19ms 0.098% 58.52% 404ms 2.07% divconqrecurse 111ms 0.57% 59.09% 380ms 1.95% std::_Rb_tree::_M_erase 144ms 0.74% 59.83% 377ms 1.94% std::_Rb_tree::_M_get_insert_unique_pos 109ms 0.56% 60.39% 374ms 1.92% mergehulls 31ms 0.16% 60.55% 360ms 1.85% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 60.57% 344ms 1.77% std::_Vector_base::_M_allocate (inline) 11ms 0.056% 60.62% 344ms 1.77% std::__new_allocator::deallocate (inline) 0 0% 60.62% 344ms 1.77% std::set::~set (inline) 0 0% 60.62% 338ms 1.74% std::allocator_traits::deallocate (inline) 337ms 1.73% 62.35% 337ms 1.73% [libchaste_cell_based.so] 18ms 0.092% 62.45% 335ms 1.72% Element::ResetIndex 0 0% 62.45% 335ms 1.72% std::_Rb_tree::_M_drop_node (inline) 13ms 0.067% 62.51% 320ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 11ms 0.056% 62.57% 317ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 62.57% 317ms 1.63% Cell::GetMutationState 156ms 0.8% 63.37% 314ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.37% 313ms 1.61% LegacyCellProliferativeTypesWriter::VisitCell 245ms 1.26% 64.63% 309ms 1.59% _int_free 0 0% 64.63% 304ms 1.56% NodeLocationWriter::Visit 4ms 0.021% 64.65% 303ms 1.56% Cell::GetCellProliferativeType 0 0% 64.65% 293ms 1.50% std::_Rb_tree::_M_put_node (inline) 287ms 1.47% 66.13% 289ms 1.48% std::vector::operator[] (inline) 16ms 0.082% 66.21% 278ms 1.43% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.01% 66.22% 275ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.13% 66.35% 269ms 1.38% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0051% 66.36% 267ms 1.37% alternateaxes 253ms 1.30% 67.66% 265ms 1.36% vertexmedian 9ms 0.046% 67.70% 263ms 1.35% std::num_put::_M_insert_float 10ms 0.051% 67.75% 262ms 1.34% std::vector::push_back (inline) 12ms 0.062% 67.81% 252ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0051% 67.82% 250ms 1.28% std::set::set (inline) 94ms 0.48% 68.30% 249ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 18ms 0.092% 68.39% 246ms 1.26% std::vector::_M_realloc_insert 51ms 0.26% 68.66% 243ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 22ms 0.11% 68.77% 241ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.036% 68.81% 236ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 89ms 0.46% 69.26% 235ms 1.21% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 22ms 0.11% 69.38% 235ms 1.21% std::_Rb_tree::_M_copy (inline) 18ms 0.092% 69.47% 229ms 1.18% TetrahedralMesh::Clear 4ms 0.021% 69.49% 226ms 1.16% std::__cxx11::collate::do_transform 0 0% 69.49% 225ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.067% 69.55% 223ms 1.14% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 69.57% 221ms 1.13% MeshBasedCellPopulation::GetDampingConstant 7ms 0.036% 69.60% 220ms 1.13% Element::MarkAsDeleted 2ms 0.01% 69.61% 219ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.015% 69.63% 218ms 1.12% ___vsnprintf 0 0% 69.63% 215ms 1.10% __vsnprintf_internal (inline) 70ms 0.36% 69.99% 211ms 1.08% std::_Rb_tree::_M_clone_node (inline) 16ms 0.082% 70.07% 210ms 1.08% __printf_buffer 2ms 0.01% 70.08% 209ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 133ms 0.68% 70.76% 200ms 1.03% AbstractElement::GetNodeGlobalIndex 0 0% 70.76% 199ms 1.02% OffLatticeSimulation::ApplyBoundaries 6ms 0.031% 70.79% 192ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.026% 70.82% 186ms 0.95% __printf_fp_l_buffer 0 0% 70.82% 186ms 0.95% __printf_fp_spec (inline) 123ms 0.63% 71.45% 186ms 0.95% malloc_consolidate 184ms 0.94% 72.39% 184ms 0.94% unlink_chunk 33ms 0.17% 72.56% 180ms 0.92% TetrahedralMesh::EdgesEnd (partial-inline) 74ms 0.38% 72.94% 174ms 0.89% __printf_fp_buffer_1 54ms 0.28% 73.22% 169ms 0.87% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 125ms 0.64% 73.86% 169ms 0.87% std::_Rb_tree::equal_range (inline) 20ms 0.1% 73.96% 166ms 0.85% AbstractTetrahedralElement::RefreshJacobian 166ms 0.85% 74.82% 166ms 0.85% std::_Rb_tree_insert_and_rebalance 2ms 0.01% 74.83% 164ms 0.84% CellPropertyCollection::HasProperty 164ms 0.84% 75.67% 164ms 0.84% std::vector::size (inline) 163ms 0.84% 76.51% 163ms 0.84% [libchaste_crypt.so] 161ms 0.83% 77.33% 161ms 0.83% AbstractCellMutationState::~AbstractCellMutationState 0 0% 77.33% 161ms 0.83% Cell::HasCellProperty (inline) 10ms 0.051% 77.38% 161ms 0.83% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 77.38% 157ms 0.81% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.015% 77.40% 157ms 0.81% CellProliferativeTypesWriter::VisitCell 157ms 0.81% 78.20% 157ms 0.81% incircle 4ms 0.021% 78.22% 156ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 78.22% 156ms 0.8% OutputFileHandler::OpenOutputFile 152ms 0.78% 79.01% 152ms 0.78% Node::GetIndex 49ms 0.25% 79.26% 149ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 55ms 0.28% 79.54% 147ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 10ms 0.051% 79.59% 146ms 0.75% Node::~Node 3ms 0.015% 79.61% 144ms 0.74% boost::numeric::ublas::vector_assign (inline) 144ms 0.74% 80.34% 144ms 0.74% std::type_info::name (inline) 0 0% 80.34% 135ms 0.69% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 81ms 0.42% 80.76% 132ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.76% 132ms 0.68% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 13ms 0.067% 80.83% 131ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.046% 80.87% 130ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 53ms 0.27% 81.15% 129ms 0.66% AbstractElement::GetNodeLocation 83ms 0.43% 81.57% 129ms 0.66% TetrahedralMesh::EdgeIterator::EdgeIterator 117ms 0.6% 82.17% 129ms 0.66% vertexsort 2ms 0.01% 82.18% 126ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.067% 82.25% 117ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 82.25% 117ms 0.6% boost::shared_ptr::~shared_ptr (inline) 2ms 0.01% 82.26% 115ms 0.59% Cell::SetCellProliferativeType 113ms 0.58% 82.84% 113ms 0.58% std::_Rb_tree_increment 30ms 0.15% 82.99% 112ms 0.57% boost::numeric::ublas::indexing_vector_assign 34ms 0.17% 83.17% 112ms 0.57% std::__ostream_insert 0 0% 83.17% 110ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.031% 83.20% 108ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.021% 83.22% 104ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 102ms 0.52% 83.74% 102ms 0.52% std::_Rb_tree_rebalance_for_erase 101ms 0.52% 84.26% 101ms 0.52% AbstractCellProperty::AbstractCellProperty 11ms 0.056% 84.32% 100ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 66ms 0.34% 84.66% 99ms 0.51% TimeStepper::AdvanceOneTimeStep 4ms 0.021% 84.68% 98ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath