File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12827ms, 86.01% of 14914ms total Dropped 720 nodes (cum <= 74.57ms) flat flat% sum% cum cum% 0 0% 0% 14876ms 99.75% __libc_start_call_main 0 0% 0% 14876ms 99.75% __libc_start_main_impl 0 0% 0% 14876ms 99.75% _start 0 0% 0% 14860ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14860ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14860ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14860ms 99.64% main 0 0% 0% 14818ms 99.36% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14818ms 99.36% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14818ms 99.36% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14798ms 99.22% AbstractCellBasedSimulation::Solve 2ms 0.013% 0.013% 11306ms 75.81% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0067% 0.02% 7131ms 47.81% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0067% 0.027% 7058ms 47.32% Cell::ReadyToDivide 8ms 0.054% 0.08% 6999ms 46.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.013% 0.094% 6898ms 46.25% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.08% 0.17% 6884ms 46.16% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.02% 0.19% 6870ms 46.06% CellCycleModelOdeHandler::SolveOdeToTime 40ms 0.27% 0.46% 6747ms 45.24% AbstractOneStepIvpOdeSolver::InternalSolve 772ms 5.18% 5.64% 6042ms 40.51% RungeKutta4IvpOdeSolver::CalculateNextYValue 2170ms 14.55% 20.19% 5108ms 34.25% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.19% 4088ms 27.41% MeshBasedCellPopulation::Update 1ms 0.0067% 20.20% 3136ms 21.03% Cylindrical2dMesh::ReMesh 53ms 0.36% 20.55% 2944ms 19.74% AbstractCellProperty::IsType (inline) 1ms 0.0067% 20.56% 1935ms 12.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 218ms 1.46% 22.02% 1895ms 12.71% AbstractCellProperty::IsSame 0 0% 22.02% 1776ms 11.91% MutableMesh::ReMesh 1ms 0.0067% 22.03% 1682ms 11.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 163ms 1.09% 23.12% 1677ms 11.24% std::type_info::operator== (inline) 8ms 0.054% 23.17% 1644ms 11.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 1592ms 10.67% 33.85% 1592ms 10.67% __strcmp_evex 1ms 0.0067% 33.85% 1550ms 10.39% AbstractCellPopulation::WriteResultsToFiles 625ms 4.19% 38.04% 1473ms 9.88% std::_Rb_tree::_M_lower_bound (inline) 137ms 0.92% 38.96% 1341ms 8.99% TetrahedralMesh::EdgeIterator::operator++ 53ms 0.36% 39.32% 1097ms 7.36% std::_Rb_tree::find (inline) 1ms 0.0067% 39.33% 928ms 6.22% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.054% 39.38% 901ms 6.04% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.04% 39.42% 863ms 5.79% TetrahedralMesh::ImportFromMesher 6ms 0.04% 39.46% 824ms 5.53% MeshBasedCellPopulation::SpringIterator::operator++ 26ms 0.17% 39.63% 783ms 5.25% operator new 174ms 1.17% 40.80% 752ms 5.04% __GI___libc_malloc 9ms 0.06% 40.86% 731ms 4.90% std::set::insert (inline) 12ms 0.08% 40.94% 722ms 4.84% std::_Rb_tree::_M_insert_unique 31ms 0.21% 41.15% 694ms 4.65% std::__new_allocator::allocate (inline) 0 0% 41.15% 691ms 4.63% std::allocator_traits::allocate (inline) 0 0% 41.15% 691ms 4.63% std::set::count (inline) 2ms 0.013% 41.16% 689ms 4.62% triangulate 0 0% 41.16% 626ms 4.20% delaunay 2ms 0.013% 41.18% 626ms 4.20% divconqdelaunay 584ms 3.92% 45.09% 584ms 3.92% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0067% 45.10% 568ms 3.81% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 55ms 0.37% 45.47% 563ms 3.77% std::map::operator[] (partial-inline) 4ms 0.027% 45.49% 561ms 3.76% CellPopulationElementWriter::Visit 544ms 3.65% 49.14% 544ms 3.65% std::_Rb_tree::_S_right (inline) 13ms 0.087% 49.23% 524ms 3.51% std::less::operator() (inline) 274ms 1.84% 51.07% 512ms 3.43% _int_malloc 0 0% 51.07% 511ms 3.43% AbstractTwoBodyInteractionForce::AddForceContribution 511ms 3.43% 54.49% 511ms 3.43% std::operator< (inline) 17ms 0.11% 54.61% 500ms 3.35% AbstractCellPopulation::GetCellUsingLocationIndex 139ms 0.93% 55.54% 468ms 3.14% __dynamic_cast 5ms 0.034% 55.57% 452ms 3.03% Element::Element 11ms 0.074% 55.65% 448ms 3.00% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.06% 55.71% 445ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.71% 441ms 2.96% std::_Rb_tree::lower_bound (inline) 0 0% 55.71% 441ms 2.96% std::map::lower_bound (inline) 0 0% 55.71% 436ms 2.92% std::_Rb_tree::_M_create_node (inline) 16ms 0.11% 55.81% 433ms 2.90% Cylindrical2dMesh::ReconstructCylindricalMesh 21ms 0.14% 55.95% 430ms 2.88% std::_Rb_tree::_M_insert_ (inline) 3ms 0.02% 55.97% 426ms 2.86% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.97% 426ms 2.86% std::_Rb_tree::_M_get_node (inline) 0 0% 55.97% 405ms 2.72% std::map::find (inline) 0 0% 55.97% 394ms 2.64% std::_Rb_tree::_Alloc_node::operator() (inline) 57ms 0.38% 56.36% 368ms 2.47% std::ostream::_M_insert 0 0% 56.36% 368ms 2.47% std::ostream::operator<< (inline) 3ms 0.02% 56.38% 364ms 2.44% MutableMesh::ReIndex 10ms 0.067% 56.44% 355ms 2.38% Element::RegisterWithNodes (inline) 1ms 0.0067% 56.45% 354ms 2.37% AbstractCellProperty::IsSubType (inline) 107ms 0.72% 57.17% 351ms 2.35% __GI___libc_free 5ms 0.034% 57.20% 346ms 2.32% Node::AddElement 200ms 1.34% 58.54% 329ms 2.21% AbstractCellMutationState::AbstractCellMutationState 10ms 0.067% 58.61% 318ms 2.13% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.1% 58.71% 302ms 2.02% Node::RemoveElement 2ms 0.013% 58.72% 302ms 2.02% std::set::erase (inline) 2ms 0.013% 58.74% 301ms 2.02% std::_Rb_tree::erase 83ms 0.56% 59.29% 300ms 2.01% std::_Rb_tree::_M_erase 16ms 0.11% 59.40% 297ms 1.99% std::__new_allocator::deallocate (inline) 15ms 0.1% 59.50% 295ms 1.98% divconqrecurse 0 0% 59.50% 292ms 1.96% std::allocator_traits::deallocate (inline) 0 0% 59.50% 288ms 1.93% std::_Rb_tree::_M_drop_node (inline) 13ms 0.087% 59.59% 285ms 1.91% std::_Rb_tree::~_Rb_tree (inline) 100ms 0.67% 60.26% 280ms 1.88% std::_Rb_tree::_M_get_insert_unique_pos 71ms 0.48% 60.73% 275ms 1.84% mergehulls 0 0% 60.73% 272ms 1.82% std::set::~set (inline) 4ms 0.027% 60.76% 269ms 1.80% std::_Vector_base::_M_allocate (inline) 0 0% 60.76% 253ms 1.70% std::_Rb_tree::_M_put_node (inline) 203ms 1.36% 62.12% 243ms 1.63% _int_free 0 0% 62.12% 235ms 1.58% Cell::GetMutationState 233ms 1.56% 63.69% 234ms 1.57% std::vector::operator[] (inline) 18ms 0.12% 63.81% 233ms 1.56% AbstractTetrahedralElement::CalculateJacobian 29ms 0.19% 64.00% 231ms 1.55% Element::ResetIndex 11ms 0.074% 64.07% 230ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.013% 64.09% 226ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.027% 64.11% 224ms 1.50% Cell::GetCellProliferativeType 32ms 0.21% 64.33% 223ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 124ms 0.83% 65.16% 223ms 1.50% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0067% 65.17% 220ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 14ms 0.094% 65.26% 208ms 1.39% std::_Rb_tree::_Rb_tree 0 0% 65.26% 207ms 1.39% alternateaxes 195ms 1.31% 66.57% 206ms 1.38% vertexmedian 204ms 1.37% 67.94% 204ms 1.37% [libchaste_cell_based.so] 0 0% 67.94% 203ms 1.36% NodeLocationWriter::Visit 0 0% 67.94% 203ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 82ms 0.55% 68.49% 202ms 1.35% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 86ms 0.58% 69.06% 198ms 1.33% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.06% 194ms 1.30% std::set::set (inline) 9ms 0.06% 69.12% 192ms 1.29% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.094% 69.22% 192ms 1.29% std::vector::push_back (inline) 3ms 0.02% 69.24% 186ms 1.25% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 25ms 0.17% 69.40% 184ms 1.23% AbstractTetrahedralElement::RefreshJacobian 6ms 0.04% 69.44% 183ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.067% 69.51% 179ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.06% 69.57% 177ms 1.19% std::num_put::_M_insert_float 10ms 0.067% 69.64% 171ms 1.15% Element::MarkAsDeleted 21ms 0.14% 69.78% 170ms 1.14% std::_Rb_tree::_M_copy (inline) 4ms 0.027% 69.81% 169ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.047% 69.85% 168ms 1.13% std::vector::_M_realloc_insert 0 0% 69.85% 167ms 1.12% OffLatticeSimulation::ApplyBoundaries 10ms 0.067% 69.92% 165ms 1.11% TetrahedralMesh::Clear 1ms 0.0067% 69.93% 159ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.26% 70.19% 156ms 1.05% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.027% 70.22% 152ms 1.02% AbstractTetrahedralElement::AbstractTetrahedralElement 104ms 0.7% 70.91% 152ms 1.02% malloc_consolidate 2ms 0.013% 70.93% 151ms 1.01% MeshBasedCellPopulation::GetDampingConstant 2ms 0.013% 70.94% 149ms 1% AbstractCentreBasedCellPopulation::GetDampingConstant 39ms 0.26% 71.20% 146ms 0.98% std::_Rb_tree::_M_clone_node (inline) 53ms 0.36% 71.56% 140ms 0.94% AbstractElement::GetNodeLocation 3ms 0.02% 71.58% 140ms 0.94% std::__cxx11::collate::do_transform 136ms 0.91% 72.49% 136ms 0.91% incircle 1ms 0.0067% 72.50% 135ms 0.91% ___vsnprintf 1ms 0.0067% 72.50% 134ms 0.9% CellProliferativeTypesWriter::VisitCell 1ms 0.0067% 72.51% 134ms 0.9% __vsnprintf_internal (inline) 25ms 0.17% 72.68% 132ms 0.89% __printf_buffer 132ms 0.89% 73.56% 132ms 0.89% std::_Rb_tree_insert_and_rebalance 88ms 0.59% 74.15% 122ms 0.82% AbstractElement::GetNodeGlobalIndex 0 0% 74.15% 120ms 0.8% Cell::HasCellProperty (inline) 2ms 0.013% 74.17% 120ms 0.8% CellPropertyCollection::HasProperty 120ms 0.8% 74.97% 120ms 0.8% unlink_chunk 107ms 0.72% 75.69% 115ms 0.77% vertexsort 111ms 0.74% 76.43% 111ms 0.74% [libchaste_crypt.so] 110ms 0.74% 77.17% 110ms 0.74% Node::GetIndex 21ms 0.14% 77.31% 110ms 0.74% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.013% 77.32% 110ms 0.74% boost::numeric::ublas::vector_assign (inline) 0 0% 77.32% 109ms 0.73% AbstractCellBasedWriter::OpenOutputFileForAppend 109ms 0.73% 78.05% 109ms 0.73% std::vector::size (inline) 35ms 0.23% 78.29% 108ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.04% 78.33% 108ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.02% 78.35% 108ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 78.35% 108ms 0.72% OutputFileHandler::OpenOutputFile 66ms 0.44% 78.79% 108ms 0.72% std::_Rb_tree::equal_range (inline) 36ms 0.24% 79.03% 107ms 0.72% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 105ms 0.7% 79.74% 105ms 0.7% AbstractCellMutationState::~AbstractCellMutationState 7ms 0.047% 79.78% 102ms 0.68% Node::~Node 10ms 0.067% 79.85% 102ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.02% 79.87% 100ms 0.67% __printf_fp_l_buffer 0 0% 79.87% 100ms 0.67% __printf_fp_spec (inline) 100ms 0.67% 80.54% 100ms 0.67% std::type_info::name (inline) 2ms 0.013% 80.56% 99ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 8ms 0.054% 80.61% 97ms 0.65% boost::detail::shared_count::~shared_count (inline) 0 0% 80.61% 97ms 0.65% boost::shared_ptr::~shared_ptr (inline) 38ms 0.25% 80.86% 94ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 58ms 0.39% 81.25% 94ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 44ms 0.3% 81.55% 93ms 0.62% __printf_fp_buffer_1 2ms 0.013% 81.56% 91ms 0.61% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 81.56% 90ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0067% 81.57% 87ms 0.58% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 22ms 0.15% 81.72% 87ms 0.58% std::num_put::_M_insert_int 49ms 0.33% 82.04% 86ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 21ms 0.14% 82.18% 86ms 0.58% std::__ostream_insert 0 0% 82.18% 85ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 84ms 0.56% 82.75% 84ms 0.56% Node::rGetLocation 84ms 0.56% 83.31% 84ms 0.56% std::_Rb_tree_increment 76ms 0.51% 83.82% 83ms 0.56% boost::detail::sp_counted_base::release 5ms 0.034% 83.85% 83ms 0.56% std::_Rb_tree_const_iterator::operator++ (inline) 80ms 0.54% 84.39% 80ms 0.54% AbstractCellProperty::AbstractCellProperty 43ms 0.29% 84.68% 80ms 0.54% AbstractTetrahedralMesh::GetElement 1ms 0.0067% 84.69% 80ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 33ms 0.22% 84.91% 78ms 0.52% std::basic_filebuf::xsputn 0 0% 84.91% 78ms 0.52% std::vector::_M_default_append 0 0% 84.91% 78ms 0.52% std::vector::resize (inline) 77ms 0.52% 85.42% 77ms 0.52% AbstractElement::IsDeleted 2ms 0.013% 85.44% 76ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 9ms 0.06% 85.50% 76ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 76ms 0.51% 86.01% 76ms 0.51% TetrahedralMesh::EdgeIterator::operator!= (partial-inline)