File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16000ms, 85.31% of 18755ms total Dropped 755 nodes (cum <= 93.78ms) flat flat% sum% cum cum% 0 0% 0% 18717ms 99.80% __libc_start_call_main 0 0% 0% 18717ms 99.80% __libc_start_main_impl 0 0% 0% 18717ms 99.80% _start 0 0% 0% 18699ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18699ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18699ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18699ms 99.70% main 0 0% 0% 18665ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18665ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18665ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0053% 0.0053% 18641ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0.0053% 13907ms 74.15% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0053% 0.011% 8429ms 44.94% AbstractCellBasedSimulation::DoCellBirth 14ms 0.075% 0.085% 8320ms 44.36% Cell::ReadyToDivide 3ms 0.016% 0.1% 8229ms 43.88% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.011% 0.11% 8066ms 43.01% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.053% 0.17% 8053ms 42.94% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.016% 0.18% 8039ms 42.86% CellCycleModelOdeHandler::SolveOdeToTime 50ms 0.27% 0.45% 7802ms 41.60% AbstractOneStepIvpOdeSolver::InternalSolve 919ms 4.90% 5.35% 7020ms 37.43% RungeKutta4IvpOdeSolver::CalculateNextYValue 2995ms 15.97% 21.32% 5889ms 31.40% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0053% 21.32% 5362ms 28.59% MeshBasedCellPopulation::Update 4ms 0.021% 21.34% 4183ms 22.30% Cylindrical2dMesh::ReMesh 210ms 1.12% 22.46% 3032ms 16.17% AbstractCellProperty::IsType (inline) 0 0% 22.46% 2665ms 14.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.46% 2421ms 12.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.037% 22.50% 2400ms 12.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0053% 22.51% 2384ms 12.71% MutableMesh::ReMesh 0 0% 22.51% 2058ms 10.97% AbstractCellPopulation::WriteResultsToFiles 754ms 4.02% 26.53% 1792ms 9.55% std::_Rb_tree::_M_lower_bound (inline) 177ms 0.94% 27.47% 1686ms 8.99% TetrahedralMesh::EdgeIterator::operator++ 53ms 0.28% 27.75% 1373ms 7.32% std::_Rb_tree::find (inline) 275ms 1.47% 29.22% 1361ms 7.26% AbstractCellProperty::IsSame 43ms 0.23% 29.45% 1322ms 7.05% operator new 455ms 2.43% 31.87% 1254ms 6.69% __GI___libc_malloc 12ms 0.064% 31.94% 1249ms 6.66% TetrahedralMesh::ImportFromMesher 1ms 0.0053% 31.94% 1135ms 6.05% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 31.96% 1106ms 5.90% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 161ms 0.86% 32.82% 1086ms 5.79% std::type_info::operator== (inline) 38ms 0.2% 33.03% 1080ms 5.76% std::__new_allocator::allocate (inline) 0 0% 33.03% 1079ms 5.75% std::allocator_traits::allocate (inline) 10ms 0.053% 33.08% 1070ms 5.71% std::set::insert (inline) 1062ms 5.66% 38.74% 1062ms 5.66% __strcmp_evex 19ms 0.1% 38.84% 1060ms 5.65% std::_Rb_tree::_M_insert_unique 13ms 0.069% 38.91% 1013ms 5.40% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 38.91% 888ms 4.73% std::set::count (inline) 3ms 0.016% 38.93% 879ms 4.69% AbstractTwoBodyInteractionForce::AddForceContribution 252ms 1.34% 40.27% 846ms 4.51% __dynamic_cast 3ms 0.016% 40.29% 844ms 4.50% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 825ms 4.40% 44.69% 825ms 4.40% [libchaste_cell_based.so] 0 0% 44.69% 798ms 4.25% triangulate 4ms 0.021% 44.71% 783ms 4.17% CellPropertyCollection::GetPropertiesType (inline) 0 0% 44.71% 768ms 4.09% std::_Rb_tree::_M_create_node (inline) 28ms 0.15% 44.86% 766ms 4.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.043% 44.90% 761ms 4.06% CellPopulationElementWriter::Visit 0 0% 44.90% 742ms 3.96% std::_Rb_tree::_M_get_node (inline) 0 0% 44.90% 710ms 3.79% delaunay 1ms 0.0053% 44.91% 710ms 3.79% divconqdelaunay 33ms 0.18% 45.08% 707ms 3.77% std::_Rb_tree::_M_insert_ (inline) 382ms 2.04% 47.12% 694ms 3.70% _int_malloc 0 0% 47.12% 688ms 3.67% std::_Rb_tree::_Alloc_node::operator() (inline) 64ms 0.34% 47.46% 681ms 3.63% std::map::operator[] (partial-inline) 9ms 0.048% 47.51% 673ms 3.59% MeshBasedCellPopulation::AcceptCellWriter 637ms 3.40% 50.90% 637ms 3.40% std::_Rb_tree::_S_right (inline) 8ms 0.043% 50.95% 615ms 3.28% AbstractCellProperty::IsSubType (inline) 609ms 3.25% 54.19% 609ms 3.25% WntCellCycleOdeSystem::CalculateStoppingEvent 12ms 0.064% 54.26% 595ms 3.17% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.027% 54.28% 572ms 3.05% Element::Element 7ms 0.037% 54.32% 556ms 2.96% Element::RegisterWithNodes (inline) 10ms 0.053% 54.37% 547ms 2.92% Node::AddElement 116ms 0.62% 54.99% 547ms 2.92% __GI___libc_free 29ms 0.15% 55.15% 533ms 2.84% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.064% 55.21% 520ms 2.77% std::less::operator() (inline) 508ms 2.71% 57.92% 508ms 2.71% std::operator< (inline) 0 0% 57.92% 500ms 2.67% std::_Rb_tree::lower_bound (inline) 0 0% 57.92% 500ms 2.67% std::map::lower_bound (inline) 65ms 0.35% 58.27% 485ms 2.59% std::_Rb_tree::~_Rb_tree (inline) 0 0% 58.27% 485ms 2.59% std::map::find (inline) 248ms 1.32% 59.59% 477ms 2.54% AbstractCellMutationState::AbstractCellMutationState 97ms 0.52% 60.11% 472ms 2.52% std::_Rb_tree::_M_erase 0 0% 60.11% 463ms 2.47% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.11% 460ms 2.45% Cell::GetMutationState 460ms 2.45% 62.56% 460ms 2.45% [libchaste_crypt.so] 0 0% 62.56% 458ms 2.44% std::set::~set (inline) 7ms 0.037% 62.60% 457ms 2.44% MutableMesh::ReIndex 196ms 1.05% 63.64% 431ms 2.30% __cxxabiv1::__si_class_type_info::__do_dyncast 359ms 1.91% 65.56% 424ms 2.26% _int_free 2ms 0.011% 65.57% 416ms 2.22% std::ostream::operator<< (inline) 2ms 0.011% 65.58% 415ms 2.21% std::set::erase (inline) 5ms 0.027% 65.60% 414ms 2.21% std::_Rb_tree::erase 96ms 0.51% 66.12% 410ms 2.19% std::ostream::_M_insert 10ms 0.053% 66.17% 408ms 2.18% std::__new_allocator::deallocate (inline) 0 0% 66.17% 400ms 2.13% std::allocator_traits::deallocate (inline) 7ms 0.037% 66.21% 397ms 2.12% Node::RemoveElement 12ms 0.064% 66.27% 393ms 2.10% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.011% 66.28% 373ms 1.99% Cell::GetCellProliferativeType 22ms 0.12% 66.40% 363ms 1.94% divconqrecurse 2ms 0.011% 66.41% 343ms 1.83% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.41% 343ms 1.83% std::_Rb_tree::_M_put_node (inline) 1ms 0.0053% 66.41% 338ms 1.80% std::_Vector_base::_M_allocate (inline) 107ms 0.57% 66.98% 334ms 1.78% std::_Rb_tree::_M_get_insert_unique_pos 75ms 0.4% 67.38% 327ms 1.74% mergehulls 13ms 0.069% 67.45% 324ms 1.73% boost::detail::shared_count::~shared_count (inline) 0 0% 67.45% 324ms 1.73% boost::shared_ptr::~shared_ptr (inline) 22ms 0.12% 67.57% 313ms 1.67% Element::ResetIndex 3ms 0.016% 67.59% 304ms 1.62% TetrahedralMesh::RefreshJacobianCachedData 300ms 1.60% 69.19% 302ms 1.61% boost::detail::sp_counted_base::release 1ms 0.0053% 69.19% 299ms 1.59% MeshBasedCellPopulation::GetDampingConstant 2ms 0.011% 69.20% 298ms 1.59% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.032% 69.23% 297ms 1.58% std::_Rb_tree::_Rb_tree 7ms 0.037% 69.27% 296ms 1.58% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.08% 69.35% 286ms 1.52% TetrahedralMesh::Clear 1ms 0.0053% 69.36% 286ms 1.52% std::set::set (inline) 22ms 0.12% 69.47% 272ms 1.45% std::_Rb_tree::_M_copy (inline) 8ms 0.043% 69.52% 263ms 1.40% AbstractTetrahedralElement::CalculateInverseJacobian 25ms 0.13% 69.65% 262ms 1.40% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.027% 69.68% 261ms 1.39% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.048% 69.73% 261ms 1.39% std::vector::push_back (inline) 12ms 0.064% 69.79% 248ms 1.32% std::_Rb_tree::_M_erase_aux (inline) 0 0% 69.79% 246ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.059% 69.85% 244ms 1.30% AbstractCellPopulation::GetLocationIndexUsingCell 27ms 0.14% 69.99% 243ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 103ms 0.55% 70.54% 243ms 1.30% std::_Rb_tree::_M_clone_node (inline) 9ms 0.048% 70.59% 240ms 1.28% AbstractTetrahedralElement::CalculateJacobian 239ms 1.27% 71.86% 239ms 1.27% [libchaste_mesh.so] 11ms 0.059% 71.92% 234ms 1.25% std::vector::_M_realloc_insert 8ms 0.043% 71.96% 227ms 1.21% alternateaxes 3ms 0.016% 71.98% 224ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 9ms 0.048% 72.03% 223ms 1.19% Element::MarkAsDeleted 197ms 1.05% 73.08% 216ms 1.15% vertexmedian 3ms 0.016% 73.10% 215ms 1.15% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0053% 73.10% 215ms 1.15% NodeLocationWriter::Visit 209ms 1.11% 74.21% 209ms 1.11% std::vector::operator[] (inline) 14ms 0.075% 74.29% 208ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 159ms 0.85% 75.14% 194ms 1.03% malloc_consolidate 5ms 0.027% 75.16% 193ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.16% 193ms 1.03% CellProliferativeTypesWriter::VisitCell 21ms 0.11% 75.28% 188ms 1.00% AbstractTetrahedralElement::RefreshJacobian 19ms 0.1% 75.38% 187ms 1% std::num_put::_M_insert_float 9ms 0.048% 75.43% 181ms 0.97% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 180ms 0.96% 76.38% 180ms 0.96% std::_Rb_tree::_S_left (inline) 1ms 0.0053% 76.39% 178ms 0.95% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 5ms 0.027% 76.42% 175ms 0.93% boost::numeric::ublas::vector_assign (inline) 3ms 0.016% 76.43% 164ms 0.87% Cylindrical2dMesh::CreateMirrorNodes 82ms 0.44% 76.87% 163ms 0.87% std::_Rb_tree::equal_range (inline) 7ms 0.037% 76.91% 159ms 0.85% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.011% 76.92% 158ms 0.84% CellPropertyCollection::HasProperty 0 0% 76.92% 156ms 0.83% Cell::HasCellProperty (inline) 0 0% 76.92% 153ms 0.82% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 152ms 0.81% 77.73% 152ms 0.81% incircle 92ms 0.49% 78.22% 149ms 0.79% AbstractElement::GetNodeLocation 2ms 0.011% 78.23% 148ms 0.79% Node::~Node 2ms 0.011% 78.24% 144ms 0.77% std::__cxx11::collate::do_transform 41ms 0.22% 78.46% 143ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.032% 78.49% 143ms 0.76% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.016% 78.51% 141ms 0.75% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 140ms 0.75% 79.25% 140ms 0.75% std::_Rb_tree_insert_and_rebalance 139ms 0.74% 79.99% 139ms 0.74% unlink_chunk 15ms 0.08% 80.07% 136ms 0.73% __printf_buffer 6ms 0.032% 80.11% 135ms 0.72% Cell::SetCellProliferativeType 1ms 0.0053% 80.11% 135ms 0.72% OffLatticeSimulation::ApplyBoundaries 0 0% 80.11% 135ms 0.72% ___vsnprintf 0 0% 80.11% 135ms 0.72% __vsnprintf_internal (inline) 135ms 0.72% 80.83% 135ms 0.72% std::type_info::name (inline) 88ms 0.47% 81.30% 134ms 0.71% AbstractElement::GetNodeGlobalIndex 3ms 0.016% 81.32% 134ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 30ms 0.16% 81.48% 133ms 0.71% boost::numeric::ublas::indexing_vector_assign 131ms 0.7% 82.18% 131ms 0.7% std::_Rb_tree_increment 71ms 0.38% 82.55% 130ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 124ms 0.66% 83.22% 124ms 0.66% AbstractCellProperty::AbstractCellProperty 6ms 0.032% 83.25% 124ms 0.66% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 83.25% 122ms 0.65% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.25% 122ms 0.65% std::__new_allocator::destroy (inline) 0 0% 83.25% 122ms 0.65% std::allocator_traits::destroy (inline) 1ms 0.0053% 83.25% 117ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.032% 83.28% 114ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.28% 112ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.037% 83.32% 112ms 0.6% __printf_fp_l_buffer 0 0% 83.32% 112ms 0.6% __printf_fp_spec (inline) 5ms 0.027% 83.35% 111ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.35% 109ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 23ms 0.12% 83.47% 107ms 0.57% TetrahedralMesh::EdgesEnd 0 0% 83.47% 106ms 0.57% OutputFileHandler::OpenOutputFile 100ms 0.53% 84.00% 106ms 0.57% vertexsort 103ms 0.55% 84.55% 103ms 0.55% Node::GetIndex 47ms 0.25% 84.80% 102ms 0.54% __printf_fp_buffer_1 0 0% 84.80% 101ms 0.54% std::vector::resize (inline) 0 0% 84.80% 100ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 84.80% 100ms 0.53% std::vector::_M_default_append 95ms 0.51% 85.31% 95ms 0.51% std::vector::size (inline)