File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13654ms, 85.64% of 15944ms total Dropped 765 nodes (cum <= 79.72ms) flat flat% sum% cum cum% 0 0% 0% 15908ms 99.77% __libc_start_call_main 0 0% 0% 15908ms 99.77% __libc_start_main_impl 0 0% 0% 15908ms 99.77% _start 0 0% 0% 15885ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15885ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15885ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15885ms 99.63% main 0 0% 0% 15851ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15851ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15851ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15830ms 99.28% AbstractCellBasedSimulation::Solve 1ms 0.0063% 0.0063% 12054ms 75.60% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0063% 0.013% 7423ms 46.56% AbstractCellBasedSimulation::DoCellBirth 5ms 0.031% 0.044% 7338ms 46.02% Cell::ReadyToDivide 2ms 0.013% 0.056% 7280ms 45.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0063% 0.063% 7138ms 44.77% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.025% 0.088% 7130ms 44.72% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0063% 0.094% 7122ms 44.67% CellCycleModelOdeHandler::SolveOdeToTime 53ms 0.33% 0.43% 6996ms 43.88% AbstractOneStepIvpOdeSolver::InternalSolve 740ms 4.64% 5.07% 6224ms 39.04% RungeKutta4IvpOdeSolver::CalculateNextYValue 2903ms 18.21% 23.28% 5221ms 32.75% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.28% 4519ms 28.34% MeshBasedCellPopulation::Update 3ms 0.019% 23.29% 3423ms 21.47% Cylindrical2dMesh::ReMesh 264ms 1.66% 24.95% 2456ms 15.40% AbstractCellProperty::IsType (inline) 0 0% 24.95% 2169ms 13.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0063% 24.96% 1871ms 11.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0063% 24.96% 1868ms 11.72% MutableMesh::ReMesh 1ms 0.0063% 24.97% 1833ms 11.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 24.97% 1603ms 10.05% AbstractCellPopulation::WriteResultsToFiles 779ms 4.89% 29.85% 1588ms 9.96% std::_Rb_tree::_M_lower_bound (inline) 146ms 0.92% 30.77% 1545ms 9.69% TetrahedralMesh::EdgeIterator::operator++ 39ms 0.24% 31.01% 1268ms 7.95% std::_Rb_tree::find (inline) 0 0% 31.01% 1064ms 6.67% MeshBasedCellPopulation::UpdateNodePairs 44ms 0.28% 31.29% 1057ms 6.63% operator new 3ms 0.019% 31.31% 1006ms 6.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 324ms 2.03% 33.34% 1006ms 6.31% __GI___libc_malloc 9ms 0.056% 33.40% 943ms 5.91% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.038% 33.44% 929ms 5.83% TetrahedralMesh::ImportFromMesher 12ms 0.075% 33.51% 914ms 5.73% std::set::insert (inline) 139ms 0.87% 34.38% 910ms 5.71% AbstractCellProperty::IsSame 15ms 0.094% 34.48% 902ms 5.66% std::_Rb_tree::_M_insert_unique 15ms 0.094% 34.57% 892ms 5.59% std::__new_allocator::allocate (inline) 0 0% 34.57% 888ms 5.57% std::allocator_traits::allocate (inline) 0 0% 34.57% 787ms 4.94% std::set::count (inline) 778ms 4.88% 39.45% 778ms 4.88% [libchaste_cell_based.so] 15ms 0.094% 39.54% 771ms 4.84% std::type_info::operator== (inline) 740ms 4.64% 44.19% 740ms 4.64% __strcmp_evex 1ms 0.0063% 44.19% 729ms 4.57% triangulate 10ms 0.063% 44.25% 668ms 4.19% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.25% 651ms 4.08% delaunay 3ms 0.019% 44.27% 651ms 4.08% divconqdelaunay 357ms 2.24% 46.51% 582ms 3.65% _int_malloc 40ms 0.25% 46.76% 580ms 3.64% std::_Rb_tree::_M_insert_ (inline) 578ms 3.63% 50.39% 578ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.025% 50.41% 573ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 50.41% 572ms 3.59% std::_Rb_tree::_M_create_node (inline) 0 0% 50.41% 558ms 3.50% std::_Rb_tree::_M_get_node (inline) 10ms 0.063% 50.48% 557ms 3.49% CellPopulationElementWriter::Visit 11ms 0.069% 50.55% 541ms 3.39% MeshBasedCellPopulation::AcceptCellWriter 49ms 0.31% 50.85% 536ms 3.36% std::map::operator[] (partial-inline) 152ms 0.95% 51.81% 525ms 3.29% __dynamic_cast 522ms 3.27% 55.08% 522ms 3.27% std::_Rb_tree::_S_right (inline) 5ms 0.031% 55.11% 506ms 3.17% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.11% 505ms 3.17% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.094% 55.21% 504ms 3.16% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.069% 55.27% 486ms 3.05% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.27% 478ms 3.00% std::map::find (inline) 18ms 0.11% 55.39% 466ms 2.92% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.031% 55.42% 457ms 2.87% Element::RegisterWithNodes (inline) 24ms 0.15% 55.57% 450ms 2.82% Node::AddElement 3ms 0.019% 55.59% 448ms 2.81% Element::Element 91ms 0.57% 56.16% 433ms 2.72% __GI___libc_free 214ms 1.34% 57.50% 431ms 2.70% AbstractCellMutationState::AbstractCellMutationState 9ms 0.056% 57.56% 415ms 2.60% std::less::operator() (inline) 406ms 2.55% 60.10% 406ms 2.55% std::operator< (inline) 4ms 0.025% 60.13% 404ms 2.53% MutableMesh::ReIndex 0 0% 60.13% 403ms 2.53% std::_Rb_tree::_M_drop_node (inline) 5ms 0.031% 60.16% 402ms 2.52% AbstractCellProperty::IsSubType (inline) 0 0% 60.16% 392ms 2.46% std::_Rb_tree::lower_bound (inline) 0 0% 60.16% 392ms 2.46% std::map::lower_bound (inline) 6ms 0.038% 60.20% 391ms 2.45% Cylindrical2dMesh::CorrectNonPeriodicMesh 52ms 0.33% 60.52% 380ms 2.38% std::_Rb_tree::~_Rb_tree (inline) 51ms 0.32% 60.84% 374ms 2.35% std::_Rb_tree::_M_erase 2ms 0.013% 60.86% 371ms 2.33% std::ostream::operator<< (inline) 51ms 0.32% 61.18% 368ms 2.31% std::ostream::_M_insert 0 0% 61.18% 363ms 2.28% std::set::~set (inline) 10ms 0.063% 61.24% 362ms 2.27% std::__new_allocator::deallocate (inline) 0 0% 61.24% 357ms 2.24% std::allocator_traits::deallocate (inline) 350ms 2.20% 63.43% 350ms 2.20% [libchaste_crypt.so] 296ms 1.86% 65.29% 336ms 2.11% _int_free 7ms 0.044% 65.33% 333ms 2.09% divconqrecurse 0 0% 65.33% 330ms 2.07% std::_Vector_base::_M_allocate (inline) 100ms 0.63% 65.96% 322ms 2.02% mergehulls 140ms 0.88% 66.84% 307ms 1.93% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.056% 66.90% 307ms 1.93% std::_Rb_tree::erase 0 0% 66.90% 307ms 1.93% std::set::erase (inline) 12ms 0.075% 66.97% 306ms 1.92% Node::RemoveElement 0 0% 66.97% 303ms 1.90% std::_Rb_tree::_M_put_node (inline) 1ms 0.0063% 66.98% 297ms 1.86% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.98% 296ms 1.86% Cell::GetCellProliferativeType 6ms 0.038% 67.02% 279ms 1.75% boost::detail::shared_count::~shared_count (inline) 0 0% 67.02% 279ms 1.75% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0063% 67.02% 276ms 1.73% Cell::GetMutationState 262ms 1.64% 68.67% 266ms 1.67% boost::detail::sp_counted_base::release 1ms 0.0063% 68.67% 265ms 1.66% AbstractCellPopulation::Iterator::operator++ (inline) 132ms 0.83% 69.50% 264ms 1.66% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.056% 69.56% 263ms 1.65% Element::ResetIndex 34ms 0.21% 69.77% 260ms 1.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 250ms 1.57% 71.34% 259ms 1.62% std::vector::operator[] (inline) 17ms 0.11% 71.44% 251ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.038% 71.48% 240ms 1.51% std::vector::push_back (inline) 12ms 0.075% 71.56% 237ms 1.49% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.025% 71.58% 230ms 1.44% std::vector::_M_realloc_insert 1ms 0.0063% 71.59% 229ms 1.44% NodeLocationWriter::Visit 0 0% 71.59% 228ms 1.43% std::set::set (inline) 6ms 0.038% 71.63% 221ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0063% 71.63% 220ms 1.38% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 33ms 0.21% 71.84% 219ms 1.37% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0063% 71.85% 219ms 1.37% alternateaxes 202ms 1.27% 73.11% 218ms 1.37% vertexmedian 0 0% 73.11% 217ms 1.36% ApcOneHitCellMutationState::ApcOneHitCellMutationState 6ms 0.038% 73.15% 213ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.11% 73.26% 210ms 1.32% std::_Rb_tree::_M_copy (inline) 16ms 0.1% 73.36% 209ms 1.31% std::num_put::_M_insert_float 0 0% 73.36% 208ms 1.30% OffLatticeSimulation::ApplyBoundaries 0 0% 73.36% 203ms 1.27% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0063% 73.36% 199ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 191ms 1.20% 74.56% 191ms 1.20% [libchaste_mesh.so] 1ms 0.0063% 74.57% 186ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 74ms 0.46% 75.03% 184ms 1.15% std::_Rb_tree::_M_clone_node (inline) 5ms 0.031% 75.06% 182ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.056% 75.12% 181ms 1.14% Element::MarkAsDeleted 8ms 0.05% 75.17% 178ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.013% 75.18% 177ms 1.11% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.18% 174ms 1.09% AbstractCentreBasedCellPopulation::GetDampingConstant 12ms 0.075% 75.26% 173ms 1.09% AbstractTetrahedralElement::CalculateJacobian 8ms 0.05% 75.31% 165ms 1.03% std::__cxx11::collate::do_transform 160ms 1.00% 76.31% 160ms 1.00% std::_Rb_tree_insert_and_rebalance 1ms 0.0063% 76.32% 151ms 0.95% TetrahedralMesh::Clear 151ms 0.95% 77.26% 151ms 0.95% incircle 114ms 0.72% 77.98% 151ms 0.95% malloc_consolidate 0 0% 77.98% 149ms 0.93% ___vsnprintf 0 0% 77.98% 149ms 0.93% __vsnprintf_internal (inline) 19ms 0.12% 78.10% 147ms 0.92% __printf_buffer 1ms 0.0063% 78.10% 141ms 0.88% CellPropertyCollection::HasProperty 31ms 0.19% 78.30% 140ms 0.88% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 41ms 0.26% 78.56% 140ms 0.88% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 78.56% 140ms 0.88% Cell::HasCellProperty (inline) 4ms 0.025% 78.58% 138ms 0.87% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 78.58% 136ms 0.85% CellProliferativeTypesWriter::VisitCell 63ms 0.4% 78.98% 134ms 0.84% AbstractElement::GetNodeGlobalIndex 127ms 0.8% 79.77% 127ms 0.8% std::type_info::name (inline) 18ms 0.11% 79.89% 122ms 0.77% AbstractTetrahedralElement::RefreshJacobian 122ms 0.77% 80.65% 122ms 0.77% std::vector::size (inline) 66ms 0.41% 81.06% 121ms 0.76% std::_Rb_tree::equal_range (inline) 4ms 0.025% 81.09% 120ms 0.75% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0063% 81.10% 120ms 0.75% __printf_fp_l_buffer 0 0% 81.10% 120ms 0.75% __printf_fp_spec (inline) 1ms 0.0063% 81.10% 112ms 0.7% Cell::SetCellProliferativeType 0 0% 81.10% 110ms 0.69% AbstractCellBasedSimulation::DoCellRemoval (inline) 110ms 0.69% 81.79% 110ms 0.69% AbstractCellProperty::AbstractCellProperty 9ms 0.056% 81.85% 110ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.038% 81.89% 109ms 0.68% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 38ms 0.24% 82.12% 109ms 0.68% __printf_fp_buffer_1 5ms 0.031% 82.16% 109ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.025% 82.18% 107ms 0.67% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 107ms 0.67% 82.85% 107ms 0.67% std::_Rb_tree::_S_left (inline) 3ms 0.019% 82.87% 106ms 0.66% AbstractTetrahedralElement::AbstractTetrahedralElement 18ms 0.11% 82.98% 104ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0063% 82.99% 104ms 0.65% boost::numeric::ublas::vector_assign (inline) 4ms 0.025% 83.02% 101ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.02% 101ms 0.63% std::__new_allocator::destroy (inline) 0 0% 83.02% 101ms 0.63% std::allocator_traits::destroy (inline) 0 0% 83.02% 100ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 42ms 0.26% 83.28% 96ms 0.6% AbstractElement::GetNodeLocation 2ms 0.013% 83.29% 96ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 47ms 0.29% 83.59% 93ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 3ms 0.019% 83.61% 92ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.031% 83.64% 91ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 84ms 0.53% 84.16% 89ms 0.56% vertexsort 6ms 0.038% 84.20% 88ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 87ms 0.55% 84.75% 87ms 0.55% unlink_chunk 0 0% 84.75% 83ms 0.52% tcache_get (inline) 83ms 0.52% 85.27% 83ms 0.52% tcache_get_n (inline) 35ms 0.22% 85.49% 82ms 0.51% std::__ostream_insert 24ms 0.15% 85.64% 80ms 0.5% std::num_put::_M_insert_int