File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16047ms, 86.27% of 18601ms total Dropped 796 nodes (cum <= 93ms) flat flat% sum% cum cum% 0 0% 0% 18560ms 99.78% __libc_start_call_main 0 0% 0% 18560ms 99.78% __libc_start_main_impl 0 0% 0% 18560ms 99.78% _start 0 0% 0% 18542ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18542ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18542ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18542ms 99.68% main 0 0% 0% 18508ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18508ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18508ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18483ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 13885ms 74.65% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.016% 0.016% 8500ms 45.70% AbstractCellBasedSimulation::DoCellBirth 12ms 0.065% 0.081% 8387ms 45.09% Cell::ReadyToDivide 3ms 0.016% 0.097% 8305ms 44.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.016% 0.11% 8151ms 43.82% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.038% 0.15% 8140ms 43.76% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.011% 0.16% 8129ms 43.70% CellCycleModelOdeHandler::SolveOdeToTime 50ms 0.27% 0.43% 7906ms 42.50% AbstractOneStepIvpOdeSolver::InternalSolve 852ms 4.58% 5.01% 7122ms 38.29% RungeKutta4IvpOdeSolver::CalculateNextYValue 3102ms 16.68% 21.69% 6101ms 32.80% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0054% 21.69% 5284ms 28.41% MeshBasedCellPopulation::Update 2ms 0.011% 21.70% 4117ms 22.13% Cylindrical2dMesh::ReMesh 217ms 1.17% 22.87% 3142ms 16.89% AbstractCellProperty::IsType (inline) 0 0% 22.87% 2551ms 13.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.022% 22.89% 2282ms 12.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0054% 22.90% 2275ms 12.23% MutableMesh::ReMesh 2ms 0.011% 22.91% 2241ms 12.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0054% 22.91% 2043ms 10.98% AbstractCellPopulation::WriteResultsToFiles 734ms 3.95% 26.86% 1811ms 9.74% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.81% 27.67% 1674ms 9.00% TetrahedralMesh::EdgeIterator::operator++ 285ms 1.53% 29.20% 1455ms 7.82% AbstractCellProperty::IsSame 47ms 0.25% 29.45% 1408ms 7.57% std::_Rb_tree::find (inline) 66ms 0.35% 29.80% 1240ms 6.67% operator new 8ms 0.043% 29.85% 1220ms 6.56% TetrahedralMesh::ImportFromMesher 185ms 0.99% 30.84% 1170ms 6.29% std::type_info::operator== (inline) 411ms 2.21% 33.05% 1149ms 6.18% __GI___libc_malloc 1ms 0.0054% 33.06% 1132ms 6.09% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.032% 33.09% 1116ms 6.00% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.091% 33.18% 1080ms 5.81% std::set::insert (inline) 19ms 0.1% 33.28% 1061ms 5.70% std::_Rb_tree::_M_insert_unique 1055ms 5.67% 38.95% 1055ms 5.67% __strcmp_evex 44ms 0.24% 39.19% 1040ms 5.59% std::__new_allocator::allocate (inline) 0 0% 39.19% 1034ms 5.56% std::allocator_traits::allocate (inline) 11ms 0.059% 39.25% 1001ms 5.38% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 39.25% 892ms 4.80% std::set::count (inline) 859ms 4.62% 43.87% 859ms 4.62% [libchaste_cell_based.so] 11ms 0.059% 43.93% 846ms 4.55% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.011% 43.94% 798ms 4.29% triangulate 9ms 0.048% 43.99% 746ms 4.01% CellPopulationElementWriter::Visit 1ms 0.0054% 43.99% 738ms 3.97% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 43.99% 735ms 3.95% std::_Rb_tree::_M_create_node (inline) 15ms 0.081% 44.07% 723ms 3.89% CellPropertyCollection::GetPropertiesType (inline) 218ms 1.17% 45.24% 722ms 3.88% __dynamic_cast 0 0% 45.24% 722ms 3.88% std::_Rb_tree::_M_get_node (inline) 0 0% 45.24% 713ms 3.83% delaunay 3ms 0.016% 45.26% 712ms 3.83% divconqdelaunay 28ms 0.15% 45.41% 691ms 3.71% std::_Rb_tree::_M_insert_ (inline) 64ms 0.34% 45.76% 673ms 3.62% std::map::operator[] (partial-inline) 669ms 3.60% 49.35% 669ms 3.60% std::_Rb_tree::_S_right (inline) 25ms 0.13% 49.49% 664ms 3.57% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.043% 49.53% 662ms 3.56% MeshBasedCellPopulation::AcceptCellWriter 0 0% 49.53% 644ms 3.46% std::_Rb_tree::_Alloc_node::operator() (inline) 387ms 2.08% 51.61% 641ms 3.45% _int_malloc 7ms 0.038% 51.65% 616ms 3.31% Element::Element 600ms 3.23% 54.87% 600ms 3.23% WntCellCycleOdeSystem::CalculateStoppingEvent 21ms 0.11% 54.99% 588ms 3.16% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.032% 55.02% 586ms 3.15% Element::RegisterWithNodes (inline) 17ms 0.091% 55.11% 576ms 3.10% Node::AddElement 6ms 0.032% 55.14% 560ms 3.01% AbstractCellProperty::IsSubType (inline) 12ms 0.065% 55.21% 560ms 3.01% std::less::operator() (inline) 548ms 2.95% 58.15% 548ms 2.95% std::operator< (inline) 36ms 0.19% 58.35% 527ms 2.83% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 58.35% 513ms 2.76% std::map::find (inline) 110ms 0.59% 58.94% 509ms 2.74% __GI___libc_free 3ms 0.016% 58.95% 500ms 2.69% MutableMesh::ReIndex 0 0% 58.95% 486ms 2.61% std::_Rb_tree::lower_bound (inline) 0 0% 58.95% 486ms 2.61% std::map::lower_bound (inline) 481ms 2.59% 61.54% 481ms 2.59% [libchaste_crypt.so] 221ms 1.19% 62.73% 467ms 2.51% AbstractCellMutationState::AbstractCellMutationState 13ms 0.07% 62.80% 450ms 2.42% Cylindrical2dMesh::CorrectNonPeriodicMesh 53ms 0.28% 63.08% 429ms 2.31% std::_Rb_tree::~_Rb_tree (inline) 75ms 0.4% 63.49% 424ms 2.28% std::_Rb_tree::_M_erase 0 0% 63.49% 423ms 2.27% std::_Rb_tree::_M_drop_node (inline) 4ms 0.022% 63.51% 415ms 2.23% Cell::GetMutationState 0 0% 63.51% 407ms 2.19% std::set::~set (inline) 1ms 0.0054% 63.51% 403ms 2.17% std::ostream::operator<< (inline) 58ms 0.31% 63.82% 399ms 2.15% std::ostream::_M_insert 10ms 0.054% 63.88% 393ms 2.11% std::__new_allocator::deallocate (inline) 1ms 0.0054% 63.88% 393ms 2.11% std::set::erase (inline) 6ms 0.032% 63.92% 392ms 2.11% std::_Rb_tree::erase 328ms 1.76% 65.68% 391ms 2.10% _int_free 0 0% 65.68% 383ms 2.06% std::allocator_traits::deallocate (inline) 8ms 0.043% 65.72% 378ms 2.03% Node::RemoveElement 182ms 0.98% 66.70% 370ms 1.99% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.016% 66.72% 366ms 1.97% Cell::GetCellProliferativeType 114ms 0.61% 67.33% 353ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 24ms 0.13% 67.46% 345ms 1.85% Element::ResetIndex 2ms 0.011% 67.47% 343ms 1.84% LegacyCellProliferativeTypesWriter::VisitCell 12ms 0.065% 67.53% 332ms 1.78% divconqrecurse 0 0% 67.53% 328ms 1.76% std::_Rb_tree::_M_put_node (inline) 0 0% 67.53% 312ms 1.68% std::_Vector_base::_M_allocate (inline) 14ms 0.075% 67.61% 308ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 67.61% 308ms 1.66% boost::shared_ptr::~shared_ptr (inline) 83ms 0.45% 68.06% 307ms 1.65% mergehulls 9ms 0.048% 68.10% 303ms 1.63% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 68.10% 289ms 1.55% MeshBasedCellPopulation::GetDampingConstant 2ms 0.011% 68.11% 286ms 1.54% AbstractCentreBasedCellPopulation::GetDampingConstant 15ms 0.081% 68.20% 286ms 1.54% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 284ms 1.53% 69.72% 286ms 1.54% boost::detail::sp_counted_base::release 5ms 0.027% 69.75% 269ms 1.45% std::set::set (inline) 9ms 0.048% 69.80% 268ms 1.44% std::_Rb_tree::_Rb_tree 0 0% 69.80% 258ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.059% 69.86% 258ms 1.39% std::vector::push_back (inline) 22ms 0.12% 69.97% 255ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.016% 69.99% 254ms 1.37% alternateaxes 231ms 1.24% 71.23% 251ms 1.35% vertexmedian 16ms 0.086% 71.32% 250ms 1.34% AbstractTetrahedralElement::CalculateJacobian 14ms 0.075% 71.39% 244ms 1.31% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.011% 71.40% 239ms 1.28% NodeLocationWriter::Visit 239ms 1.28% 72.69% 239ms 1.28% [libchaste_mesh.so] 2ms 0.011% 72.70% 238ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 20ms 0.11% 72.81% 237ms 1.27% std::_Rb_tree::_M_copy (inline) 0 0% 72.81% 234ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 22ms 0.12% 72.93% 233ms 1.25% TetrahedralMesh::Clear 1ms 0.0054% 72.93% 231ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 9ms 0.048% 72.98% 227ms 1.22% std::vector::_M_realloc_insert 0 0% 72.98% 221ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.054% 73.03% 220ms 1.18% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.091% 73.13% 220ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 102ms 0.55% 73.67% 214ms 1.15% std::_Rb_tree::_M_clone_node (inline) 18ms 0.097% 73.77% 212ms 1.14% std::num_put::_M_insert_float 12ms 0.065% 73.83% 210ms 1.13% Element::MarkAsDeleted 3ms 0.016% 73.85% 196ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.011% 73.86% 191ms 1.03% CellProliferativeTypesWriter::VisitCell 1ms 0.0054% 73.87% 189ms 1.02% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 7ms 0.038% 73.90% 187ms 1.01% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 25ms 0.13% 74.04% 183ms 0.98% AbstractTetrahedralElement::RefreshJacobian 2ms 0.011% 74.05% 173ms 0.93% boost::numeric::ublas::vector_assign (inline) 171ms 0.92% 74.97% 171ms 0.92% std::_Rb_tree::_S_left (inline) 1ms 0.0054% 74.97% 169ms 0.91% OffLatticeSimulation::ApplyBoundaries 4ms 0.022% 75.00% 167ms 0.9% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 167ms 0.9% 75.89% 167ms 0.9% std::vector::operator[] (inline) 2ms 0.011% 75.90% 163ms 0.88% std::__cxx11::collate::do_transform 2ms 0.011% 75.92% 162ms 0.87% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0054% 75.92% 158ms 0.85% ___vsnprintf 21ms 0.11% 76.03% 157ms 0.84% __printf_buffer 0 0% 76.03% 157ms 0.84% __vsnprintf_internal (inline) 5ms 0.027% 76.06% 156ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.011% 76.07% 154ms 0.83% CellPropertyCollection::HasProperty 1ms 0.0054% 76.08% 152ms 0.82% Cell::HasCellProperty (inline) 2ms 0.011% 76.09% 152ms 0.82% Cylindrical2dMesh::CreateMirrorNodes 6ms 0.032% 76.12% 152ms 0.82% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.016% 76.14% 150ms 0.81% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 73ms 0.39% 76.53% 147ms 0.79% std::_Rb_tree::equal_range (inline) 143ms 0.77% 77.30% 143ms 0.77% Node::GetIndex 117ms 0.63% 77.93% 140ms 0.75% malloc_consolidate 138ms 0.74% 78.67% 138ms 0.74% incircle 138ms 0.74% 79.41% 138ms 0.74% std::_Rb_tree_insert_and_rebalance 37ms 0.2% 79.61% 137ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 12ms 0.065% 79.67% 136ms 0.73% std::_Rb_tree_const_iterator::operator++ (inline) 85ms 0.46% 80.13% 135ms 0.73% AbstractElement::GetNodeGlobalIndex 9ms 0.048% 80.18% 132ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 79ms 0.42% 80.60% 131ms 0.7% AbstractElement::GetNodeLocation 131ms 0.7% 81.31% 131ms 0.7% unlink_chunk 8ms 0.043% 81.35% 130ms 0.7% __printf_fp_l_buffer 0 0% 81.35% 130ms 0.7% __printf_fp_spec (inline) 1ms 0.0054% 81.36% 128ms 0.69% Cell::SetCellProliferativeType 128ms 0.69% 82.04% 128ms 0.69% std::_Rb_tree_increment 125ms 0.67% 82.72% 125ms 0.67% AbstractCellProperty::AbstractCellProperty 0 0% 82.72% 124ms 0.67% Node::~Node 39ms 0.21% 82.93% 124ms 0.67% std::__ostream_insert 25ms 0.13% 83.06% 123ms 0.66% boost::numeric::ublas::indexing_vector_assign 58ms 0.31% 83.37% 122ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 7ms 0.038% 83.41% 121ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.038% 83.45% 118ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 53ms 0.28% 83.73% 116ms 0.62% __printf_fp_buffer_1 103ms 0.55% 84.29% 113ms 0.61% vertexsort 112ms 0.6% 84.89% 112ms 0.6% std::type_info::name (inline) 21ms 0.11% 85.00% 107ms 0.58% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 85.00% 101ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.011% 85.01% 101ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 17ms 0.091% 85.10% 100ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.022% 85.12% 98ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.12% 85.24% 98ms 0.53% std::num_put::_M_insert_int 97ms 0.52% 85.76% 97ms 0.52% [libstdc++.so.6.0.33] 0 0% 85.76% 95ms 0.51% std::_Rb_tree::_M_destroy_node (inline) 0 0% 85.76% 95ms 0.51% std::__new_allocator::destroy (inline) 0 0% 85.76% 95ms 0.51% std::allocator_traits::destroy (inline) 0 0% 85.76% 95ms 0.51% std::operator<< (inline) 94ms 0.51% 86.27% 94ms 0.51% std::_Rb_tree_rebalance_for_erase