File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16992ms, 83.59% of 20328ms total Dropped 848 nodes (cum <= 101.64ms) flat flat% sum% cum cum% 0 0% 0% 20283ms 99.78% __libc_start_call_main 0 0% 0% 20283ms 99.78% __libc_start_main_impl 0 0% 0% 20283ms 99.78% _start 0 0% 0% 20262ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20262ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20262ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20262ms 99.68% main 0 0% 0% 20216ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20216ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20216ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 3ms 0.015% 0.015% 20189ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.015% 15289ms 75.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.02% 9433ms 46.40% AbstractCellBasedSimulation::DoCellBirth 15ms 0.074% 0.093% 9322ms 45.86% Cell::ReadyToDivide 8ms 0.039% 0.13% 9191ms 45.21% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0049% 0.14% 9032ms 44.43% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.098% 0.24% 9025ms 44.40% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.25% 9001ms 44.28% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.34% 0.6% 8797ms 43.28% AbstractOneStepIvpOdeSolver::InternalSolve 1025ms 5.04% 5.64% 7897ms 38.85% RungeKutta4IvpOdeSolver::CalculateNextYValue 2755ms 13.55% 19.19% 6690ms 32.91% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.19% 5725ms 28.16% MeshBasedCellPopulation::Update 5ms 0.025% 19.21% 4503ms 22.15% Cylindrical2dMesh::ReMesh 60ms 0.3% 19.51% 3974ms 19.55% AbstractCellProperty::IsType (inline) 2ms 0.0098% 19.52% 2756ms 13.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.52% 2569ms 12.64% MutableMesh::ReMesh 333ms 1.64% 21.16% 2561ms 12.60% AbstractCellProperty::IsSame 0 0% 21.16% 2406ms 11.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.069% 21.23% 2360ms 11.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 225ms 1.11% 22.33% 2228ms 10.96% std::type_info::operator== (inline) 0 0% 22.33% 2131ms 10.48% AbstractCellPopulation::WriteResultsToFiles 2131ms 10.48% 32.82% 2131ms 10.48% __strcmp_avx2 800ms 3.94% 36.75% 1921ms 9.45% std::_Rb_tree::_M_lower_bound (inline) 180ms 0.89% 37.64% 1727ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 63ms 0.31% 37.95% 1436ms 7.06% std::_Rb_tree::find (inline) 16ms 0.079% 38.03% 1325ms 6.52% TetrahedralMesh::ImportFromMesher 0 0% 38.03% 1182ms 5.81% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 38.05% 1140ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 44ms 0.22% 38.26% 1125ms 5.53% operator new 251ms 1.23% 39.50% 1071ms 5.27% __GI___libc_malloc 5ms 0.025% 39.52% 1064ms 5.23% MeshBasedCellPopulation::SpringIterator::operator++ 31ms 0.15% 39.67% 959ms 4.72% std::__new_allocator::allocate (inline) 0 0% 39.67% 957ms 4.71% std::allocator_traits::allocate (inline) 15ms 0.074% 39.75% 922ms 4.54% std::set::insert (inline) 12ms 0.059% 39.81% 907ms 4.46% std::_Rb_tree::_M_insert_unique 1ms 0.0049% 39.81% 892ms 4.39% triangulate 0 0% 39.81% 888ms 4.37% std::set::count (inline) 1ms 0.0049% 39.82% 844ms 4.15% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0049% 39.82% 798ms 3.93% delaunay 5ms 0.025% 39.85% 795ms 3.91% divconqdelaunay 71ms 0.35% 40.20% 781ms 3.84% std::map::operator[] (partial-inline) 27ms 0.13% 40.33% 752ms 3.70% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0049% 40.33% 740ms 3.64% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 391ms 1.92% 42.26% 737ms 3.63% _int_malloc 268ms 1.32% 43.58% 731ms 3.60% __dynamic_cast 725ms 3.57% 47.14% 725ms 3.57% WntCellCycleOdeSystem::CalculateStoppingEvent 724ms 3.56% 50.70% 724ms 3.56% std::_Rb_tree::_S_right (inline) 8ms 0.039% 50.74% 705ms 3.47% CellPopulationElementWriter::Visit 14ms 0.069% 50.81% 703ms 3.46% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.064% 50.88% 654ms 3.22% std::less::operator() (inline) 21ms 0.1% 50.98% 653ms 3.21% AbstractCellPopulation::GetCellUsingLocationIndex 641ms 3.15% 54.13% 641ms 3.15% std::operator< (inline) 0 0% 54.13% 635ms 3.12% std::_Rb_tree::_M_create_node (inline) 3ms 0.015% 54.15% 591ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.15% 591ms 2.91% std::_Rb_tree::_M_get_node (inline) 0 0% 54.15% 582ms 2.86% std::_Rb_tree::lower_bound (inline) 0 0% 54.15% 582ms 2.86% std::map::lower_bound (inline) 35ms 0.17% 54.32% 573ms 2.82% std::_Rb_tree::_M_insert_ (inline) 190ms 0.93% 55.25% 549ms 2.70% __GI___libc_free 4ms 0.02% 55.27% 548ms 2.70% AbstractCellProperty::IsSubType (inline) 0 0% 55.27% 548ms 2.70% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.27% 548ms 2.70% std::map::find (inline) 1ms 0.0049% 55.28% 540ms 2.66% std::ostream::operator<< (inline) 77ms 0.38% 55.66% 538ms 2.65% std::ostream::_M_insert 13ms 0.064% 55.72% 527ms 2.59% MutableMesh::ReIndex 10ms 0.049% 55.77% 521ms 2.56% Element::Element 15ms 0.074% 55.84% 498ms 2.45% Cylindrical2dMesh::ReconstructCylindricalMesh 170ms 0.84% 56.68% 479ms 2.36% std::_Rb_tree::_M_erase 12ms 0.059% 56.74% 472ms 2.32% Cylindrical2dMesh::CorrectNonPeriodicMesh 14ms 0.069% 56.81% 455ms 2.24% Element::RegisterWithNodes (inline) 25ms 0.12% 56.93% 455ms 2.24% std::_Rb_tree::~_Rb_tree (inline) 305ms 1.50% 58.43% 450ms 2.21% AbstractCellMutationState::AbstractCellMutationState 9ms 0.044% 58.48% 436ms 2.14% Node::AddElement 45ms 0.22% 58.70% 425ms 2.09% TetrahedralMesh::Clear 0 0% 58.70% 418ms 2.06% std::set::~set (inline) 5ms 0.025% 58.72% 395ms 1.94% Cell::GetMutationState 6ms 0.03% 58.75% 394ms 1.94% std::__new_allocator::deallocate (inline) 0 0% 58.75% 388ms 1.91% std::allocator_traits::deallocate (inline) 22ms 0.11% 58.86% 385ms 1.89% divconqrecurse 11ms 0.054% 58.91% 382ms 1.88% std::_Rb_tree::erase 1ms 0.0049% 58.92% 381ms 1.87% std::set::erase (inline) 10ms 0.049% 58.97% 373ms 1.83% Node::RemoveElement 0 0% 58.97% 366ms 1.80% std::_Vector_base::_M_allocate (inline) 0 0% 58.97% 363ms 1.79% std::_Rb_tree::_M_drop_node (inline) 291ms 1.43% 60.40% 357ms 1.76% _int_free 105ms 0.52% 60.92% 345ms 1.70% mergehulls 2ms 0.0098% 60.93% 342ms 1.68% Cell::GetCellProliferativeType 172ms 0.85% 61.77% 335ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.77% 333ms 1.64% std::_Rb_tree::_M_put_node (inline) 11ms 0.054% 61.83% 330ms 1.62% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 61.83% 330ms 1.62% NodeLocationWriter::Visit 329ms 1.62% 63.44% 329ms 1.62% [libchaste_cell_based.so] 0 0% 63.44% 327ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.098% 63.54% 326ms 1.60% Element::ResetIndex 54ms 0.27% 63.81% 324ms 1.59% AbstractCellPopulation::Iterator::IsRealCell (inline) 151ms 0.74% 64.55% 322ms 1.58% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0098% 64.56% 312ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.089% 64.65% 312ms 1.53% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.039% 64.69% 309ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.0098% 64.70% 287ms 1.41% LegacyCellProliferativeTypesWriter::VisitCell 15ms 0.074% 64.77% 287ms 1.41% std::num_put::_M_insert_float 15ms 0.074% 64.85% 286ms 1.41% std::vector::push_back (inline) 0 0% 64.85% 285ms 1.40% MeshBasedCellPopulation::GetDampingConstant 5ms 0.025% 64.87% 283ms 1.39% AbstractCentreBasedCellPopulation::GetDampingConstant 23ms 0.11% 64.98% 283ms 1.39% AbstractTetrahedralElement::CalculateJacobian 4ms 0.02% 65.00% 281ms 1.38% std::set::set (inline) 275ms 1.35% 66.36% 276ms 1.36% std::vector::operator[] (inline) 1ms 0.0049% 66.36% 272ms 1.34% alternateaxes 257ms 1.26% 67.63% 271ms 1.33% vertexmedian 14ms 0.069% 67.69% 269ms 1.32% Node::~Node 13ms 0.064% 67.76% 266ms 1.31% AbstractTetrahedralElement::CalculateInverseJacobian 22ms 0.11% 67.87% 262ms 1.29% std::_Rb_tree::_M_copy (inline) 20ms 0.098% 67.97% 256ms 1.26% std::vector::_M_realloc_insert 13ms 0.064% 68.03% 255ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.039% 68.07% 244ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.015% 68.08% 242ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.28% 68.36% 242ms 1.19% ApcOneHitCellMutationState::ApcOneHitCellMutationState 89ms 0.44% 68.80% 242ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 103ms 0.51% 69.31% 242ms 1.19% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.02% 69.33% 242ms 1.19% std::__cxx11::collate::do_transform 1ms 0.0049% 69.33% 236ms 1.16% ___vsnprintf 24ms 0.12% 69.45% 235ms 1.16% __printf_buffer 0 0% 69.45% 235ms 1.16% __vsnprintf_internal (inline) 72ms 0.35% 69.81% 231ms 1.14% std::_Rb_tree::_M_clone_node (inline) 31ms 0.15% 69.96% 229ms 1.13% AbstractTetrahedralElement::RefreshJacobian 8ms 0.039% 70.00% 228ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.00% 221ms 1.09% OffLatticeSimulation::ApplyBoundaries 1ms 0.0049% 70.00% 207ms 1.02% CellPropertyCollection::HasProperty 0 0% 70.00% 206ms 1.01% Cell::HasCellProperty (inline) 158ms 0.78% 70.78% 206ms 1.01% malloc_consolidate 148ms 0.73% 71.51% 203ms 1% AbstractElement::GetNodeGlobalIndex 8ms 0.039% 71.55% 200ms 0.98% __printf_fp_l_buffer 0 0% 71.55% 200ms 0.98% __printf_fp_spec (inline) 4ms 0.02% 71.57% 196ms 0.96% CellProliferativeTypesWriter::VisitCell 11ms 0.054% 71.62% 190ms 0.93% Element::MarkAsDeleted 91ms 0.45% 72.07% 188ms 0.92% __printf_fp_buffer_1 188ms 0.92% 72.99% 188ms 0.92% unlink_chunk 86ms 0.42% 73.42% 176ms 0.87% AbstractElement::GetNodeLocation 6ms 0.03% 73.45% 176ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 174ms 0.86% 74.30% 174ms 0.86% std::_Rb_tree_insert_and_rebalance 10ms 0.049% 74.35% 171ms 0.84% Cylindrical2dMesh::CreateMirrorNodes 14ms 0.069% 74.42% 160ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 159ms 0.78% 75.20% 159ms 0.78% AbstractCellMutationState::~AbstractCellMutationState 9ms 0.044% 75.25% 158ms 0.78% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 51ms 0.25% 75.50% 155ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 50ms 0.25% 75.74% 153ms 0.75% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 153ms 0.75% 76.50% 153ms 0.75% Node::GetIndex 148ms 0.73% 77.22% 148ms 0.73% incircle 148ms 0.73% 77.95% 148ms 0.73% std::vector::size (inline) 102ms 0.5% 78.45% 146ms 0.72% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 78.45% 145ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 44ms 0.22% 78.67% 144ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.015% 78.68% 144ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 89ms 0.44% 79.12% 144ms 0.71% std::_Rb_tree::equal_range (inline) 1ms 0.0049% 79.13% 141ms 0.69% OutputFileHandler::OpenOutputFile 35ms 0.17% 79.30% 141ms 0.69% TetrahedralMesh::EdgesEnd (partial-inline) 141ms 0.69% 79.99% 141ms 0.69% std::_Rb_tree_increment 140ms 0.69% 80.68% 140ms 0.69% [libchaste_crypt.so] 3ms 0.015% 80.70% 137ms 0.67% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.025% 80.72% 136ms 0.67% boost::numeric::ublas::vector_assign (inline) 6ms 0.03% 80.75% 135ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 131ms 0.64% 81.40% 131ms 0.64% std::type_info::name (inline) 0 0% 81.40% 129ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.02% 81.41% 128ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.41% 127ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 117ms 0.58% 81.99% 126ms 0.62% vertexsort 3ms 0.015% 82.01% 124ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 15ms 0.074% 82.08% 124ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.015% 82.09% 123ms 0.61% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0049% 82.10% 121ms 0.6% Cell::SetCellProliferativeType 33ms 0.16% 82.26% 115ms 0.57% boost::numeric::ublas::indexing_vector_assign 22ms 0.11% 82.37% 113ms 0.56% std::num_put::_M_insert_int 57ms 0.28% 82.65% 111ms 0.55% std::_Vector_base::_M_deallocate (inline) 8ms 0.039% 82.69% 109ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.0098% 82.70% 106ms 0.52% Element::~Element 0 0% 82.70% 105ms 0.52% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 75ms 0.37% 83.07% 104ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 104ms 0.51% 83.58% 104ms 0.51% boost::shared_ptr::operator-> (inline) 2ms 0.0098% 83.59% 102ms 0.5% std::vector::_M_default_append 0 0% 83.59% 102ms 0.5% std::vector::resize (inline)