File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16977ms, 83.93% of 20227ms total Dropped 822 nodes (cum <= 101.14ms) flat flat% sum% cum cum% 0 0% 0% 20182ms 99.78% __libc_start_call_main 0 0% 0% 20182ms 99.78% __libc_start_main_impl 0 0% 0% 20182ms 99.78% _start 0 0% 0% 20163ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20163ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20163ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20163ms 99.68% main 0 0% 0% 20122ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20122ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20122ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20095ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15555ms 76.90% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0099% 0.0099% 10197ms 50.41% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.035% 10089ms 49.88% Cell::ReadyToDivide 8ms 0.04% 0.074% 10012ms 49.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0049% 0.079% 9867ms 48.78% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.054% 0.13% 9858ms 48.74% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.025% 0.16% 9838ms 48.64% CellCycleModelOdeHandler::SolveOdeToTime 69ms 0.34% 0.5% 9645ms 47.68% AbstractOneStepIvpOdeSolver::InternalSolve 882ms 4.36% 4.86% 8837ms 43.69% RungeKutta4IvpOdeSolver::CalculateNextYValue 3362ms 16.62% 21.48% 7736ms 38.25% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 21.49% 5257ms 25.99% MeshBasedCellPopulation::Update 159ms 0.79% 22.27% 4427ms 21.89% AbstractCellProperty::IsType (inline) 4ms 0.02% 22.29% 4119ms 20.36% Cylindrical2dMesh::ReMesh 560ms 2.77% 25.06% 3187ms 15.76% AbstractCellProperty::IsSame 381ms 1.88% 26.94% 2627ms 12.99% std::type_info::operator== (inline) 0 0% 26.94% 2512ms 12.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.015% 26.96% 2284ms 11.29% MutableMesh::ReMesh 0 0% 26.96% 2203ms 10.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 2197ms 10.86% 37.82% 2197ms 10.86% __strcmp_avx2 8ms 0.04% 37.86% 2155ms 10.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0049% 37.87% 2019ms 9.98% AbstractCellPopulation::WriteResultsToFiles 741ms 3.66% 41.53% 1803ms 8.91% std::_Rb_tree::_M_lower_bound (inline) 136ms 0.67% 42.20% 1623ms 8.02% TetrahedralMesh::EdgeIterator::operator++ 55ms 0.27% 42.47% 1327ms 6.56% std::_Rb_tree::find (inline) 12ms 0.059% 42.53% 1176ms 5.81% TetrahedralMesh::ImportFromMesher 47ms 0.23% 42.76% 1116ms 5.52% operator new 2ms 0.0099% 42.77% 1099ms 5.43% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 42.77% 1091ms 5.39% MeshBasedCellPopulation::UpdateNodePairs 240ms 1.19% 43.96% 1061ms 5.25% __GI___libc_malloc 4ms 0.02% 43.98% 1012ms 5.00% std::set::insert (inline) 10ms 0.049% 44.03% 1008ms 4.98% std::_Rb_tree::_M_insert_unique 43ms 0.21% 44.24% 970ms 4.80% std::__new_allocator::allocate (inline) 0 0% 44.24% 962ms 4.76% std::allocator_traits::allocate (inline) 5ms 0.025% 44.27% 941ms 4.65% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0049% 44.27% 841ms 4.16% triangulate 0 0% 44.27% 800ms 3.96% std::set::count (inline) 1ms 0.0049% 44.28% 754ms 3.73% delaunay 6ms 0.03% 44.31% 751ms 3.71% divconqdelaunay 3ms 0.015% 44.32% 741ms 3.66% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.015% 44.34% 726ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 409ms 2.02% 46.36% 721ms 3.56% _int_malloc 7ms 0.035% 46.39% 719ms 3.55% CellPopulationElementWriter::Visit 707ms 3.50% 49.89% 707ms 3.50% std::_Rb_tree::_S_right (inline) 61ms 0.3% 50.19% 690ms 3.41% std::map::operator[] (partial-inline) 212ms 1.05% 51.24% 652ms 3.22% __dynamic_cast 17ms 0.084% 51.32% 635ms 3.14% std::less::operator() (inline) 0 0% 51.32% 629ms 3.11% std::_Rb_tree::_M_create_node (inline) 618ms 3.06% 54.38% 625ms 3.09% WntCellCycleOdeSystem::CalculateStoppingEvent 9ms 0.044% 54.42% 618ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 18ms 0.089% 54.51% 618ms 3.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 618ms 3.06% 57.57% 618ms 3.06% std::operator< (inline) 22ms 0.11% 57.68% 617ms 3.05% std::_Rb_tree::_M_insert_ (inline) 20ms 0.099% 57.77% 612ms 3.03% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.77% 600ms 2.97% std::_Rb_tree::_M_get_node (inline) 1ms 0.0049% 57.78% 591ms 2.92% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.78% 569ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 57.80% 558ms 2.76% Element::Element 0 0% 57.80% 538ms 2.66% std::_Rb_tree::lower_bound (inline) 0 0% 57.80% 538ms 2.66% std::map::lower_bound (inline) 2ms 0.0099% 57.81% 535ms 2.64% std::ostream::operator<< (inline) 81ms 0.4% 58.21% 532ms 2.63% std::ostream::_M_insert 0 0% 58.21% 524ms 2.59% std::map::find (inline) 9ms 0.044% 58.25% 523ms 2.59% MutableMesh::ReIndex 380ms 1.88% 60.13% 520ms 2.57% AbstractCellMutationState::AbstractCellMutationState 12ms 0.059% 60.19% 501ms 2.48% Element::RegisterWithNodes (inline) 9ms 0.044% 60.24% 497ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 60.25% 492ms 2.43% AbstractCellProperty::IsSubType (inline) 12ms 0.059% 60.31% 490ms 2.42% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.064% 60.37% 483ms 2.39% Node::AddElement 161ms 0.8% 61.17% 444ms 2.20% __GI___libc_free 15ms 0.074% 61.24% 382ms 1.89% divconqrecurse 136ms 0.67% 61.92% 382ms 1.89% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.054% 61.97% 375ms 1.85% std::_Rb_tree::erase 1ms 0.0049% 61.98% 375ms 1.85% std::set::erase (inline) 121ms 0.6% 62.57% 373ms 1.84% std::_Rb_tree::_M_erase 12ms 0.059% 62.63% 368ms 1.82% Node::RemoveElement 3ms 0.015% 62.65% 365ms 1.80% std::_Vector_base::_M_allocate (inline) 102ms 0.5% 63.15% 359ms 1.77% mergehulls 2ms 0.0099% 63.16% 351ms 1.74% Cell::GetMutationState 35ms 0.17% 63.34% 351ms 1.74% Element::ResetIndex 24ms 0.12% 63.45% 346ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.044% 63.50% 342ms 1.69% std::__new_allocator::deallocate (inline) 0 0% 63.50% 336ms 1.66% std::allocator_traits::deallocate (inline) 330ms 1.63% 65.13% 330ms 1.63% std::type_info::name (inline) 3ms 0.015% 65.15% 319ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 65.15% 319ms 1.58% std::set::~set (inline) 11ms 0.054% 65.20% 316ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 12ms 0.059% 65.26% 313ms 1.55% Cell::GetCellProliferativeType 4ms 0.02% 65.28% 312ms 1.54% NodeLocationWriter::Visit 153ms 0.76% 66.04% 312ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.04% 304ms 1.50% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0049% 66.04% 287ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 39ms 0.19% 66.23% 285ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 218ms 1.08% 67.31% 281ms 1.39% _int_free 22ms 0.11% 67.42% 276ms 1.36% std::num_put::_M_insert_float 4ms 0.02% 67.44% 269ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.44% 268ms 1.32% std::_Rb_tree::_M_put_node (inline) 15ms 0.074% 67.51% 262ms 1.30% AbstractTetrahedralElement::CalculateJacobian 35ms 0.17% 67.69% 258ms 1.28% TetrahedralMesh::Clear 14ms 0.069% 67.76% 258ms 1.28% std::_Rb_tree::_Rb_tree 252ms 1.25% 69.00% 255ms 1.26% std::vector::operator[] (inline) 251ms 1.24% 70.24% 251ms 1.24% [libchaste_cell_based.so] 1ms 0.0049% 70.25% 250ms 1.24% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0049% 70.25% 247ms 1.22% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0049% 70.26% 245ms 1.21% std::set::set (inline) 9ms 0.044% 70.30% 245ms 1.21% std::vector::push_back (inline) 3ms 0.015% 70.32% 244ms 1.21% alternateaxes 226ms 1.12% 71.43% 240ms 1.19% vertexmedian 5ms 0.025% 71.46% 235ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 71.46% 235ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.054% 71.51% 232ms 1.15% std::vector::_M_realloc_insert 47ms 0.23% 71.75% 229ms 1.13% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 18ms 0.089% 71.83% 225ms 1.11% std::_Rb_tree::_M_copy (inline) 8ms 0.04% 71.87% 222ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.04% 71.91% 217ms 1.07% std::_Rb_tree::_M_erase_aux (inline) 57ms 0.28% 72.20% 213ms 1.05% ApcOneHitCellMutationState::ApcOneHitCellMutationState 34ms 0.17% 72.36% 212ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 3ms 0.015% 72.38% 211ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0099% 72.39% 210ms 1.04% std::__cxx11::collate::do_transform 152ms 0.75% 73.14% 205ms 1.01% AbstractElement::GetNodeGlobalIndex 68ms 0.34% 73.48% 204ms 1.01% std::_Rb_tree::_M_clone_node (inline) 8ms 0.04% 73.52% 201ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 23ms 0.11% 73.63% 201ms 0.99% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0099% 73.64% 201ms 0.99% ___vsnprintf 0 0% 73.64% 199ms 0.98% __vsnprintf_internal (inline) 16ms 0.079% 73.72% 198ms 0.98% __printf_buffer 1ms 0.0049% 73.72% 196ms 0.97% OffLatticeSimulation::ApplyBoundaries 13ms 0.064% 73.79% 193ms 0.95% Element::MarkAsDeleted 135ms 0.67% 74.45% 188ms 0.93% malloc_consolidate 6ms 0.03% 74.48% 186ms 0.92% CellProliferativeTypesWriter::VisitCell 179ms 0.88% 75.37% 179ms 0.88% std::_Rb_tree_insert_and_rebalance 4ms 0.02% 75.39% 169ms 0.84% CellPropertyCollection::HasProperty 5ms 0.025% 75.41% 168ms 0.83% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 75.41% 167ms 0.83% Cell::HasCellProperty (inline) 7ms 0.035% 75.45% 166ms 0.82% __printf_fp_l_buffer 0 0% 75.45% 166ms 0.82% __printf_fp_spec (inline) 165ms 0.82% 76.26% 165ms 0.82% unlink_chunk 161ms 0.8% 77.06% 161ms 0.8% incircle 103ms 0.51% 77.57% 157ms 0.78% std::_Rb_tree::equal_range (inline) 80ms 0.4% 77.97% 156ms 0.77% __printf_fp_buffer_1 30ms 0.15% 78.11% 155ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 56ms 0.28% 78.39% 153ms 0.76% AbstractElement::GetNodeLocation 153ms 0.76% 79.15% 153ms 0.76% Node::GetIndex 7ms 0.035% 79.18% 151ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 15ms 0.074% 79.26% 141ms 0.7% Node::~Node 138ms 0.68% 79.94% 138ms 0.68% std::vector::size (inline) 4ms 0.02% 79.96% 136ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 31ms 0.15% 80.11% 136ms 0.67% std::num_put::_M_insert_int 10ms 0.049% 80.16% 132ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 132ms 0.65% 80.81% 132ms 0.65% std::_Rb_tree_increment 17ms 0.084% 80.90% 131ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 80.90% 131ms 0.65% boost::numeric::ublas::vector_assign (inline) 1ms 0.0049% 80.90% 130ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 55ms 0.27% 81.17% 127ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 122ms 0.6% 81.78% 122ms 0.6% boost::shared_ptr::operator-> (inline) 45ms 0.22% 82.00% 113ms 0.56% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 67ms 0.33% 82.33% 113ms 0.56% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.049% 82.38% 113ms 0.56% boost::detail::shared_count::~shared_count (inline) 0 0% 82.38% 113ms 0.56% boost::shared_ptr::~shared_ptr (inline) 7ms 0.035% 82.41% 110ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 102ms 0.5% 82.92% 110ms 0.54% vertexsort 1ms 0.0049% 82.92% 109ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 93ms 0.46% 83.38% 109ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0049% 83.39% 109ms 0.54% std::vector::resize (inline) 1ms 0.0049% 83.39% 108ms 0.53% std::vector::_M_default_append 0 0% 83.39% 107ms 0.53% Cell::SetCellProliferativeType 6ms 0.03% 83.42% 104ms 0.51% MeshBasedCellPopulation::SpringsEnd (inline) 103ms 0.51% 83.93% 103ms 0.51% [libchaste_mesh.so]