File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16754ms, 86.03% of 19474ms total Dropped 787 nodes (cum <= 97.37ms) flat flat% sum% cum cum% 0 0% 0% 19430ms 99.77% __libc_start_call_main 0 0% 0% 19430ms 99.77% __libc_start_main_impl 0 0% 0% 19430ms 99.77% _start 0 0% 0% 19408ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19408ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19408ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19408ms 99.66% main 0 0% 0% 19367ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19367ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19367ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19340ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14777ms 75.88% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9283ms 47.67% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.031% 9183ms 47.16% Cell::ReadyToDivide 1ms 0.0051% 0.036% 9103ms 46.74% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.041% 8961ms 46.02% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.072% 0.11% 8954ms 45.98% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.12% 8936ms 45.89% CellCycleModelOdeHandler::SolveOdeToTime 41ms 0.21% 0.33% 8774ms 45.05% AbstractOneStepIvpOdeSolver::InternalSolve 1007ms 5.17% 5.50% 7882ms 40.47% RungeKutta4IvpOdeSolver::CalculateNextYValue 2780ms 14.28% 19.78% 6670ms 34.25% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.78% 5366ms 27.55% MeshBasedCellPopulation::Update 1ms 0.0051% 19.78% 4164ms 21.38% Cylindrical2dMesh::ReMesh 65ms 0.33% 20.11% 3880ms 19.92% AbstractCellProperty::IsType (inline) 0 0% 20.11% 2577ms 13.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 358ms 1.84% 21.95% 2489ms 12.78% AbstractCellProperty::IsSame 1ms 0.0051% 21.96% 2328ms 11.95% MutableMesh::ReMesh 2ms 0.01% 21.97% 2265ms 11.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.036% 22.00% 2212ms 11.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 212ms 1.09% 23.09% 2131ms 10.94% std::type_info::operator== (inline) 2038ms 10.47% 33.56% 2038ms 10.47% __strcmp_avx2 0 0% 33.56% 1981ms 10.17% AbstractCellPopulation::WriteResultsToFiles 824ms 4.23% 37.79% 1896ms 9.74% std::_Rb_tree::_M_lower_bound (inline) 163ms 0.84% 38.63% 1715ms 8.81% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.34% 38.96% 1386ms 7.12% std::_Rb_tree::find (inline) 14ms 0.072% 39.04% 1172ms 6.02% TetrahedralMesh::ImportFromMesher 1ms 0.0051% 39.04% 1169ms 6.00% MeshBasedCellPopulation::UpdateNodePairs 13ms 0.067% 39.11% 1142ms 5.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 46ms 0.24% 39.34% 1060ms 5.44% operator new 20ms 0.1% 39.45% 1044ms 5.36% MeshBasedCellPopulation::SpringIterator::operator++ 270ms 1.39% 40.83% 1004ms 5.16% __GI___libc_malloc 12ms 0.062% 40.90% 979ms 5.03% std::set::insert (inline) 4ms 0.021% 40.92% 967ms 4.97% std::_Rb_tree::_M_insert_unique 34ms 0.17% 41.09% 902ms 4.63% std::__new_allocator::allocate (inline) 0 0% 41.09% 898ms 4.61% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.10% 879ms 4.51% triangulate 0 0% 41.10% 857ms 4.40% std::set::count (inline) 0 0% 41.10% 789ms 4.05% delaunay 2ms 0.01% 41.11% 789ms 4.05% divconqdelaunay 62ms 0.32% 41.42% 759ms 3.90% std::map::operator[] (partial-inline) 1ms 0.0051% 41.43% 743ms 3.82% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.026% 41.46% 742ms 3.81% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 721ms 3.70% 45.16% 721ms 3.70% WntCellCycleOdeSystem::CalculateStoppingEvent 711ms 3.65% 48.81% 711ms 3.65% std::_Rb_tree::_S_right (inline) 8ms 0.041% 48.85% 705ms 3.62% CellPopulationElementWriter::Visit 22ms 0.11% 48.96% 660ms 3.39% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 20ms 0.1% 49.07% 653ms 3.35% AbstractCellPopulation::GetCellUsingLocationIndex 359ms 1.84% 50.91% 643ms 3.30% _int_malloc 187ms 0.96% 51.87% 641ms 3.29% __dynamic_cast 14ms 0.072% 51.94% 628ms 3.22% std::less::operator() (inline) 614ms 3.15% 55.09% 614ms 3.15% std::operator< (inline) 0 0% 55.09% 600ms 3.08% std::_Rb_tree::_M_create_node (inline) 13ms 0.067% 55.16% 596ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.16% 589ms 3.02% std::_Rb_tree::lower_bound (inline) 0 0% 55.16% 589ms 3.02% std::map::lower_bound (inline) 13ms 0.067% 55.23% 587ms 3.01% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.23% 579ms 2.97% std::_Rb_tree::_M_get_node (inline) 32ms 0.16% 55.39% 579ms 2.97% std::_Rb_tree::_M_insert_ (inline) 10ms 0.051% 55.44% 562ms 2.89% Element::Element 0 0% 55.44% 533ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.44% 526ms 2.70% std::map::find (inline) 12ms 0.062% 55.50% 518ms 2.66% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.051% 55.56% 506ms 2.60% MutableMesh::ReIndex 11ms 0.056% 55.61% 496ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.0051% 55.62% 473ms 2.43% AbstractCellProperty::IsSubType (inline) 2ms 0.01% 55.63% 469ms 2.41% std::ostream::operator<< (inline) 6ms 0.031% 55.66% 466ms 2.39% Element::RegisterWithNodes (inline) 58ms 0.3% 55.96% 466ms 2.39% std::ostream::_M_insert 134ms 0.69% 56.64% 459ms 2.36% __GI___libc_free 9ms 0.046% 56.69% 452ms 2.32% Node::AddElement 302ms 1.55% 58.24% 436ms 2.24% AbstractCellMutationState::AbstractCellMutationState 12ms 0.062% 58.30% 408ms 2.10% std::_Rb_tree::erase 0 0% 58.30% 408ms 2.10% std::set::erase (inline) 12ms 0.062% 58.36% 401ms 2.06% Node::RemoveElement 150ms 0.77% 59.14% 384ms 1.97% std::_Rb_tree::_M_get_insert_unique_pos 12ms 0.062% 59.20% 378ms 1.94% std::__new_allocator::deallocate (inline) 0 0% 59.20% 375ms 1.93% std::allocator_traits::deallocate (inline) 115ms 0.59% 59.79% 373ms 1.92% std::_Rb_tree::_M_erase 10ms 0.051% 59.84% 366ms 1.88% divconqrecurse 28ms 0.14% 59.98% 354ms 1.82% std::_Rb_tree::~_Rb_tree (inline) 95ms 0.49% 60.47% 346ms 1.78% mergehulls 2ms 0.01% 60.48% 338ms 1.74% Cell::GetMutationState 21ms 0.11% 60.59% 338ms 1.74% Element::ResetIndex 6ms 0.031% 60.62% 330ms 1.69% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 60.62% 330ms 1.69% std::set::~set (inline) 0 0% 60.62% 327ms 1.68% std::_Rb_tree::_M_drop_node (inline) 325ms 1.67% 62.29% 325ms 1.67% [libchaste_cell_based.so] 265ms 1.36% 63.65% 325ms 1.67% _int_free 160ms 0.82% 64.47% 324ms 1.66% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0051% 64.48% 320ms 1.64% std::_Vector_base::_M_allocate (inline) 5ms 0.026% 64.50% 319ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 310ms 1.59% 66.09% 312ms 1.60% std::vector::operator[] (inline) 0 0% 66.09% 299ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0051% 66.10% 299ms 1.54% Cell::GetCellProliferativeType 1ms 0.0051% 66.10% 299ms 1.54% NodeLocationWriter::Visit 0 0% 66.10% 295ms 1.51% std::_Rb_tree::_M_put_node (inline) 4ms 0.021% 66.12% 292ms 1.50% alternateaxes 26ms 0.13% 66.26% 291ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 275ms 1.41% 67.67% 288ms 1.48% vertexmedian 3ms 0.015% 67.69% 270ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 24ms 0.12% 67.81% 267ms 1.37% AbstractTetrahedralElement::CalculateJacobian 15ms 0.077% 67.89% 267ms 1.37% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.046% 67.93% 266ms 1.37% std::vector::push_back (inline) 32ms 0.16% 68.10% 263ms 1.35% std::num_put::_M_insert_float 91ms 0.47% 68.56% 255ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 5ms 0.026% 68.59% 251ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.072% 68.66% 248ms 1.27% std::vector::_M_realloc_insert 6ms 0.031% 68.69% 246ms 1.26% std::set::set (inline) 96ms 0.49% 69.18% 241ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.18% 240ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.082% 69.27% 237ms 1.22% Element::MarkAsDeleted 14ms 0.072% 69.34% 236ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 16ms 0.082% 69.42% 234ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 69.43% 232ms 1.19% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 69.44% 229ms 1.18% AbstractCentreBasedCellPopulation::GetDampingConstant 61ms 0.31% 69.75% 228ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 169ms 0.87% 70.62% 224ms 1.15% AbstractElement::GetNodeGlobalIndex 1ms 0.0051% 70.63% 222ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 11ms 0.056% 70.68% 212ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.072% 70.76% 212ms 1.09% TetrahedralMesh::Clear 21ms 0.11% 70.86% 207ms 1.06% std::_Rb_tree::_M_copy (inline) 6ms 0.031% 70.89% 202ms 1.04% AbstractTetrahedralElement::AbstractTetrahedralElement 32ms 0.16% 71.06% 201ms 1.03% AbstractTetrahedralElement::RefreshJacobian 0 0% 71.06% 188ms 0.97% OffLatticeSimulation::ApplyBoundaries 56ms 0.29% 71.35% 184ms 0.94% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.35% 184ms 0.94% std::__cxx11::collate::do_transform 178ms 0.91% 72.26% 178ms 0.91% Node::GetIndex 121ms 0.62% 72.88% 177ms 0.91% malloc_consolidate 2ms 0.01% 72.89% 176ms 0.9% ___vsnprintf 1ms 0.0051% 72.90% 174ms 0.89% __vsnprintf_internal (inline) 25ms 0.13% 73.03% 171ms 0.88% __printf_buffer 106ms 0.54% 73.57% 168ms 0.86% std::_Rb_tree::equal_range (inline) 166ms 0.85% 74.42% 166ms 0.85% std::_Rb_tree_insert_and_rebalance 165ms 0.85% 75.27% 165ms 0.85% unlink_chunk 5ms 0.026% 75.30% 161ms 0.83% CellProliferativeTypesWriter::VisitCell 4ms 0.021% 75.32% 157ms 0.81% CellPropertyCollection::HasProperty 0 0% 75.32% 154ms 0.79% Cell::HasCellProperty (inline) 154ms 0.79% 76.11% 154ms 0.79% [libchaste_crypt.so] 41ms 0.21% 76.32% 151ms 0.78% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 63ms 0.32% 76.64% 150ms 0.77% AbstractElement::GetNodeLocation 146ms 0.75% 77.39% 146ms 0.75% incircle 146ms 0.75% 78.14% 146ms 0.75% std::vector::size (inline) 6ms 0.031% 78.17% 145ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 142ms 0.73% 78.90% 142ms 0.73% AbstractCellMutationState::~AbstractCellMutationState 141ms 0.72% 79.62% 141ms 0.72% std::type_info::name (inline) 7ms 0.036% 79.66% 140ms 0.72% __printf_fp_l_buffer 0 0% 79.66% 140ms 0.72% __printf_fp_spec (inline) 92ms 0.47% 80.13% 139ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.01% 80.14% 138ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 8ms 0.041% 80.18% 135ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.031% 80.21% 132ms 0.68% Node::~Node 47ms 0.24% 80.46% 131ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 24ms 0.12% 80.58% 131ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 55ms 0.28% 80.86% 131ms 0.67% __printf_fp_buffer_1 9ms 0.046% 80.91% 131ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.91% 125ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 80.91% 125ms 0.64% boost::numeric::ublas::vector_assign (inline) 41ms 0.21% 81.12% 123ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 11ms 0.056% 81.17% 123ms 0.63% boost::detail::shared_count::~shared_count (inline) 0 0% 81.17% 123ms 0.63% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 81.19% 119ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 9ms 0.046% 81.24% 118ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 105ms 0.54% 81.78% 117ms 0.6% vertexsort 2ms 0.01% 81.79% 111ms 0.57% Cell::SetCellProliferativeType 1ms 0.0051% 81.79% 108ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 30ms 0.15% 81.95% 108ms 0.55% std::__ostream_insert 107ms 0.55% 82.49% 107ms 0.55% TetrahedralMesh::EdgeIterator::operator!= 99ms 0.51% 83.00% 107ms 0.55% boost::detail::sp_counted_base::release 107ms 0.55% 83.55% 107ms 0.55% std::_Rb_tree_rebalance_for_erase 65ms 0.33% 83.89% 106ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator 20ms 0.1% 83.99% 105ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 35ms 0.18% 84.17% 104ms 0.53% boost::numeric::ublas::indexing_vector_assign 50ms 0.26% 84.43% 103ms 0.53% std::basic_filebuf::xsputn 22ms 0.11% 84.54% 102ms 0.52% std::_Vector_base::_M_deallocate (inline) 3ms 0.015% 84.55% 101ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 81ms 0.42% 84.97% 101ms 0.52% TimeStepper::AdvanceOneTimeStep 101ms 0.52% 85.49% 101ms 0.52% counterclockwise 100ms 0.51% 86.00% 100ms 0.51% boost::shared_ptr::operator-> (inline) 6ms 0.031% 86.03% 99ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline)