File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17186ms, 85.35% of 20136ms total Dropped 844 nodes (cum <= 100.68ms) flat flat% sum% cum cum% 0 0% 0% 20084ms 99.74% __libc_start_call_main 0 0% 0% 20084ms 99.74% __libc_start_main_impl 0 0% 0% 20084ms 99.74% _start 0 0% 0% 20060ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20060ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20060ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20060ms 99.62% main 0 0% 0% 20013ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20013ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20013ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19985ms 99.25% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15161ms 75.29% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.0099% 9434ms 46.85% AbstractCellBasedSimulation::DoCellBirth 8ms 0.04% 0.05% 9345ms 46.41% Cell::ReadyToDivide 4ms 0.02% 0.07% 9221ms 45.79% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.07% 9083ms 45.11% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.13% 9068ms 45.03% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.15% 9054ms 44.96% CellCycleModelOdeHandler::SolveOdeToTime 65ms 0.32% 0.47% 8808ms 43.74% AbstractOneStepIvpOdeSolver::InternalSolve 995ms 4.94% 5.41% 7901ms 39.24% RungeKutta4IvpOdeSolver::CalculateNextYValue 2809ms 13.95% 19.36% 6743ms 33.49% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 19.37% 5609ms 27.86% MeshBasedCellPopulation::Update 3ms 0.015% 19.38% 4407ms 21.89% Cylindrical2dMesh::ReMesh 67ms 0.33% 19.72% 3955ms 19.64% AbstractCellProperty::IsType (inline) 1ms 0.005% 19.72% 2719ms 13.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 359ms 1.78% 21.50% 2571ms 12.77% AbstractCellProperty::IsSame 0 0% 21.50% 2476ms 12.30% MutableMesh::ReMesh 1ms 0.005% 21.51% 2376ms 11.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.04% 21.55% 2327ms 11.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 269ms 1.34% 22.88% 2212ms 10.99% std::type_info::operator== (inline) 0 0% 22.88% 2096ms 10.41% AbstractCellPopulation::WriteResultsToFiles 2061ms 10.24% 33.12% 2061ms 10.24% __strcmp_avx2 840ms 4.17% 37.29% 1899ms 9.43% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.78% 38.08% 1697ms 8.43% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.31% 38.38% 1408ms 6.99% std::_Rb_tree::find (inline) 13ms 0.065% 38.45% 1251ms 6.21% TetrahedralMesh::ImportFromMesher 0 0% 38.45% 1169ms 5.81% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.05% 38.50% 1129ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 45ms 0.22% 38.72% 1086ms 5.39% operator new 11ms 0.055% 38.78% 1041ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 222ms 1.10% 39.88% 1037ms 5.15% __GI___libc_malloc 9ms 0.045% 39.92% 955ms 4.74% std::set::insert (inline) 13ms 0.065% 39.99% 946ms 4.70% std::_Rb_tree::_M_insert_unique 33ms 0.16% 40.15% 937ms 4.65% std::__new_allocator::allocate (inline) 0 0% 40.15% 935ms 4.64% std::allocator_traits::allocate (inline) 1ms 0.005% 40.16% 898ms 4.46% triangulate 0 0% 40.16% 856ms 4.25% std::set::count (inline) 0 0% 40.16% 824ms 4.09% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.02% 40.18% 823ms 4.09% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 40.18% 815ms 4.05% delaunay 7ms 0.035% 40.21% 812ms 4.03% divconqdelaunay 735ms 3.65% 43.86% 735ms 3.65% WntCellCycleOdeSystem::CalculateStoppingEvent 399ms 1.98% 45.84% 734ms 3.65% _int_malloc 277ms 1.38% 47.22% 732ms 3.64% __dynamic_cast 18ms 0.089% 47.31% 731ms 3.63% CellPropertyCollection::GetPropertiesType (inline) 51ms 0.25% 47.56% 728ms 3.62% std::map::operator[] (partial-inline) 726ms 3.61% 51.17% 726ms 3.61% std::_Rb_tree::_S_right (inline) 15ms 0.074% 51.24% 719ms 3.57% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.03% 51.27% 708ms 3.52% CellPopulationElementWriter::Visit 20ms 0.099% 51.37% 659ms 3.27% std::less::operator() (inline) 1ms 0.005% 51.38% 650ms 3.23% MeshBasedCellPopulation::AcceptCellWriter 19ms 0.094% 51.47% 649ms 3.22% AbstractCellPopulation::GetCellUsingLocationIndex 639ms 3.17% 54.64% 639ms 3.17% std::operator< (inline) 0 0% 54.64% 602ms 2.99% std::_Rb_tree::_M_create_node (inline) 0 0% 54.64% 571ms 2.84% std::_Rb_tree::_M_get_node (inline) 0 0% 54.64% 567ms 2.82% std::_Rb_tree::lower_bound (inline) 0 0% 54.64% 567ms 2.82% std::map::lower_bound (inline) 9ms 0.045% 54.69% 556ms 2.76% Element::Element 2ms 0.0099% 54.70% 552ms 2.74% AbstractCellProperty::IsSubType (inline) 0 0% 54.70% 546ms 2.71% std::map::find (inline) 36ms 0.18% 54.88% 541ms 2.69% std::_Rb_tree::_M_insert_ (inline) 0 0% 54.88% 533ms 2.65% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.055% 54.93% 527ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 173ms 0.86% 55.79% 516ms 2.56% __GI___libc_free 6ms 0.03% 55.82% 512ms 2.54% MutableMesh::ReIndex 3ms 0.015% 55.84% 501ms 2.49% std::ostream::operator<< (inline) 90ms 0.45% 56.28% 496ms 2.46% std::ostream::_M_insert 11ms 0.055% 56.34% 475ms 2.36% Cylindrical2dMesh::CorrectNonPeriodicMesh 138ms 0.69% 57.02% 456ms 2.26% std::_Rb_tree::_M_erase 10ms 0.05% 57.07% 453ms 2.25% Element::RegisterWithNodes (inline) 9ms 0.045% 57.12% 440ms 2.19% Node::AddElement 18ms 0.089% 57.21% 425ms 2.11% std::__new_allocator::deallocate (inline) 2ms 0.0099% 57.22% 422ms 2.10% std::_Rb_tree::erase 1ms 0.005% 57.22% 421ms 2.09% std::set::erase (inline) 13ms 0.065% 57.29% 420ms 2.09% Node::RemoveElement 3ms 0.015% 57.30% 419ms 2.08% Cell::GetMutationState 0 0% 57.30% 419ms 2.08% std::allocator_traits::deallocate (inline) 283ms 1.41% 58.71% 417ms 2.07% AbstractCellMutationState::AbstractCellMutationState 34ms 0.17% 58.87% 414ms 2.06% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.065% 58.94% 405ms 2.01% divconqrecurse 141ms 0.7% 59.64% 392ms 1.95% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 59.64% 390ms 1.94% std::_Rb_tree::_M_drop_node (inline) 111ms 0.55% 60.19% 387ms 1.92% mergehulls 0 0% 60.19% 383ms 1.90% std::set::~set (inline) 2ms 0.0099% 60.20% 366ms 1.82% std::_Vector_base::_M_allocate (inline) 5ms 0.025% 60.23% 363ms 1.80% Cell::GetCellProliferativeType 0 0% 60.23% 348ms 1.73% std::_Rb_tree::_M_put_node (inline) 346ms 1.72% 61.94% 346ms 1.72% [libchaste_cell_based.so] 279ms 1.39% 63.33% 342ms 1.70% _int_free 41ms 0.2% 63.53% 334ms 1.66% TetrahedralMesh::Clear 151ms 0.75% 64.28% 332ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.089% 64.37% 323ms 1.60% Element::ResetIndex 1ms 0.005% 64.38% 311ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 9ms 0.045% 64.42% 309ms 1.53% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.005% 64.43% 304ms 1.51% TetrahedralMesh::RefreshJacobianCachedData 21ms 0.1% 64.53% 303ms 1.50% AbstractTetrahedralElement::CalculateJacobian 3ms 0.015% 64.55% 298ms 1.48% NodeLocationWriter::Visit 13ms 0.065% 64.61% 296ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.074% 64.69% 296ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 64.69% 290ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 48ms 0.24% 64.92% 287ms 1.43% AbstractCellPopulation::Iterator::IsRealCell 11ms 0.055% 64.98% 279ms 1.39% std::vector::push_back (inline) 0 0% 64.98% 277ms 1.38% MeshBasedCellPopulation::GetDampingConstant 1ms 0.005% 64.98% 276ms 1.37% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.025% 65.01% 271ms 1.35% alternateaxes 15ms 0.074% 65.08% 267ms 1.33% std::_Rb_tree::_M_erase_aux (inline) 251ms 1.25% 66.33% 266ms 1.32% vertexmedian 3ms 0.015% 66.34% 264ms 1.31% std::set::set (inline) 263ms 1.31% 67.65% 264ms 1.31% std::vector::operator[] (inline) 18ms 0.089% 67.74% 259ms 1.29% std::num_put::_M_insert_float 6ms 0.03% 67.77% 258ms 1.28% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.074% 67.84% 254ms 1.26% std::vector::_M_realloc_insert 97ms 0.48% 68.33% 249ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 22ms 0.11% 68.43% 249ms 1.24% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 68.46% 246ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.05% 68.51% 239ms 1.19% Element::MarkAsDeleted 61ms 0.3% 68.81% 230ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 32ms 0.16% 68.97% 226ms 1.12% AbstractTetrahedralElement::RefreshJacobian 96ms 0.48% 69.45% 226ms 1.12% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.05% 69.50% 224ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.03% 69.53% 224ms 1.11% CellProliferativeTypesWriter::VisitCell 66ms 0.33% 69.85% 223ms 1.11% std::_Rb_tree::_M_clone_node (inline) 0 0% 69.85% 219ms 1.09% OffLatticeSimulation::ApplyBoundaries 2ms 0.0099% 69.86% 210ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0099% 69.87% 209ms 1.04% CellPropertyCollection::HasProperty 0 0% 69.87% 207ms 1.03% Cell::HasCellProperty (inline) 7ms 0.035% 69.91% 204ms 1.01% AbstractTetrahedralElement::AbstractTetrahedralElement 146ms 0.73% 70.63% 201ms 1% AbstractElement::GetNodeGlobalIndex 142ms 0.71% 71.34% 200ms 0.99% malloc_consolidate 3ms 0.015% 71.35% 200ms 0.99% std::__cxx11::collate::do_transform 7ms 0.035% 71.39% 195ms 0.97% Node::~Node 18ms 0.089% 71.48% 195ms 0.97% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 193ms 0.96% 72.44% 193ms 0.96% unlink_chunk 0 0% 72.44% 189ms 0.94% ___vsnprintf 0 0% 72.44% 189ms 0.94% __vsnprintf_internal (inline) 18ms 0.089% 72.53% 188ms 0.93% __printf_buffer 179ms 0.89% 73.42% 179ms 0.89% incircle 178ms 0.88% 74.30% 178ms 0.88% Node::GetIndex 76ms 0.38% 74.68% 169ms 0.84% AbstractElement::GetNodeLocation 3ms 0.015% 74.69% 162ms 0.8% __printf_fp_l_buffer 0 0% 74.69% 162ms 0.8% __printf_fp_spec (inline) 100ms 0.5% 75.19% 162ms 0.8% std::_Rb_tree::equal_range (inline) 160ms 0.79% 75.98% 160ms 0.79% [libchaste_crypt.so] 160ms 0.79% 76.78% 160ms 0.79% std::_Rb_tree_increment 8ms 0.04% 76.82% 158ms 0.78% std::_Rb_tree_const_iterator::operator++ (inline) 155ms 0.77% 77.59% 155ms 0.77% std::type_info::name (inline) 6ms 0.03% 77.62% 154ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 57ms 0.28% 77.90% 153ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 89ms 0.44% 78.34% 153ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.0099% 78.35% 153ms 0.76% boost::numeric::ublas::vector_assign (inline) 152ms 0.75% 79.11% 152ms 0.75% std::_Rb_tree_insert_and_rebalance 19ms 0.094% 79.20% 150ms 0.74% boost::numeric::ublas::c_vector::c_vector (inline) 65ms 0.32% 79.52% 146ms 0.73% __printf_fp_buffer_1 142ms 0.71% 80.23% 142ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 141ms 0.7% 80.93% 141ms 0.7% std::vector::size (inline) 40ms 0.2% 81.13% 139ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 41ms 0.2% 81.33% 139ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.025% 81.36% 134ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.099% 81.46% 133ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 81.46% 133ms 0.66% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 81.47% 131ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 32ms 0.16% 81.63% 127ms 0.63% boost::numeric::ublas::indexing_vector_assign 120ms 0.6% 82.23% 124ms 0.62% vertexsort 5ms 0.025% 82.25% 118ms 0.59% Cylindrical2dMesh::CreateMirrorNodes 18ms 0.089% 82.34% 117ms 0.58% TetrahedralMesh::EdgesEnd 116ms 0.58% 82.92% 116ms 0.58% TetrahedralMesh::EdgeIterator::operator!= 0 0% 82.92% 115ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.02% 82.94% 112ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 112ms 0.56% 83.49% 112ms 0.56% boost::shared_ptr::operator-> (inline) 2ms 0.0099% 83.50% 110ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.50% 109ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.5% 84.00% 108ms 0.54% boost::detail::sp_counted_base::release 108ms 0.54% 84.54% 108ms 0.54% std::_Rb_tree_rebalance_for_erase 3ms 0.015% 84.56% 107ms 0.53% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 20ms 0.099% 84.65% 107ms 0.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 66ms 0.33% 84.98% 104ms 0.52% boost::numeric::ublas::c_matrix::operator() 1ms 0.005% 84.99% 103ms 0.51% Cell::SetCellProliferativeType 32ms 0.16% 85.15% 103ms 0.51% std::_Vector_base::_M_deallocate (inline) 40ms 0.2% 85.34% 103ms 0.51% std::__ostream_insert 1ms 0.005% 85.35% 101ms 0.5% std::vector::_M_default_append 0 0% 85.35% 101ms 0.5% std::vector::resize (inline)