File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16443ms, 83.15% of 19774ms total Dropped 775 nodes (cum <= 98.87ms) flat flat% sum% cum cum% 0 0% 0% 19725ms 99.75% __libc_start_call_main 0 0% 0% 19725ms 99.75% __libc_start_main_impl 0 0% 0% 19725ms 99.75% _start 0 0% 0% 19705ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19705ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19705ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19705ms 99.65% main 0 0% 0% 19669ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19669ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19669ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19642ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 15255ms 77.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0051% 9958ms 50.36% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.03% 9869ms 49.91% Cell::ReadyToDivide 7ms 0.035% 0.066% 9776ms 49.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.071% 9630ms 48.70% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.081% 0.15% 9621ms 48.65% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.16% 9601ms 48.55% CellCycleModelOdeHandler::SolveOdeToTime 73ms 0.37% 0.53% 9424ms 47.66% AbstractOneStepIvpOdeSolver::InternalSolve 854ms 4.32% 4.85% 8602ms 43.50% RungeKutta4IvpOdeSolver::CalculateNextYValue 3508ms 17.74% 22.59% 7520ms 38.03% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.59% 5165ms 26.12% MeshBasedCellPopulation::Update 125ms 0.63% 23.22% 4098ms 20.72% AbstractCellProperty::IsType (inline) 12ms 0.061% 23.28% 3976ms 20.11% Cylindrical2dMesh::ReMesh 574ms 2.90% 26.19% 2828ms 14.30% AbstractCellProperty::IsSame 2ms 0.01% 26.20% 2443ms 12.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 428ms 2.16% 28.36% 2254ms 11.40% std::type_info::operator== (inline) 0 0% 28.36% 2144ms 10.84% MutableMesh::ReMesh 1ms 0.0051% 28.37% 2132ms 10.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.04% 28.41% 2064ms 10.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.01% 28.42% 1939ms 9.81% AbstractCellPopulation::WriteResultsToFiles 863ms 4.36% 32.78% 1863ms 9.42% std::_Rb_tree::_M_lower_bound (inline) 1768ms 8.94% 41.72% 1768ms 8.94% __strcmp_avx2 171ms 0.86% 42.59% 1683ms 8.51% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.33% 42.92% 1396ms 7.06% std::_Rb_tree::find (inline) 0 0% 42.92% 1138ms 5.76% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 42.94% 1104ms 5.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 52ms 0.26% 43.20% 1100ms 5.56% operator new 15ms 0.076% 43.27% 1088ms 5.50% TetrahedralMesh::ImportFromMesher 259ms 1.31% 44.58% 1040ms 5.26% __GI___libc_malloc 6ms 0.03% 44.61% 1015ms 5.13% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.061% 44.67% 979ms 4.95% std::set::insert (inline) 47ms 0.24% 44.91% 973ms 4.92% std::__new_allocator::allocate (inline) 0 0% 44.91% 968ms 4.90% std::allocator_traits::allocate (inline) 18ms 0.091% 45.00% 967ms 4.89% std::_Rb_tree::_M_insert_unique 0 0% 45.00% 839ms 4.24% std::set::count (inline) 3ms 0.015% 45.02% 791ms 4.00% triangulate 1ms 0.0051% 45.02% 716ms 3.62% delaunay 4ms 0.02% 45.04% 713ms 3.61% divconqdelaunay 3ms 0.015% 45.06% 700ms 3.54% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 46ms 0.23% 45.29% 686ms 3.47% std::map::operator[] (partial-inline) 369ms 1.87% 47.16% 682ms 3.45% _int_malloc 3ms 0.015% 47.17% 680ms 3.44% CellPopulationElementWriter::Visit 3ms 0.015% 47.19% 652ms 3.30% AbstractTwoBodyInteractionForce::AddForceContribution 640ms 3.24% 50.42% 648ms 3.28% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 50.42% 639ms 3.23% std::_Rb_tree::_M_create_node (inline) 29ms 0.15% 50.57% 636ms 3.22% std::_Rb_tree::_M_insert_ (inline) 633ms 3.20% 53.77% 633ms 3.20% std::_Rb_tree::_S_right (inline) 0 0% 53.77% 609ms 3.08% std::_Rb_tree::_M_get_node (inline) 11ms 0.056% 53.83% 607ms 3.07% std::less::operator() (inline) 150ms 0.76% 54.59% 599ms 3.03% __dynamic_cast 596ms 3.01% 57.60% 596ms 3.01% std::operator< (inline) 0 0% 57.60% 589ms 2.98% std::_Rb_tree::_Alloc_node::operator() (inline) 22ms 0.11% 57.71% 572ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 31ms 0.16% 57.87% 565ms 2.86% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.87% 558ms 2.82% std::_Rb_tree::lower_bound (inline) 0 0% 57.87% 558ms 2.82% std::map::lower_bound (inline) 5ms 0.025% 57.89% 557ms 2.82% Element::Element 5ms 0.025% 57.92% 557ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.92% 552ms 2.79% std::map::find (inline) 2ms 0.01% 57.93% 546ms 2.76% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.04% 57.97% 534ms 2.70% MutableMesh::ReIndex 10ms 0.051% 58.02% 500ms 2.53% Cylindrical2dMesh::CorrectNonPeriodicMesh 340ms 1.72% 59.74% 491ms 2.48% AbstractCellMutationState::AbstractCellMutationState 2ms 0.01% 59.75% 490ms 2.48% std::ostream::operator<< (inline) 50ms 0.25% 60.00% 485ms 2.45% std::ostream::_M_insert 15ms 0.076% 60.08% 479ms 2.42% Element::RegisterWithNodes (inline) 10ms 0.051% 60.13% 462ms 2.34% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.056% 60.19% 460ms 2.33% Node::AddElement 4ms 0.02% 60.21% 447ms 2.26% AbstractCellProperty::IsSubType (inline) 144ms 0.73% 60.93% 408ms 2.06% __GI___libc_free 3ms 0.015% 60.95% 377ms 1.91% std::set::erase (inline) 8ms 0.04% 60.99% 376ms 1.90% std::_Rb_tree::erase 9ms 0.046% 61.03% 366ms 1.85% Node::RemoveElement 0 0% 61.03% 359ms 1.82% std::_Vector_base::_M_allocate (inline) 38ms 0.19% 61.23% 355ms 1.80% Element::ResetIndex 8ms 0.04% 61.27% 353ms 1.79% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 159ms 0.8% 62.07% 352ms 1.78% __cxxabiv1::__si_class_type_info::__do_dyncast 108ms 0.55% 62.62% 352ms 1.78% std::_Rb_tree::_M_erase 351ms 1.78% 64.39% 351ms 1.78% std::type_info::name (inline) 16ms 0.081% 64.47% 349ms 1.76% std::__new_allocator::deallocate (inline) 0 0% 64.47% 345ms 1.74% std::allocator_traits::deallocate (inline) 13ms 0.066% 64.54% 337ms 1.70% divconqrecurse 1ms 0.0051% 64.54% 331ms 1.67% NodeLocationWriter::Visit 21ms 0.11% 64.65% 329ms 1.66% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.035% 64.69% 320ms 1.62% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.02% 64.71% 317ms 1.60% Cell::GetMutationState 87ms 0.44% 65.15% 316ms 1.60% mergehulls 0 0% 65.15% 313ms 1.58% std::_Rb_tree::_M_drop_node (inline) 119ms 0.6% 65.75% 313ms 1.58% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 65.75% 308ms 1.56% std::set::~set (inline) 0 0% 65.75% 307ms 1.55% AbstractCellPopulation::Iterator::operator++ (inline) 6ms 0.03% 65.78% 305ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 19ms 0.096% 65.87% 305ms 1.54% std::num_put::_M_insert_float 34ms 0.17% 66.05% 304ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 66.06% 288ms 1.46% Cell::GetCellProliferativeType 12ms 0.061% 66.12% 280ms 1.42% std::_Rb_tree::_Rb_tree (partial-inline) 31ms 0.16% 66.28% 279ms 1.41% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.28% 274ms 1.39% std::_Rb_tree::_M_put_node (inline) 219ms 1.11% 67.39% 264ms 1.34% _int_free 6ms 0.03% 67.42% 262ms 1.32% std::vector::push_back (inline) 2ms 0.01% 67.43% 259ms 1.31% std::set::set (inline) 6ms 0.03% 67.46% 254ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 254ms 1.28% 68.74% 254ms 1.28% std::vector::operator[] (inline) 3ms 0.015% 68.76% 251ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.061% 68.82% 248ms 1.25% std::vector::_M_realloc_insert 26ms 0.13% 68.95% 247ms 1.25% std::_Rb_tree::_M_copy (inline) 69ms 0.35% 69.30% 243ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 69.30% 243ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 69.31% 242ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.025% 69.34% 235ms 1.19% alternateaxes 10ms 0.051% 69.39% 234ms 1.18% std::__cxx11::collate::do_transform 223ms 1.13% 70.52% 230ms 1.16% vertexmedian 44ms 0.22% 70.74% 228ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 13ms 0.066% 70.81% 225ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 64ms 0.32% 71.13% 219ms 1.11% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.13% 216ms 1.09% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.13% 216ms 1.09% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 71.13% 211ms 1.07% ___vsnprintf 210ms 1.06% 72.20% 210ms 1.06% [libchaste_cell_based.so] 26ms 0.13% 72.33% 210ms 1.06% __printf_buffer 0 0% 72.33% 210ms 1.06% __vsnprintf_internal (inline) 7ms 0.035% 72.36% 209ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 72.36% 209ms 1.06% OffLatticeSimulation::ApplyBoundaries 23ms 0.12% 72.48% 208ms 1.05% AbstractTetrahedralElement::RefreshJacobian 43ms 0.22% 72.70% 206ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.056% 72.75% 192ms 0.97% AbstractTetrahedralElement::AbstractTetrahedralElement 192ms 0.97% 73.72% 192ms 0.97% std::_Rb_tree_insert_and_rebalance 13ms 0.066% 73.79% 189ms 0.96% Element::MarkAsDeleted 5ms 0.025% 73.81% 186ms 0.94% CellPropertyCollection::HasProperty 135ms 0.68% 74.50% 185ms 0.94% malloc_consolidate 0 0% 74.50% 182ms 0.92% Cell::HasCellProperty (inline) 174ms 0.88% 75.38% 174ms 0.88% Node::GetIndex 3ms 0.015% 75.39% 173ms 0.87% __printf_fp_l_buffer 0 0% 75.39% 173ms 0.87% __printf_fp_spec (inline) 12ms 0.061% 75.45% 170ms 0.86% TetrahedralMesh::Clear 71ms 0.36% 75.81% 165ms 0.83% AbstractElement::GetNodeLocation 84ms 0.42% 76.24% 165ms 0.83% __printf_fp_buffer_1 120ms 0.61% 76.84% 158ms 0.8% AbstractElement::GetNodeGlobalIndex 151ms 0.76% 77.61% 151ms 0.76% unlink_chunk 10ms 0.051% 77.66% 150ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 77.67% 146ms 0.74% CellProliferativeTypesWriter::VisitCell 100ms 0.51% 78.18% 145ms 0.73% std::_Rb_tree::equal_range (inline) 3ms 0.015% 78.19% 143ms 0.72% boost::numeric::ublas::vector_assign (inline) 0 0% 78.19% 138ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 135ms 0.68% 78.88% 135ms 0.68% incircle 134ms 0.68% 79.55% 134ms 0.68% AbstractCellMutationState::~AbstractCellMutationState 8ms 0.04% 79.59% 133ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 79.59% 132ms 0.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 19ms 0.096% 79.69% 129ms 0.65% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.025% 79.72% 128ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.02% 79.74% 128ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 113ms 0.57% 80.31% 128ms 0.65% vertexsort 127ms 0.64% 80.95% 127ms 0.64% std::vector::size (inline) 39ms 0.2% 81.15% 125ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 39ms 0.2% 81.34% 121ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 71ms 0.36% 81.70% 119ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0051% 81.71% 118ms 0.6% Cell::SetCellProliferativeType 29ms 0.15% 81.85% 114ms 0.58% TetrahedralMesh::EdgesEnd 12ms 0.061% 81.92% 112ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 81.92% 112ms 0.57% boost::shared_ptr::~shared_ptr (inline) 111ms 0.56% 82.48% 111ms 0.56% AbstractElement::IsDeleted 30ms 0.15% 82.63% 109ms 0.55% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 39ms 0.2% 82.83% 109ms 0.55% boost::numeric::ublas::indexing_vector_assign 47ms 0.24% 83.06% 109ms 0.55% std::__ostream_insert 0 0% 83.06% 107ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.02% 83.08% 107ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 83.08% 106ms 0.54% OutputFileHandler::OpenOutputFile 13ms 0.066% 83.15% 103ms 0.52% Node::~Node 0 0% 83.15% 103ms 0.52% std::vector::resize (inline) 0 0% 83.15% 102ms 0.52% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.0051% 83.15% 101ms 0.51% std::vector::_M_default_append