File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17987ms, 85.34% of 21076ms total Dropped 815 nodes (cum <= 105.38ms) flat flat% sum% cum cum% 0 0% 0% 21027ms 99.77% __libc_start_call_main 0 0% 0% 21027ms 99.77% __libc_start_main_impl 0 0% 0% 21027ms 99.77% _start 0 0% 0% 21006ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21006ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21006ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21006ms 99.67% main 0 0% 0% 20964ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20964ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20963ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0047% 0.0047% 20936ms 99.34% AbstractCellBasedSimulation::Solve 1ms 0.0047% 0.0095% 16020ms 76.01% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0047% 0.014% 10112ms 47.98% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0095% 0.024% 9988ms 47.39% Cell::ReadyToDivide 3ms 0.014% 0.038% 9855ms 46.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0095% 0.047% 9702ms 46.03% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 21ms 0.1% 0.15% 9689ms 45.97% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.033% 0.18% 9664ms 45.85% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.32% 0.5% 9451ms 44.84% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.16% 4.66% 8665ms 41.11% RungeKutta4IvpOdeSolver::CalculateNextYValue 3588ms 17.02% 21.68% 7604ms 36.08% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0047% 21.69% 5787ms 27.46% MeshBasedCellPopulation::Update 1ms 0.0047% 21.69% 4564ms 21.65% Cylindrical2dMesh::ReMesh 86ms 0.41% 22.10% 4111ms 19.51% AbstractCellProperty::IsType (inline) 647ms 3.07% 25.17% 2877ms 13.65% AbstractCellProperty::IsSame 2ms 0.0095% 25.18% 2691ms 12.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.18% 2591ms 12.29% MutableMesh::ReMesh 1ms 0.0047% 25.19% 2369ms 11.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.038% 25.22% 2321ms 11.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 391ms 1.86% 27.08% 2230ms 10.58% std::type_info::operator== (inline) 0 0% 27.08% 2216ms 10.51% AbstractCellPopulation::WriteResultsToFiles 826ms 3.92% 31.00% 1892ms 8.98% std::_Rb_tree::_M_lower_bound (inline) 1787ms 8.48% 39.48% 1787ms 8.48% __strcmp_avx2 188ms 0.89% 40.37% 1736ms 8.24% TetrahedralMesh::EdgeIterator::operator++ 72ms 0.34% 40.71% 1466ms 6.96% std::_Rb_tree::find (inline) 29ms 0.14% 40.85% 1433ms 6.80% TetrahedralMesh::ImportFromMesher 81ms 0.38% 41.23% 1276ms 6.05% operator new 246ms 1.17% 42.40% 1180ms 5.60% __GI___libc_malloc 0 0% 42.40% 1166ms 5.53% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.014% 42.41% 1160ms 5.50% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 63ms 0.3% 42.71% 1136ms 5.39% std::__new_allocator::allocate (inline) 0 0% 42.71% 1129ms 5.36% std::allocator_traits::allocate (inline) 9ms 0.043% 42.75% 1076ms 5.11% std::set::insert (inline) 19ms 0.09% 42.84% 1067ms 5.06% std::_Rb_tree::_M_insert_unique 9ms 0.043% 42.89% 1032ms 4.90% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 42.89% 895ms 4.25% std::set::count (inline) 473ms 2.24% 45.13% 854ms 4.05% _int_malloc 7ms 0.033% 45.17% 839ms 3.98% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.0095% 45.17% 825ms 3.91% triangulate 2ms 0.0095% 45.18% 762ms 3.62% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.18% 758ms 3.60% delaunay 3ms 0.014% 45.20% 758ms 3.60% divconqdelaunay 29ms 0.14% 45.34% 756ms 3.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 45.34% 741ms 3.52% std::_Rb_tree::_M_create_node (inline) 10ms 0.047% 45.38% 737ms 3.50% CellPopulationElementWriter::Visit 0 0% 45.38% 712ms 3.38% std::_Rb_tree::_M_get_node (inline) 270ms 1.28% 46.66% 709ms 3.36% __dynamic_cast 21ms 0.1% 46.76% 699ms 3.32% std::_Rb_tree::_M_insert_ (inline) 49ms 0.23% 47.00% 696ms 3.30% std::map::operator[] (partial-inline) 688ms 3.26% 50.26% 688ms 3.26% std::_Rb_tree::_S_right (inline) 4ms 0.019% 50.28% 684ms 3.25% MeshBasedCellPopulation::AcceptCellWriter 0 0% 50.28% 657ms 3.12% std::_Rb_tree::_Alloc_node::operator() (inline) 16ms 0.076% 50.36% 652ms 3.09% std::less::operator() (inline) 636ms 3.02% 53.37% 636ms 3.02% std::operator< (inline) 23ms 0.11% 53.48% 620ms 2.94% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 600ms 2.85% 56.33% 614ms 2.91% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.024% 56.35% 601ms 2.85% Element::Element 18ms 0.085% 56.44% 591ms 2.80% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.028% 56.47% 587ms 2.79% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0047% 56.47% 563ms 2.67% AbstractCellProperty::IsSubType (inline) 0 0% 56.47% 560ms 2.66% std::map::find (inline) 4ms 0.019% 56.49% 545ms 2.59% Element::RegisterWithNodes (inline) 6ms 0.028% 56.52% 542ms 2.57% Node::AddElement 0 0% 56.52% 529ms 2.51% std::_Rb_tree::lower_bound (inline) 0 0% 56.52% 529ms 2.51% std::map::lower_bound (inline) 4ms 0.019% 56.54% 523ms 2.48% MutableMesh::ReIndex 2ms 0.0095% 56.55% 522ms 2.48% std::ostream::operator<< (inline) 73ms 0.35% 56.89% 520ms 2.47% std::ostream::_M_insert 185ms 0.88% 57.77% 503ms 2.39% __GI___libc_free 339ms 1.61% 59.38% 497ms 2.36% AbstractCellMutationState::AbstractCellMutationState 9ms 0.043% 59.42% 469ms 2.23% Cylindrical2dMesh::CorrectNonPeriodicMesh 143ms 0.68% 60.10% 428ms 2.03% std::_Rb_tree::_M_erase 3ms 0.014% 60.12% 420ms 1.99% std::_Vector_base::_M_allocate (inline) 4ms 0.019% 60.13% 402ms 1.91% Cell::GetMutationState 9ms 0.043% 60.18% 399ms 1.89% std::_Rb_tree::erase 0 0% 60.18% 399ms 1.89% std::set::erase (inline) 65ms 0.31% 60.49% 398ms 1.89% TetrahedralMesh::Clear 12ms 0.057% 60.54% 397ms 1.88% Node::RemoveElement 29ms 0.14% 60.68% 395ms 1.87% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.014% 60.69% 387ms 1.84% Cell::GetCellProliferativeType 15ms 0.071% 60.77% 380ms 1.80% divconqrecurse 0 0% 60.77% 376ms 1.78% std::set::~set (inline) 93ms 0.44% 61.21% 358ms 1.70% mergehulls 11ms 0.052% 61.26% 356ms 1.69% std::__new_allocator::deallocate (inline) 0 0% 61.26% 354ms 1.68% std::allocator_traits::deallocate (inline) 150ms 0.71% 61.97% 349ms 1.66% std::_Rb_tree::_M_get_insert_unique_pos 160ms 0.76% 62.73% 334ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.13% 62.86% 333ms 1.58% Element::ResetIndex 333ms 1.58% 64.44% 333ms 1.58% std::type_info::name (inline) 10ms 0.047% 64.49% 325ms 1.54% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.49% 321ms 1.52% NodeLocationWriter::Visit 236ms 1.12% 65.61% 318ms 1.51% _int_free 13ms 0.062% 65.67% 313ms 1.49% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 65.67% 312ms 1.48% MeshBasedCellPopulation::GetDampingConstant 0 0% 65.67% 312ms 1.48% std::_Rb_tree::_M_drop_node (inline) 3ms 0.014% 65.69% 311ms 1.48% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 65.69% 301ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.095% 65.78% 300ms 1.42% AbstractTetrahedralElement::CalculateJacobian 4ms 0.019% 65.80% 300ms 1.42% LegacyCellProliferativeTypesWriter::VisitCell 55ms 0.26% 66.06% 297ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0095% 66.07% 294ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.019% 66.09% 292ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.0095% 66.10% 291ms 1.38% std::set::set (inline) 19ms 0.09% 66.19% 286ms 1.36% std::num_put::_M_insert_float 0 0% 66.19% 277ms 1.31% std::_Rb_tree::_M_put_node (inline) 10ms 0.047% 66.24% 276ms 1.31% std::vector::push_back (inline) 22ms 0.1% 66.34% 272ms 1.29% std::_Rb_tree::_M_copy (inline) 19ms 0.09% 66.43% 260ms 1.23% std::vector::_M_realloc_insert 7ms 0.033% 66.46% 256ms 1.21% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.019% 66.48% 253ms 1.20% CellProliferativeTypesWriter::VisitCell 85ms 0.4% 66.89% 246ms 1.17% std::_Rb_tree::_M_clone_node (inline) 5ms 0.024% 66.91% 243ms 1.15% CellPropertyCollection::HasProperty 242ms 1.15% 68.06% 243ms 1.15% std::vector::operator[] (inline) 27ms 0.13% 68.19% 242ms 1.15% AbstractTetrahedralElement::RefreshJacobian 11ms 0.052% 68.24% 241ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 9ms 0.043% 68.28% 239ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 68.28% 237ms 1.12% Cell::HasCellProperty (inline) 5ms 0.024% 68.31% 237ms 1.12% alternateaxes 173ms 0.82% 69.13% 236ms 1.12% malloc_consolidate 19ms 0.09% 69.22% 232ms 1.10% Node::~Node 216ms 1.02% 70.24% 231ms 1.10% vertexmedian 7ms 0.033% 70.27% 229ms 1.09% Element::MarkAsDeleted 3ms 0.014% 70.29% 227ms 1.08% std::__cxx11::collate::do_transform 9ms 0.043% 70.33% 226ms 1.07% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 63ms 0.3% 70.63% 226ms 1.07% ApcOneHitCellMutationState::ApcOneHitCellMutationState 37ms 0.18% 70.81% 224ms 1.06% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 44ms 0.21% 71.01% 221ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 71.01% 214ms 1.02% OffLatticeSimulation::ApplyBoundaries 2ms 0.0095% 71.02% 214ms 1.02% ___vsnprintf 0 0% 71.02% 212ms 1.01% __vsnprintf_internal (inline) 31ms 0.15% 71.17% 210ms 1% __printf_buffer 210ms 1% 72.17% 210ms 1% unlink_chunk 3ms 0.014% 72.18% 209ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 202ms 0.96% 73.14% 202ms 0.96% std::_Rb_tree_insert_and_rebalance 197ms 0.93% 74.07% 197ms 0.93% [libchaste_cell_based.so] 84ms 0.4% 74.47% 193ms 0.92% AbstractElement::GetNodeLocation 139ms 0.66% 75.13% 192ms 0.91% AbstractElement::GetNodeGlobalIndex 3ms 0.014% 75.15% 176ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 12ms 0.057% 75.20% 171ms 0.81% std::_Rb_tree_const_iterator::operator++ (inline) 170ms 0.81% 76.01% 170ms 0.81% std::_Rb_tree_increment 17ms 0.081% 76.09% 169ms 0.8% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.014% 76.11% 166ms 0.79% __printf_fp_l_buffer 0 0% 76.11% 166ms 0.79% __printf_fp_spec (inline) 166ms 0.79% 76.89% 166ms 0.79% incircle 164ms 0.78% 77.67% 164ms 0.78% std::vector::size (inline) 161ms 0.76% 78.44% 161ms 0.76% Node::GetIndex 7ms 0.033% 78.47% 160ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 107ms 0.51% 78.98% 157ms 0.74% std::_Rb_tree::equal_range (inline) 71ms 0.34% 79.31% 156ms 0.74% __printf_fp_buffer_1 145ms 0.69% 80.00% 145ms 0.69% AbstractElement::IsDeleted 3ms 0.014% 80.02% 144ms 0.68% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0047% 80.02% 142ms 0.67% boost::numeric::ublas::vector_assign (inline) 0 0% 80.02% 141ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 44ms 0.21% 80.23% 141ms 0.67% std::__ostream_insert 0 0% 80.23% 139ms 0.66% OutputFileHandler::OpenOutputFile 40ms 0.19% 80.42% 135ms 0.64% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 30ms 0.14% 80.56% 135ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 135ms 0.64% 81.20% 135ms 0.64% std::_Rb_tree_rebalance_for_erase 10ms 0.047% 81.25% 134ms 0.64% Cylindrical2dMesh::CreateMirrorNodes 127ms 0.6% 81.85% 132ms 0.63% vertexsort 56ms 0.27% 82.12% 131ms 0.62% std::_Vector_base::_M_deallocate (inline) 3ms 0.014% 82.13% 129ms 0.61% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 49ms 0.23% 82.36% 129ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 127ms 0.6% 82.97% 127ms 0.6% AbstractCellMutationState::~AbstractCellMutationState 78ms 0.37% 83.34% 127ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 13ms 0.062% 83.40% 124ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0047% 83.40% 123ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.024% 83.43% 123ms 0.58% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 4ms 0.019% 83.45% 121ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.45% 119ms 0.56% Cell::SetCellProliferativeType 6ms 0.028% 83.47% 118ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.024% 83.50% 118ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.50% 117ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 42ms 0.2% 83.70% 117ms 0.56% boost::numeric::ublas::indexing_vector_assign 116ms 0.55% 84.25% 116ms 0.55% AbstractCellProperty::~AbstractCellProperty 37ms 0.18% 84.42% 115ms 0.55% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 51ms 0.24% 84.67% 115ms 0.55% std::basic_filebuf::xsputn 20ms 0.095% 84.76% 112ms 0.53% std::num_put::_M_insert_int 5ms 0.024% 84.78% 111ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 84.78% 111ms 0.53% std::vector::vector (inline) 2ms 0.0095% 84.79% 109ms 0.52% std::operator<< (inline) 0 0% 84.79% 109ms 0.52% std::vector::_M_default_append 0 0% 84.79% 109ms 0.52% std::vector::resize (inline) 9ms 0.043% 84.84% 108ms 0.51% boost::detail::shared_count::~shared_count (inline) 0 0% 84.84% 108ms 0.51% boost::shared_ptr::~shared_ptr (inline) 107ms 0.51% 85.34% 107ms 0.51% boost::shared_ptr::operator-> (inline)