File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16578ms, 84.21% of 19687ms total Dropped 832 nodes (cum <= 98.44ms) flat flat% sum% cum cum% 0 0% 0% 19640ms 99.76% __libc_start_call_main 0 0% 0% 19640ms 99.76% __libc_start_main_impl 0 0% 0% 19640ms 99.76% _start 0 0% 0% 19619ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19619ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19619ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19619ms 99.65% main 0 0% 0% 19576ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19576ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19576ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19549ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 14878ms 75.57% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 9310ms 47.29% AbstractCellBasedSimulation::DoCellBirth 11ms 0.056% 0.061% 9206ms 46.76% Cell::ReadyToDivide 8ms 0.041% 0.1% 9106ms 46.25% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.11% 8950ms 45.46% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.046% 0.15% 8943ms 45.43% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.025% 0.18% 8930ms 45.36% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.36% 0.53% 8762ms 44.51% AbstractOneStepIvpOdeSolver::InternalSolve 1019ms 5.18% 5.71% 7825ms 39.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 2684ms 13.63% 19.34% 6626ms 33.66% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 19.35% 5459ms 27.73% MeshBasedCellPopulation::Update 2ms 0.01% 19.36% 4212ms 21.39% Cylindrical2dMesh::ReMesh 54ms 0.27% 19.64% 3954ms 20.08% AbstractCellProperty::IsType (inline) 1ms 0.0051% 19.64% 2609ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 323ms 1.64% 21.28% 2571ms 13.06% AbstractCellProperty::IsSame 0 0% 21.28% 2317ms 11.77% MutableMesh::ReMesh 0 0% 21.28% 2279ms 11.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 210ms 1.07% 22.35% 2248ms 11.42% std::type_info::operator== (inline) 11ms 0.056% 22.41% 2225ms 11.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 2152ms 10.93% 33.34% 2152ms 10.93% __strcmp_avx2 2ms 0.01% 33.35% 2056ms 10.44% AbstractCellPopulation::WriteResultsToFiles 825ms 4.19% 37.54% 1883ms 9.56% std::_Rb_tree::_M_lower_bound (inline) 171ms 0.87% 38.41% 1735ms 8.81% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.34% 38.75% 1360ms 6.91% std::_Rb_tree::find (inline) 0 0% 38.75% 1202ms 6.11% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.036% 38.78% 1168ms 5.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.071% 38.85% 1156ms 5.87% TetrahedralMesh::ImportFromMesher 47ms 0.24% 39.09% 1126ms 5.72% operator new 11ms 0.056% 39.15% 1077ms 5.47% MeshBasedCellPopulation::SpringIterator::operator++ 245ms 1.24% 40.39% 1072ms 5.45% __GI___libc_malloc 10ms 0.051% 40.44% 1044ms 5.30% std::set::insert (inline) 10ms 0.051% 40.49% 1033ms 5.25% std::_Rb_tree::_M_insert_unique 35ms 0.18% 40.67% 967ms 4.91% std::__new_allocator::allocate (inline) 0 0% 40.67% 961ms 4.88% std::allocator_traits::allocate (inline) 6ms 0.03% 40.70% 894ms 4.54% triangulate 0 0% 40.70% 813ms 4.13% std::set::count (inline) 0 0% 40.70% 804ms 4.08% delaunay 1ms 0.0051% 40.71% 800ms 4.06% divconqdelaunay 72ms 0.37% 41.07% 794ms 4.03% std::map::operator[] (partial-inline) 747ms 3.79% 44.87% 747ms 3.79% WntCellCycleOdeSystem::CalculateStoppingEvent 2ms 0.01% 44.88% 743ms 3.77% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 736ms 3.74% 48.62% 736ms 3.74% std::_Rb_tree::_S_right (inline) 0 0% 48.62% 735ms 3.73% AbstractTwoBodyInteractionForce::AddForceContribution 403ms 2.05% 50.66% 723ms 3.67% _int_malloc 4ms 0.02% 50.68% 699ms 3.55% CellPopulationElementWriter::Visit 216ms 1.10% 51.78% 680ms 3.45% __dynamic_cast 26ms 0.13% 51.91% 656ms 3.33% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 51.91% 654ms 3.32% std::_Rb_tree::_M_create_node (inline) 18ms 0.091% 52.00% 634ms 3.22% AbstractCellPopulation::GetCellUsingLocationIndex 37ms 0.19% 52.19% 632ms 3.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 52.19% 628ms 3.19% std::_Rb_tree::_M_get_node (inline) 0 0% 52.19% 611ms 3.10% std::_Rb_tree::lower_bound (inline) 0 0% 52.19% 611ms 3.10% std::map::lower_bound (inline) 15ms 0.076% 52.27% 608ms 3.09% std::less::operator() (inline) 593ms 3.01% 55.28% 593ms 3.01% std::operator< (inline) 4ms 0.02% 55.30% 582ms 2.96% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.015% 55.32% 581ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.32% 581ms 2.95% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 55.34% 576ms 2.93% Element::Element 10ms 0.051% 55.39% 544ms 2.76% MutableMesh::ReIndex 0 0% 55.39% 543ms 2.76% std::map::find (inline) 13ms 0.066% 55.46% 512ms 2.60% Element::RegisterWithNodes (inline) 22ms 0.11% 55.57% 506ms 2.57% Cylindrical2dMesh::CorrectNonPeriodicMesh 20ms 0.1% 55.67% 498ms 2.53% Node::AddElement 2ms 0.01% 55.68% 491ms 2.49% AbstractCellProperty::IsSubType (inline) 18ms 0.091% 55.77% 488ms 2.48% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 55.77% 477ms 2.42% std::ostream::operator<< (inline) 68ms 0.35% 56.12% 476ms 2.42% std::ostream::_M_insert 137ms 0.7% 56.81% 459ms 2.33% __GI___libc_free 271ms 1.38% 58.19% 415ms 2.11% AbstractCellMutationState::AbstractCellMutationState 136ms 0.69% 58.88% 404ms 2.05% std::_Rb_tree::_M_erase 2ms 0.01% 58.89% 401ms 2.04% std::set::erase (inline) 10ms 0.051% 58.94% 400ms 2.03% std::_Rb_tree::erase 161ms 0.82% 59.76% 395ms 2.01% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.066% 59.83% 392ms 1.99% Node::RemoveElement 14ms 0.071% 59.90% 379ms 1.93% divconqrecurse 25ms 0.13% 60.02% 379ms 1.93% std::_Rb_tree::~_Rb_tree (inline) 0 0% 60.02% 357ms 1.81% std::set::~set (inline) 102ms 0.52% 60.54% 353ms 1.79% mergehulls 35ms 0.18% 60.72% 352ms 1.79% Element::ResetIndex 12ms 0.061% 60.78% 348ms 1.77% std::__new_allocator::deallocate (inline) 193ms 0.98% 61.76% 347ms 1.76% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.76% 342ms 1.74% std::allocator_traits::deallocate (inline) 2ms 0.01% 61.77% 335ms 1.70% std::_Vector_base::_M_allocate (inline) 0 0% 61.77% 327ms 1.66% std::_Rb_tree::_M_drop_node (inline) 245ms 1.24% 63.02% 322ms 1.64% _int_free 10ms 0.051% 63.07% 320ms 1.63% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0051% 63.07% 312ms 1.58% Cell::GetCellProliferativeType 2ms 0.01% 63.08% 312ms 1.58% Cell::GetMutationState 306ms 1.55% 64.64% 306ms 1.55% [libchaste_cell_based.so] 6ms 0.03% 64.67% 302ms 1.53% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0051% 64.67% 297ms 1.51% NodeLocationWriter::Visit 5ms 0.025% 64.70% 293ms 1.49% alternateaxes 0 0% 64.70% 292ms 1.48% std::_Rb_tree::_M_put_node (inline) 1ms 0.0051% 64.70% 291ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.076% 64.78% 289ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.02% 64.80% 288ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 270ms 1.37% 66.17% 288ms 1.46% vertexmedian 51ms 0.26% 66.43% 286ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.025% 66.46% 277ms 1.41% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.081% 66.54% 270ms 1.37% std::num_put::_M_insert_float 266ms 1.35% 67.89% 268ms 1.36% std::vector::operator[] (inline) 3ms 0.015% 67.90% 259ms 1.32% std::set::set (inline) 13ms 0.066% 67.97% 251ms 1.27% std::vector::push_back (inline) 29ms 0.15% 68.12% 246ms 1.25% std::_Rb_tree::_M_copy (inline) 94ms 0.48% 68.59% 245ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 109ms 0.55% 69.15% 244ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 17ms 0.086% 69.23% 241ms 1.22% AbstractTetrahedralElement::CalculateJacobian 20ms 0.1% 69.34% 240ms 1.22% TetrahedralMesh::Clear 1ms 0.0051% 69.34% 232ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 14ms 0.071% 69.41% 231ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 15ms 0.076% 69.49% 224ms 1.14% std::vector::_M_realloc_insert 1ms 0.0051% 69.49% 223ms 1.13% MeshBasedCellPopulation::GetDampingConstant 4ms 0.02% 69.51% 222ms 1.13% std::__cxx11::collate::do_transform 0 0% 69.51% 220ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 10ms 0.051% 69.56% 218ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 59ms 0.3% 69.86% 218ms 1.11% ApcOneHitCellMutationState::ApcOneHitCellMutationState 12ms 0.061% 69.92% 217ms 1.10% Element::MarkAsDeleted 76ms 0.39% 70.31% 215ms 1.09% std::_Rb_tree::_M_clone_node (inline) 2ms 0.01% 70.32% 208ms 1.06% ___vsnprintf 0 0% 70.32% 206ms 1.05% __vsnprintf_internal (inline) 12ms 0.061% 70.38% 203ms 1.03% __printf_buffer 3ms 0.015% 70.40% 201ms 1.02% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.041% 70.44% 200ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0051% 70.44% 200ms 1.02% OffLatticeSimulation::ApplyBoundaries 138ms 0.7% 71.14% 197ms 1.00% malloc_consolidate 151ms 0.77% 71.91% 196ms 1% AbstractElement::GetNodeGlobalIndex 23ms 0.12% 72.03% 194ms 0.99% AbstractTetrahedralElement::RefreshJacobian 180ms 0.91% 72.94% 180ms 0.91% unlink_chunk 6ms 0.03% 72.97% 176ms 0.89% __printf_fp_l_buffer 0 0% 72.97% 176ms 0.89% __printf_fp_spec (inline) 2ms 0.01% 72.98% 175ms 0.89% CellPropertyCollection::HasProperty 0 0% 72.98% 174ms 0.88% Cell::HasCellProperty (inline) 4ms 0.02% 73.00% 171ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 114ms 0.58% 73.58% 171ms 0.87% std::_Rb_tree::equal_range (inline) 169ms 0.86% 74.44% 169ms 0.86% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 74.47% 168ms 0.85% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 4ms 0.02% 74.49% 164ms 0.83% CellProliferativeTypesWriter::VisitCell 70ms 0.36% 74.85% 163ms 0.83% __printf_fp_buffer_1 162ms 0.82% 75.67% 162ms 0.82% std::vector::size (inline) 2ms 0.01% 75.68% 160ms 0.81% boost::numeric::ublas::vector_assign (inline) 72ms 0.37% 76.05% 158ms 0.8% AbstractElement::GetNodeLocation 51ms 0.26% 76.30% 157ms 0.8% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 155ms 0.79% 77.09% 155ms 0.79% AbstractCellMutationState::~AbstractCellMutationState 155ms 0.79% 77.88% 155ms 0.79% [libchaste_crypt.so] 155ms 0.79% 78.67% 155ms 0.79% incircle 153ms 0.78% 79.44% 153ms 0.78% Node::GetIndex 55ms 0.28% 79.72% 152ms 0.77% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 7ms 0.036% 79.76% 152ms 0.77% Node::~Node 0 0% 79.76% 147ms 0.75% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.76% 147ms 0.75% OutputFileHandler::OpenOutputFile 3ms 0.015% 79.77% 144ms 0.73% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 74ms 0.38% 80.15% 135ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.041% 80.19% 134ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 24ms 0.12% 80.31% 134ms 0.68% TetrahedralMesh::EdgesEnd (partial-inline) 5ms 0.025% 80.34% 132ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 8ms 0.041% 80.38% 131ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 129ms 0.66% 81.03% 129ms 0.66% std::type_info::name (inline) 38ms 0.19% 81.23% 128ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.23% 126ms 0.64% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 81.23% 125ms 0.63% Cell::SetCellProliferativeType 9ms 0.046% 81.27% 118ms 0.6% Cylindrical2dMesh::CreateMirrorNodes 109ms 0.55% 81.83% 118ms 0.6% vertexsort 29ms 0.15% 81.97% 114ms 0.58% boost::numeric::ublas::indexing_vector_assign 114ms 0.58% 82.55% 114ms 0.58% std::_Rb_tree_increment 9ms 0.046% 82.60% 113ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 33ms 0.17% 82.77% 112ms 0.57% std::__ostream_insert 2ms 0.01% 82.78% 111ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 3ms 0.015% 82.79% 111ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 109ms 0.55% 83.34% 109ms 0.55% std::_Rb_tree_rebalance_for_erase 0 0% 83.34% 108ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 60ms 0.3% 83.65% 107ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator 2ms 0.01% 83.66% 103ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.15% 83.81% 103ms 0.52% std::num_put::_M_insert_int 61ms 0.31% 84.12% 102ms 0.52% TimeStepper::AdvanceOneTimeStep 17ms 0.086% 84.21% 100ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator