File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16826ms, 84.04% of 20022ms total Dropped 795 nodes (cum <= 100.11ms) flat flat% sum% cum cum% 0 0% 0% 19974ms 99.76% __libc_start_call_main 0 0% 0% 19974ms 99.76% __libc_start_main_impl 0 0% 0% 19974ms 99.76% _start 0 0% 0% 19951ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19951ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19951ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19951ms 99.65% main 0 0% 0% 19909ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19909ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19908ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19880ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 15175ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 9562ms 47.76% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.03% 9450ms 47.20% Cell::ReadyToDivide 6ms 0.03% 0.06% 9339ms 46.64% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.065% 9172ms 45.81% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 27ms 0.13% 0.2% 9166ms 45.78% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.21% 9137ms 45.63% CellCycleModelOdeHandler::SolveOdeToTime 66ms 0.33% 0.54% 8946ms 44.68% AbstractOneStepIvpOdeSolver::InternalSolve 973ms 4.86% 5.40% 8063ms 40.27% RungeKutta4IvpOdeSolver::CalculateNextYValue 2783ms 13.90% 19.30% 6901ms 34.47% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.30% 5489ms 27.41% MeshBasedCellPopulation::Update 6ms 0.03% 19.33% 4265ms 21.30% Cylindrical2dMesh::ReMesh 70ms 0.35% 19.68% 4136ms 20.66% AbstractCellProperty::IsType (inline) 414ms 2.07% 21.75% 2731ms 13.64% AbstractCellProperty::IsSame 2ms 0.01% 21.76% 2598ms 12.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.76% 2368ms 11.83% MutableMesh::ReMesh 277ms 1.38% 23.14% 2317ms 11.57% std::type_info::operator== (inline) 1ms 0.005% 23.14% 2281ms 11.39% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.055% 23.20% 2229ms 11.13% AbstractNumericalMethod::ComputeForcesIncludingDamping 2143ms 10.70% 33.90% 2143ms 10.70% __strcmp_avx2 1ms 0.005% 33.91% 2097ms 10.47% AbstractCellPopulation::WriteResultsToFiles 797ms 3.98% 37.89% 1865ms 9.31% std::_Rb_tree::_M_lower_bound (inline) 155ms 0.77% 38.66% 1715ms 8.57% TetrahedralMesh::EdgeIterator::operator++ 87ms 0.43% 39.10% 1350ms 6.74% std::_Rb_tree::find (inline) 10ms 0.05% 39.15% 1192ms 5.95% TetrahedralMesh::ImportFromMesher 0 0% 39.15% 1187ms 5.93% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.01% 39.16% 1143ms 5.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 49ms 0.24% 39.40% 1121ms 5.60% operator new 13ms 0.065% 39.47% 1061ms 5.30% MeshBasedCellPopulation::SpringIterator::operator++ 239ms 1.19% 40.66% 1055ms 5.27% __GI___libc_malloc 17ms 0.085% 40.75% 994ms 4.96% std::set::insert (inline) 23ms 0.11% 40.86% 975ms 4.87% std::_Rb_tree::_M_insert_unique 35ms 0.17% 41.03% 962ms 4.80% std::__new_allocator::allocate (inline) 0 0% 41.03% 958ms 4.78% std::allocator_traits::allocate (inline) 2ms 0.01% 41.04% 882ms 4.41% triangulate 0 0% 41.04% 800ms 4.00% std::set::count (inline) 0 0% 41.04% 786ms 3.93% delaunay 4ms 0.02% 41.06% 783ms 3.91% divconqdelaunay 66ms 0.33% 41.39% 781ms 3.90% std::map::operator[] (partial-inline) 767ms 3.83% 45.23% 767ms 3.83% std::_Rb_tree::_S_right (inline) 6ms 0.03% 45.26% 759ms 3.79% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 396ms 1.98% 47.23% 744ms 3.72% _int_malloc 2ms 0.01% 47.24% 732ms 3.66% CellPopulationElementWriter::Visit 1ms 0.005% 47.25% 728ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 700ms 3.50% 50.74% 700ms 3.50% WntCellCycleOdeSystem::CalculateStoppingEvent 204ms 1.02% 51.76% 658ms 3.29% __dynamic_cast 17ms 0.085% 51.85% 645ms 3.22% CellPropertyCollection::GetPropertiesType (inline) 21ms 0.1% 51.95% 642ms 3.21% AbstractCellPopulation::GetCellUsingLocationIndex 31ms 0.15% 52.11% 639ms 3.19% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 52.11% 618ms 3.09% std::_Rb_tree::lower_bound (inline) 0 0% 52.11% 618ms 3.09% std::map::lower_bound (inline) 0 0% 52.11% 612ms 3.06% std::_Rb_tree::_M_create_node (inline) 8ms 0.04% 52.15% 598ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 9ms 0.045% 52.19% 597ms 2.98% std::less::operator() (inline) 588ms 2.94% 55.13% 588ms 2.94% std::operator< (inline) 0 0% 55.13% 582ms 2.91% std::_Rb_tree::_M_get_node (inline) 37ms 0.18% 55.31% 557ms 2.78% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.31% 545ms 2.72% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.31% 541ms 2.70% std::map::find (inline) 10ms 0.05% 55.36% 539ms 2.69% Element::Element 7ms 0.035% 55.40% 539ms 2.69% MutableMesh::ReIndex 2ms 0.01% 55.41% 511ms 2.55% AbstractCellProperty::IsSubType (inline) 0 0% 55.41% 494ms 2.47% std::ostream::operator<< (inline) 60ms 0.3% 55.71% 493ms 2.46% std::ostream::_M_insert 158ms 0.79% 56.50% 484ms 2.42% __GI___libc_free 9ms 0.045% 56.54% 483ms 2.41% Cylindrical2dMesh::CorrectNonPeriodicMesh 14ms 0.07% 56.61% 477ms 2.38% Cylindrical2dMesh::ReconstructCylindricalMesh 308ms 1.54% 58.15% 474ms 2.37% AbstractCellMutationState::AbstractCellMutationState 14ms 0.07% 58.22% 438ms 2.19% Element::RegisterWithNodes (inline) 9ms 0.045% 58.27% 427ms 2.13% Node::AddElement 123ms 0.61% 58.88% 406ms 2.03% std::_Rb_tree::_M_erase 148ms 0.74% 59.62% 397ms 1.98% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.04% 59.66% 380ms 1.90% std::_Rb_tree::erase 0 0% 59.66% 379ms 1.89% std::set::erase (inline) 1ms 0.005% 59.66% 377ms 1.88% std::_Vector_base::_M_allocate (inline) 24ms 0.12% 59.78% 374ms 1.87% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.06% 59.84% 370ms 1.85% std::__new_allocator::deallocate (inline) 369ms 1.84% 61.69% 369ms 1.84% [libchaste_cell_based.so] 12ms 0.06% 61.75% 367ms 1.83% Node::RemoveElement 0 0% 61.75% 366ms 1.83% std::allocator_traits::deallocate (inline) 7ms 0.035% 61.78% 357ms 1.78% divconqrecurse 0 0% 61.78% 357ms 1.78% std::set::~set (inline) 4ms 0.02% 61.80% 350ms 1.75% Cell::GetMutationState 25ms 0.12% 61.93% 346ms 1.73% Element::ResetIndex 0 0% 61.93% 345ms 1.72% std::_Rb_tree::_M_drop_node (inline) 98ms 0.49% 62.42% 343ms 1.71% mergehulls 12ms 0.06% 62.48% 336ms 1.68% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 4ms 0.02% 62.50% 329ms 1.64% Cell::GetCellProliferativeType 261ms 1.30% 63.80% 325ms 1.62% _int_free 149ms 0.74% 64.54% 320ms 1.60% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 64.56% 306ms 1.53% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.015% 64.58% 305ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 38ms 0.19% 64.77% 304ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 64.77% 304ms 1.52% std::_Rb_tree::_M_put_node (inline) 0 0% 64.77% 303ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.075% 64.84% 301ms 1.50% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 64.85% 299ms 1.49% NodeLocationWriter::Visit 36ms 0.18% 65.03% 294ms 1.47% TetrahedralMesh::Clear 3ms 0.015% 65.05% 288ms 1.44% alternateaxes 282ms 1.41% 66.46% 285ms 1.42% std::vector::operator[] (inline) 265ms 1.32% 67.78% 284ms 1.42% vertexmedian 12ms 0.06% 67.84% 279ms 1.39% std::_Rb_tree::_Rb_tree (partial-inline) 25ms 0.12% 67.97% 273ms 1.36% std::num_put::_M_insert_float 13ms 0.065% 68.03% 273ms 1.36% std::vector::push_back (inline) 1ms 0.005% 68.04% 266ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.05% 68.09% 264ms 1.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 68.10% 254ms 1.27% MeshBasedCellPopulation::GetDampingConstant 13ms 0.065% 68.16% 251ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 68.18% 250ms 1.25% AbstractCentreBasedCellPopulation::GetDampingConstant 90ms 0.45% 68.62% 249ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.04% 68.66% 249ms 1.24% std::vector::_M_realloc_insert 2ms 0.01% 68.67% 241ms 1.20% std::set::set (inline) 77ms 0.38% 69.06% 240ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 24ms 0.12% 69.18% 238ms 1.19% std::_Rb_tree::_M_copy (inline) 9ms 0.045% 69.22% 235ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.055% 69.28% 233ms 1.16% std::_Rb_tree::_M_erase_aux (inline) 54ms 0.27% 69.55% 231ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 45ms 0.22% 69.77% 227ms 1.13% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 69.79% 223ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 69.81% 213ms 1.06% std::__cxx11::collate::do_transform 6ms 0.03% 69.84% 212ms 1.06% AbstractTetrahedralElement::AbstractTetrahedralElement 64ms 0.32% 70.16% 209ms 1.04% std::_Rb_tree::_M_clone_node (inline) 1ms 0.005% 70.16% 205ms 1.02% ___vsnprintf 0 0% 70.16% 204ms 1.02% __vsnprintf_internal (inline) 202ms 1.01% 71.17% 202ms 1.01% [libchaste_crypt.so] 36ms 0.18% 71.35% 201ms 1.00% __printf_buffer 141ms 0.7% 72.06% 197ms 0.98% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 72.06% 196ms 0.98% OffLatticeSimulation::ApplyBoundaries 193ms 0.96% 73.02% 193ms 0.96% unlink_chunk 3ms 0.015% 73.04% 191ms 0.95% CellPropertyCollection::HasProperty 132ms 0.66% 73.70% 190ms 0.95% malloc_consolidate 0 0% 73.70% 189ms 0.94% Cell::HasCellProperty (inline) 8ms 0.04% 73.74% 179ms 0.89% Element::MarkAsDeleted 173ms 0.86% 74.60% 173ms 0.86% Node::GetIndex 4ms 0.02% 74.62% 169ms 0.84% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 10ms 0.05% 74.67% 168ms 0.84% Node::~Node 68ms 0.34% 75.01% 166ms 0.83% AbstractElement::GetNodeLocation 5ms 0.025% 75.04% 165ms 0.82% CellProliferativeTypesWriter::VisitCell 164ms 0.82% 75.86% 164ms 0.82% incircle 3ms 0.015% 75.87% 162ms 0.81% __printf_fp_l_buffer 0 0% 75.87% 162ms 0.81% __printf_fp_spec (inline) 60ms 0.3% 76.17% 157ms 0.78% __printf_fp_buffer_1 2ms 0.01% 76.18% 155ms 0.77% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 154ms 0.77% 76.95% 154ms 0.77% std::type_info::name (inline) 149ms 0.74% 77.69% 149ms 0.74% std::vector::size (inline) 48ms 0.24% 77.93% 148ms 0.74% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 96ms 0.48% 78.41% 147ms 0.73% std::_Rb_tree::equal_range (inline) 5ms 0.025% 78.44% 144ms 0.72% boost::numeric::ublas::vector_assign (inline) 7ms 0.035% 78.47% 142ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 6ms 0.03% 78.50% 139ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 78.50% 138ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 78.50% 137ms 0.68% OutputFileHandler::OpenOutputFile 4ms 0.02% 78.52% 136ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 84ms 0.42% 78.94% 133ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 113ms 0.56% 79.51% 131ms 0.65% vertexsort 1ms 0.005% 79.51% 129ms 0.64% Cell::SetCellProliferativeType 129ms 0.64% 80.16% 129ms 0.64% std::_Rb_tree_insert_and_rebalance 40ms 0.2% 80.36% 127ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 25ms 0.12% 80.48% 127ms 0.63% TetrahedralMesh::EdgesEnd (partial-inline) 19ms 0.095% 80.58% 123ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 80.58% 123ms 0.61% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.58% 122ms 0.61% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 10ms 0.05% 80.63% 122ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.63% 121ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 80.64% 119ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.015% 80.66% 117ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 116ms 0.58% 81.24% 116ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 115ms 0.57% 81.81% 115ms 0.57% std::_Rb_tree_increment 19ms 0.095% 81.90% 114ms 0.57% std::num_put::_M_insert_int 8ms 0.04% 81.94% 112ms 0.56% Cylindrical2dMesh::CreateMirrorNodes 36ms 0.18% 82.12% 112ms 0.56% boost::numeric::ublas::indexing_vector_assign 12ms 0.06% 82.18% 108ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 108ms 0.54% 82.72% 108ms 0.54% TetrahedralMesh::EdgeIterator::operator!= 53ms 0.26% 82.99% 107ms 0.53% boost::shared_ptr::shared_ptr (inline) 38ms 0.19% 83.18% 104ms 0.52% std::__ostream_insert 103ms 0.51% 83.69% 103ms 0.51% AbstractCellProperty::AbstractCellProperty 69ms 0.34% 84.04% 103ms 0.51% TimeStepper::AdvanceOneTimeStep