File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16769ms, 85.73% of 19561ms total Dropped 767 nodes (cum <= 97.81ms) flat flat% sum% cum cum% 0 0% 0% 19514ms 99.76% __libc_start_call_main 0 0% 0% 19514ms 99.76% __libc_start_main_impl 0 0% 0% 19514ms 99.76% _start 0 0% 0% 19491ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19491ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19491ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19491ms 99.64% main 0 0% 0% 19451ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19451ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19451ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19423ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 14825ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9397ms 48.04% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.02% 9296ms 47.52% Cell::ReadyToDivide 2ms 0.01% 0.031% 9191ms 46.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.031% 9036ms 46.19% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.072% 9031ms 46.17% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.082% 9021ms 46.12% CellCycleModelOdeHandler::SolveOdeToTime 59ms 0.3% 0.38% 8833ms 45.16% AbstractOneStepIvpOdeSolver::InternalSolve 1031ms 5.27% 5.65% 7908ms 40.43% RungeKutta4IvpOdeSolver::CalculateNextYValue 2703ms 13.82% 19.47% 6715ms 34.33% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.47% 5314ms 27.17% MeshBasedCellPopulation::Update 4ms 0.02% 19.49% 4102ms 20.97% Cylindrical2dMesh::ReMesh 65ms 0.33% 19.83% 4019ms 20.55% AbstractCellProperty::IsType (inline) 359ms 1.84% 21.66% 2583ms 13.20% AbstractCellProperty::IsSame 0 0% 21.66% 2554ms 13.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.01% 21.67% 2249ms 11.50% MutableMesh::ReMesh 246ms 1.26% 22.93% 2224ms 11.37% std::type_info::operator== (inline) 1ms 0.0051% 22.93% 2219ms 11.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.036% 22.97% 2162ms 11.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 2084ms 10.65% 33.62% 2084ms 10.65% __strcmp_avx2 1ms 0.0051% 33.63% 2039ms 10.42% AbstractCellPopulation::WriteResultsToFiles 874ms 4.47% 38.10% 1941ms 9.92% std::_Rb_tree::_M_lower_bound (inline) 187ms 0.96% 39.05% 1733ms 8.86% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.31% 39.36% 1422ms 7.27% std::_Rb_tree::find (partial-inline) 0 0% 39.36% 1176ms 6.01% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.041% 39.40% 1155ms 5.90% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 20ms 0.1% 39.50% 1123ms 5.74% TetrahedralMesh::ImportFromMesher 48ms 0.25% 39.75% 1097ms 5.61% operator new 9ms 0.046% 39.79% 1053ms 5.38% MeshBasedCellPopulation::SpringIterator::operator++ 237ms 1.21% 41.01% 1027ms 5.25% __GI___libc_malloc 12ms 0.061% 41.07% 976ms 4.99% std::set::insert (inline) 17ms 0.087% 41.15% 964ms 4.93% std::_Rb_tree::_M_insert_unique 26ms 0.13% 41.29% 957ms 4.89% std::__new_allocator::allocate (inline) 0 0% 41.29% 954ms 4.88% std::allocator_traits::allocate (inline) 2ms 0.01% 41.30% 899ms 4.60% triangulate 0 0% 41.30% 883ms 4.51% std::set::count (inline) 0 0% 41.30% 818ms 4.18% delaunay 6ms 0.031% 41.33% 818ms 4.18% divconqdelaunay 2ms 0.01% 41.34% 764ms 3.91% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 54ms 0.28% 41.61% 747ms 3.82% std::map::operator[] (partial-inline) 731ms 3.74% 45.35% 731ms 3.74% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0051% 45.36% 697ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.031% 45.39% 697ms 3.56% CellPopulationElementWriter::Visit 360ms 1.84% 47.23% 682ms 3.49% _int_malloc 674ms 3.45% 50.67% 674ms 3.45% std::_Rb_tree::_S_right (inline) 0 0% 50.67% 647ms 3.31% std::_Rb_tree::_M_create_node (inline) 20ms 0.1% 50.77% 644ms 3.29% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.061% 50.84% 637ms 3.26% std::less::operator() (inline) 624ms 3.19% 54.03% 625ms 3.20% std::operator< (inline) 6ms 0.031% 54.06% 618ms 3.16% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.06% 608ms 3.11% std::_Rb_tree::_M_get_node (inline) 193ms 0.99% 55.04% 606ms 3.10% __dynamic_cast 41ms 0.21% 55.25% 601ms 3.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.25% 599ms 3.06% std::_Rb_tree::lower_bound (inline) 0 0% 55.25% 599ms 3.06% std::map::lower_bound (inline) 5ms 0.026% 55.28% 590ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 28ms 0.14% 55.42% 583ms 2.98% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 3ms 0.015% 55.44% 578ms 2.95% Element::Element 0 0% 55.44% 578ms 2.95% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.051% 55.49% 535ms 2.74% MutableMesh::ReIndex 0 0% 55.49% 534ms 2.73% std::map::find (inline) 16ms 0.082% 55.57% 506ms 2.59% Cylindrical2dMesh::CorrectNonPeriodicMesh 18ms 0.092% 55.66% 496ms 2.54% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.072% 55.73% 493ms 2.52% Element::RegisterWithNodes (inline) 12ms 0.061% 55.79% 479ms 2.45% Node::AddElement 1ms 0.0051% 55.80% 470ms 2.40% AbstractCellProperty::IsSubType (inline) 3ms 0.015% 55.82% 469ms 2.40% std::ostream::operator<< (inline) 68ms 0.35% 56.16% 465ms 2.38% std::ostream::_M_insert 306ms 1.56% 57.73% 451ms 2.31% AbstractCellMutationState::AbstractCellMutationState 152ms 0.78% 58.50% 436ms 2.23% __GI___libc_free 21ms 0.11% 58.61% 394ms 2.01% Node::RemoveElement 107ms 0.55% 59.16% 392ms 2.00% std::_Rb_tree::_M_erase 13ms 0.066% 59.22% 384ms 1.96% std::_Rb_tree::erase 1ms 0.0051% 59.23% 384ms 1.96% std::set::erase (inline) 13ms 0.066% 59.30% 380ms 1.94% divconqrecurse 36ms 0.18% 59.48% 379ms 1.94% std::_Rb_tree::~_Rb_tree (inline) 377ms 1.93% 61.41% 377ms 1.93% [libchaste_cell_based.so] 17ms 0.087% 61.49% 372ms 1.90% std::__new_allocator::deallocate (inline) 0 0% 61.49% 369ms 1.89% std::allocator_traits::deallocate (inline) 90ms 0.46% 61.95% 359ms 1.84% mergehulls 33ms 0.17% 62.12% 358ms 1.83% Element::ResetIndex 0 0% 62.12% 356ms 1.82% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.12% 350ms 1.79% std::set::~set (inline) 3ms 0.015% 62.14% 349ms 1.78% std::_Vector_base::_M_allocate (inline) 141ms 0.72% 62.86% 346ms 1.77% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.056% 62.92% 340ms 1.74% Cell::GetCellProliferativeType 7ms 0.036% 62.95% 323ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.031% 62.98% 318ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 62.99% 310ms 1.58% Cell::GetMutationState 1ms 0.0051% 62.99% 309ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0051% 63.00% 303ms 1.55% NodeLocationWriter::Visit 124ms 0.63% 63.63% 301ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.63% 299ms 1.53% std::_Rb_tree::_M_put_node (inline) 13ms 0.066% 63.70% 295ms 1.51% std::_Rb_tree::_Rb_tree (partial-inline) 112ms 0.57% 64.27% 290ms 1.48% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 234ms 1.20% 65.47% 284ms 1.45% _int_free 1ms 0.0051% 65.47% 283ms 1.45% alternateaxes 271ms 1.39% 66.86% 282ms 1.44% vertexmedian 2ms 0.01% 66.87% 281ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.14% 67.01% 277ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 262ms 1.34% 68.35% 268ms 1.37% std::vector::operator[] (inline) 13ms 0.066% 68.42% 266ms 1.36% std::num_put::_M_insert_float 3ms 0.015% 68.43% 265ms 1.35% std::set::set (inline) 13ms 0.066% 68.50% 263ms 1.34% std::vector::push_back (inline) 5ms 0.026% 68.52% 261ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.072% 68.60% 255ms 1.30% AbstractTetrahedralElement::CalculateJacobian 26ms 0.13% 68.73% 247ms 1.26% std::_Rb_tree::_M_copy (inline) 20ms 0.1% 68.83% 244ms 1.25% std::vector::_M_realloc_insert 9ms 0.046% 68.88% 242ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 90ms 0.46% 69.34% 234ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.031% 69.37% 229ms 1.17% std::__cxx11::collate::do_transform 14ms 0.072% 69.44% 228ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 69.45% 219ms 1.12% ___vsnprintf 60ms 0.31% 69.76% 218ms 1.11% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 69.78% 217ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 69.78% 217ms 1.11% __vsnprintf_internal (inline) 67ms 0.34% 70.12% 217ms 1.11% std::_Rb_tree::_M_clone_node (inline) 20ms 0.1% 70.23% 216ms 1.10% __printf_buffer 12ms 0.061% 70.29% 215ms 1.10% Element::MarkAsDeleted 3ms 0.015% 70.30% 213ms 1.09% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.30% 213ms 1.09% MeshBasedCellPopulation::GetDampingConstant 0 0% 70.30% 207ms 1.06% TetrahedralMesh::RefreshJacobianCachedData 0 0% 70.30% 205ms 1.05% OffLatticeSimulation::ApplyBoundaries 134ms 0.69% 70.99% 204ms 1.04% malloc_consolidate 203ms 1.04% 72.03% 203ms 1.04% [libchaste_crypt.so] 6ms 0.031% 72.06% 198ms 1.01% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.031% 72.09% 197ms 1.01% CellPropertyCollection::HasProperty 127ms 0.65% 72.74% 196ms 1.00% AbstractElement::GetNodeGlobalIndex 15ms 0.077% 72.81% 194ms 0.99% TetrahedralMesh::Clear 0 0% 72.81% 193ms 0.99% Cell::HasCellProperty (inline) 9ms 0.046% 72.86% 185ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 28ms 0.14% 73.00% 185ms 0.95% AbstractTetrahedralElement::RefreshJacobian 8ms 0.041% 73.04% 180ms 0.92% __printf_fp_l_buffer 0 0% 73.04% 180ms 0.92% __printf_fp_spec (inline) 4ms 0.02% 73.06% 178ms 0.91% CellProliferativeTypesWriter::VisitCell 176ms 0.9% 73.96% 176ms 0.9% incircle 168ms 0.86% 74.82% 168ms 0.86% std::vector::size (inline) 168ms 0.86% 75.68% 168ms 0.86% unlink_chunk 85ms 0.43% 76.12% 167ms 0.85% __printf_fp_buffer_1 2ms 0.01% 76.13% 165ms 0.84% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 160ms 0.82% 76.94% 160ms 0.82% Node::GetIndex 17ms 0.087% 77.03% 159ms 0.81% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 159ms 0.81% 77.84% 159ms 0.81% std::type_info::name (inline) 22ms 0.11% 77.96% 157ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.01% 77.97% 151ms 0.77% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 7ms 0.036% 78.00% 150ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 108ms 0.55% 78.55% 149ms 0.76% std::_Rb_tree::equal_range (inline) 56ms 0.29% 78.84% 143ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.02% 78.86% 143ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 135ms 0.69% 79.55% 143ms 0.73% vertexsort 52ms 0.27% 79.82% 139ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 44ms 0.22% 80.04% 138ms 0.71% AbstractElement::GetNodeLocation 138ms 0.71% 80.75% 138ms 0.71% std::_Rb_tree_insert_and_rebalance 2ms 0.01% 80.76% 133ms 0.68% boost::numeric::ublas::vector_assign (inline) 78ms 0.4% 81.16% 132ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.01% 81.17% 131ms 0.67% Cell::SetCellProliferativeType 20ms 0.1% 81.27% 125ms 0.64% boost::detail::shared_count::~shared_count (inline) 0 0% 81.27% 125ms 0.64% boost::shared_ptr::~shared_ptr (inline) 84ms 0.43% 81.70% 122ms 0.62% TetrahedralMesh::EdgeIterator::EdgeIterator 14ms 0.072% 81.77% 122ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.77% 121ms 0.62% OutputFileHandler::OpenOutputFile 0 0% 81.77% 120ms 0.61% AbstractCellBasedWriter::OpenOutputFileForAppend 82ms 0.42% 82.19% 119ms 0.61% TimeStepper::AdvanceOneTimeStep 119ms 0.61% 82.80% 119ms 0.61% std::_Rb_tree_increment 10ms 0.051% 82.85% 117ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.036% 82.88% 114ms 0.58% Node::~Node 0 0% 82.88% 113ms 0.58% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.036% 82.92% 109ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 82.92% 105ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 25ms 0.13% 83.05% 105ms 0.54% boost::numeric::ublas::indexing_vector_assign 48ms 0.25% 83.29% 105ms 0.54% boost::shared_ptr::shared_ptr (inline) 1ms 0.0051% 83.30% 103ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.52% 83.81% 101ms 0.52% [libchaste_mesh.so] 35ms 0.18% 83.99% 101ms 0.52% std::__ostream_insert 0 0% 83.99% 100ms 0.51% tcache_get (inline) 100ms 0.51% 84.50% 100ms 0.51% tcache_get_n (inline) 99ms 0.51% 85.01% 99ms 0.51% AbstractCellMutationState::~AbstractCellMutationState 41ms 0.21% 85.22% 99ms 0.51% AbstractTetrahedralMesh::GetElement 99ms 0.51% 85.73% 99ms 0.51% boost::shared_ptr::operator-> (inline)