File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16886ms, 85.99% of 19637ms total Dropped 786 nodes (cum <= 98.19ms) flat flat% sum% cum cum% 0 0% 0% 19592ms 99.77% __libc_start_call_main 0 0% 0% 19592ms 99.77% __libc_start_main_impl 0 0% 0% 19592ms 99.77% _start 0 0% 0% 19571ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19571ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19571ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19571ms 99.66% main 0 0% 0% 19529ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19529ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19529ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19502ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14858ms 75.66% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9394ms 47.84% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.025% 9299ms 47.35% Cell::ReadyToDivide 7ms 0.036% 0.061% 9213ms 46.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.071% 9058ms 46.13% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.061% 0.13% 9052ms 46.10% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.15% 9036ms 46.02% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.32% 0.47% 8854ms 45.09% AbstractOneStepIvpOdeSolver::InternalSolve 1012ms 5.15% 5.62% 7942ms 40.44% RungeKutta4IvpOdeSolver::CalculateNextYValue 2747ms 13.99% 19.61% 6748ms 34.36% WntCellCycleOdeSystem::EvaluateYDerivatives 4ms 0.02% 19.63% 5361ms 27.30% MeshBasedCellPopulation::Update 7ms 0.036% 19.67% 4139ms 21.08% Cylindrical2dMesh::ReMesh 75ms 0.38% 20.05% 4030ms 20.52% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.05% 2580ms 13.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 386ms 1.97% 22.02% 2560ms 13.04% AbstractCellProperty::IsSame 0 0% 22.02% 2261ms 11.51% MutableMesh::ReMesh 0 0% 22.02% 2222ms 11.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 22.07% 2176ms 11.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 234ms 1.19% 23.26% 2174ms 11.07% std::type_info::operator== (inline) 2061ms 10.50% 33.76% 2061ms 10.50% __strcmp_avx2 0 0% 33.76% 2059ms 10.49% AbstractCellPopulation::WriteResultsToFiles 793ms 4.04% 37.80% 1860ms 9.47% std::_Rb_tree::_M_lower_bound (inline) 149ms 0.76% 38.55% 1703ms 8.67% TetrahedralMesh::EdgeIterator::operator++ 71ms 0.36% 38.92% 1394ms 7.10% std::_Rb_tree::find (inline) 0 0% 38.92% 1183ms 6.02% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 38.96% 1171ms 5.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.051% 39.01% 1129ms 5.75% TetrahedralMesh::ImportFromMesher 59ms 0.3% 39.31% 1085ms 5.53% operator new 15ms 0.076% 39.39% 1039ms 5.29% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.066% 39.46% 1032ms 5.26% std::set::insert (inline) 9ms 0.046% 39.50% 1019ms 5.19% std::_Rb_tree::_M_insert_unique 240ms 1.22% 40.72% 1013ms 5.16% __GI___libc_malloc 31ms 0.16% 40.88% 955ms 4.86% std::__new_allocator::allocate (inline) 0 0% 40.88% 951ms 4.84% std::allocator_traits::allocate (inline) 3ms 0.015% 40.90% 900ms 4.58% triangulate 0 0% 40.90% 844ms 4.30% std::set::count (inline) 0 0% 40.90% 825ms 4.20% delaunay 5ms 0.025% 40.92% 825ms 4.20% divconqdelaunay 2ms 0.01% 40.93% 813ms 4.14% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 739ms 3.76% 44.70% 739ms 3.76% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.015% 44.71% 715ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 55ms 0.28% 44.99% 711ms 3.62% std::map::operator[] (partial-inline) 705ms 3.59% 48.58% 705ms 3.59% std::_Rb_tree::_S_right (inline) 199ms 1.01% 49.60% 703ms 3.58% __dynamic_cast 393ms 2.00% 51.60% 685ms 3.49% _int_malloc 5ms 0.025% 51.62% 656ms 3.34% CellPopulationElementWriter::Visit 4ms 0.02% 51.64% 652ms 3.32% MeshBasedCellPopulation::AcceptCellWriter 16ms 0.081% 51.72% 652ms 3.32% std::less::operator() (inline) 636ms 3.24% 54.96% 636ms 3.24% std::operator< (inline) 5ms 0.025% 54.99% 629ms 3.20% CellPropertyCollection::GetPropertiesType (inline) 34ms 0.17% 55.16% 624ms 3.18% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.16% 620ms 3.16% std::_Rb_tree::_M_create_node (inline) 23ms 0.12% 55.28% 617ms 3.14% AbstractCellPopulation::GetCellUsingLocationIndex 14ms 0.071% 55.35% 605ms 3.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 55.35% 596ms 3.04% std::_Rb_tree::_M_get_node (inline) 5ms 0.025% 55.38% 572ms 2.91% Element::Element 0 0% 55.38% 565ms 2.88% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.38% 562ms 2.86% std::_Rb_tree::lower_bound (inline) 0 0% 55.38% 562ms 2.86% std::map::lower_bound (inline) 8ms 0.041% 55.42% 549ms 2.80% MutableMesh::ReIndex 0 0% 55.42% 547ms 2.79% std::map::find (inline) 1ms 0.0051% 55.42% 542ms 2.76% AbstractCellProperty::IsSubType (inline) 17ms 0.087% 55.51% 515ms 2.62% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.056% 55.56% 497ms 2.53% Element::RegisterWithNodes (inline) 7ms 0.036% 55.60% 488ms 2.49% Cylindrical2dMesh::ReconstructCylindricalMesh 17ms 0.087% 55.69% 482ms 2.45% Node::AddElement 151ms 0.77% 56.45% 475ms 2.42% __GI___libc_free 287ms 1.46% 57.92% 450ms 2.29% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0051% 57.92% 448ms 2.28% std::ostream::operator<< (inline) 77ms 0.39% 58.31% 446ms 2.27% std::ostream::_M_insert 130ms 0.66% 58.98% 435ms 2.22% std::_Rb_tree::_M_erase 32ms 0.16% 59.14% 408ms 2.08% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.076% 59.21% 397ms 2.02% std::__new_allocator::deallocate (inline) 14ms 0.071% 59.29% 390ms 1.99% divconqrecurse 0 0% 59.29% 390ms 1.99% std::allocator_traits::deallocate (inline) 136ms 0.69% 59.98% 386ms 1.97% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.01% 59.99% 385ms 1.96% std::set::erase (inline) 15ms 0.076% 60.07% 384ms 1.96% Node::RemoveElement 17ms 0.087% 60.15% 384ms 1.96% std::_Rb_tree::erase 0 0% 60.15% 376ms 1.91% std::set::~set (inline) 0 0% 60.15% 375ms 1.91% std::_Rb_tree::_M_drop_node (inline) 98ms 0.5% 60.65% 366ms 1.86% mergehulls 0 0% 60.65% 355ms 1.81% std::_Vector_base::_M_allocate (inline) 2ms 0.01% 60.66% 352ms 1.79% Cell::GetCellProliferativeType 4ms 0.02% 60.68% 345ms 1.76% LegacyCellProliferativeTypesWriter::VisitCell 21ms 0.11% 60.79% 341ms 1.74% Element::ResetIndex 172ms 0.88% 61.66% 337ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 8ms 0.041% 61.70% 335ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 335ms 1.71% 63.41% 335ms 1.71% [libchaste_cell_based.so] 0 0% 63.41% 333ms 1.70% std::_Rb_tree::_M_put_node (inline) 254ms 1.29% 64.70% 323ms 1.64% _int_free 1ms 0.0051% 64.71% 319ms 1.62% Cell::GetMutationState 0 0% 64.71% 308ms 1.57% NodeLocationWriter::Visit 8ms 0.041% 64.75% 305ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.75% 299ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 25ms 0.13% 64.88% 297ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0051% 64.88% 275ms 1.40% alternateaxes 262ms 1.33% 66.22% 274ms 1.40% vertexmedian 63ms 0.32% 66.54% 267ms 1.36% ApcOneHitCellMutationState::ApcOneHitCellMutationState 8ms 0.041% 66.58% 267ms 1.36% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.046% 66.62% 264ms 1.34% std::vector::push_back (inline) 256ms 1.30% 67.93% 262ms 1.33% std::vector::operator[] (inline) 8ms 0.041% 67.97% 257ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 21ms 0.11% 68.08% 254ms 1.29% std::num_put::_M_insert_float 17ms 0.087% 68.16% 242ms 1.23% std::vector::_M_realloc_insert 6ms 0.031% 68.19% 241ms 1.23% std::set::set (inline) 5ms 0.025% 68.22% 240ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 96ms 0.49% 68.71% 240ms 1.22% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.036% 68.74% 239ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.071% 68.81% 234ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 27ms 0.14% 68.95% 232ms 1.18% std::_Rb_tree::_M_copy (inline) 18ms 0.092% 69.04% 230ms 1.17% AbstractTetrahedralElement::CalculateJacobian 94ms 0.48% 69.52% 229ms 1.17% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.52% 217ms 1.11% OffLatticeSimulation::ApplyBoundaries 146ms 0.74% 70.27% 214ms 1.09% AbstractElement::GetNodeGlobalIndex 20ms 0.1% 70.37% 212ms 1.08% TetrahedralMesh::Clear 1ms 0.0051% 70.37% 206ms 1.05% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.025% 70.40% 204ms 1.04% std::__cxx11::collate::do_transform 33ms 0.17% 70.57% 199ms 1.01% TetrahedralMesh::EdgesEnd (partial-inline) 70ms 0.36% 70.92% 199ms 1.01% std::_Rb_tree::_M_clone_node (inline) 5ms 0.025% 70.95% 197ms 1.00% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 70.96% 194ms 0.99% CellProliferativeTypesWriter::VisitCell 9ms 0.046% 71.01% 193ms 0.98% Element::MarkAsDeleted 1ms 0.0051% 71.01% 192ms 0.98% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.01% 192ms 0.98% ___vsnprintf 0 0% 71.01% 192ms 0.98% __vsnprintf_internal (inline) 24ms 0.12% 71.14% 191ms 0.97% __printf_buffer 7ms 0.036% 71.17% 184ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.051% 71.22% 180ms 0.92% AbstractTetrahedralElement::CalculateInverseJacobian 179ms 0.91% 72.13% 179ms 0.91% std::type_info::name (inline) 121ms 0.62% 72.75% 178ms 0.91% malloc_consolidate 4ms 0.02% 72.77% 177ms 0.9% CellPropertyCollection::HasProperty 0 0% 72.77% 175ms 0.89% Cell::HasCellProperty (inline) 66ms 0.34% 73.11% 173ms 0.88% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 25ms 0.13% 73.23% 170ms 0.87% AbstractTetrahedralElement::RefreshJacobian 170ms 0.87% 74.10% 170ms 0.87% std::_Rb_tree_insert_and_rebalance 168ms 0.86% 74.96% 168ms 0.86% std::vector::size (inline) 167ms 0.85% 75.81% 167ms 0.85% Node::GetIndex 54ms 0.27% 76.08% 161ms 0.82% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 157ms 0.8% 76.88% 157ms 0.8% incircle 157ms 0.8% 77.68% 157ms 0.8% unlink_chunk 8ms 0.041% 77.72% 156ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 77.74% 156ms 0.79% __printf_fp_l_buffer 0 0% 77.74% 156ms 0.79% __printf_fp_spec (inline) 155ms 0.79% 78.53% 155ms 0.79% AbstractCellMutationState::~AbstractCellMutationState 150ms 0.76% 79.29% 150ms 0.76% [libchaste_crypt.so] 72ms 0.37% 79.66% 150ms 0.76% __printf_fp_buffer_1 91ms 0.46% 80.12% 146ms 0.74% TetrahedralMesh::EdgeIterator::EdgeIterator 128ms 0.65% 80.77% 145ms 0.74% vertexsort 3ms 0.015% 80.79% 144ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 17ms 0.087% 80.87% 144ms 0.73% boost::detail::shared_count::~shared_count (inline) 0 0% 80.87% 144ms 0.73% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 80.89% 142ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 91ms 0.46% 81.35% 142ms 0.72% std::_Rb_tree::equal_range 52ms 0.26% 81.62% 141ms 0.72% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.62% 132ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 59ms 0.3% 81.92% 132ms 0.67% AbstractElement::GetNodeLocation 5ms 0.025% 81.94% 132ms 0.67% Node::~Node 3ms 0.015% 81.96% 131ms 0.67% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 81.98% 131ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.015% 82.00% 127ms 0.65% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0051% 82.00% 127ms 0.65% OutputFileHandler::OpenOutputFile 0 0% 82.00% 120ms 0.61% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 82.01% 117ms 0.6% Cell::SetCellProliferativeType 116ms 0.59% 82.60% 116ms 0.59% AbstractCellProperty::AbstractCellProperty 110ms 0.56% 83.16% 115ms 0.59% boost::detail::sp_counted_base::release 68ms 0.35% 83.51% 114ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 11ms 0.056% 83.57% 113ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 107ms 0.54% 84.11% 107ms 0.54% counterclockwise 107ms 0.54% 84.66% 107ms 0.54% std::_Rb_tree_increment 31ms 0.16% 84.81% 106ms 0.54% std::__ostream_insert 6ms 0.031% 84.84% 104ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 103ms 0.52% 85.37% 103ms 0.52% [libchaste_mesh.so] 102ms 0.52% 85.89% 102ms 0.52% boost::shared_ptr::operator-> (inline) 20ms 0.1% 85.99% 100ms 0.51% boost::numeric::ublas::indexing_vector_assign 0 0% 85.99% 100ms 0.51% std::vector::vector (inline) 0 0% 85.99% 99ms 0.5% AbstractCellBasedSimulation::DoCellRemoval (inline)