File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16565ms, 83.20% of 19911ms total Dropped 783 nodes (cum <= 99.56ms) flat flat% sum% cum cum% 0 0% 0% 19869ms 99.79% __libc_start_call_main 0 0% 0% 19869ms 99.79% __libc_start_main_impl 0 0% 0% 19869ms 99.79% _start 0 0% 0% 19850ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19850ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19850ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19850ms 99.69% main 0 0% 0% 19813ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19813ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19813ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19786ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 15378ms 77.23% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10156ms 51.01% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 10059ms 50.52% Cell::ReadyToDivide 7ms 0.035% 0.055% 10004ms 50.24% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.06% 9858ms 49.51% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.12% 9851ms 49.48% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.13% 9838ms 49.41% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.35% 0.48% 9664ms 48.54% AbstractOneStepIvpOdeSolver::InternalSolve 859ms 4.31% 4.79% 8873ms 44.56% RungeKutta4IvpOdeSolver::CalculateNextYValue 3702ms 18.59% 23.38% 7812ms 39.23% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.39% 5103ms 25.63% MeshBasedCellPopulation::Update 209ms 1.05% 24.44% 4140ms 20.79% AbstractCellProperty::IsType (inline) 1ms 0.005% 24.44% 3928ms 19.73% Cylindrical2dMesh::ReMesh 596ms 2.99% 27.44% 2918ms 14.66% AbstractCellProperty::IsSame 1ms 0.005% 27.44% 2464ms 12.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 409ms 2.05% 29.50% 2322ms 11.66% std::type_info::operator== (inline) 0 0% 29.50% 2155ms 10.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.50% 2115ms 10.62% MutableMesh::ReMesh 7ms 0.035% 29.53% 2109ms 10.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 29.54% 1940ms 9.74% AbstractCellPopulation::WriteResultsToFiles 1920ms 9.64% 39.18% 1920ms 9.64% __strcmp_avx2 777ms 3.90% 43.08% 1818ms 9.13% std::_Rb_tree::_M_lower_bound (inline) 171ms 0.86% 43.94% 1659ms 8.33% TetrahedralMesh::EdgeIterator::operator++ 48ms 0.24% 44.18% 1372ms 6.89% std::_Rb_tree::find (inline) 0 0% 44.18% 1140ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.04% 44.22% 1120ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 41ms 0.21% 44.43% 1087ms 5.46% operator new 14ms 0.07% 44.50% 1067ms 5.36% TetrahedralMesh::ImportFromMesher 251ms 1.26% 45.76% 1034ms 5.19% __GI___libc_malloc 12ms 0.06% 45.82% 1015ms 5.10% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.05% 45.87% 957ms 4.81% std::set::insert (inline) 38ms 0.19% 46.06% 948ms 4.76% std::__new_allocator::allocate (inline) 18ms 0.09% 46.15% 947ms 4.76% std::_Rb_tree::_M_insert_unique 0 0% 46.15% 939ms 4.72% std::allocator_traits::allocate (inline) 0 0% 46.15% 843ms 4.23% std::set::count (inline) 0 0% 46.15% 791ms 3.97% triangulate 0 0% 46.15% 721ms 3.62% delaunay 0 0% 46.15% 719ms 3.61% divconqdelaunay 3ms 0.015% 46.17% 690ms 3.47% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 46.18% 689ms 3.46% AbstractTwoBodyInteractionForce::AddForceContribution 388ms 1.95% 48.12% 688ms 3.46% _int_malloc 4ms 0.02% 48.14% 665ms 3.34% CellPopulationElementWriter::Visit 17ms 0.085% 48.23% 653ms 3.28% std::less::operator() (inline) 651ms 3.27% 51.50% 651ms 3.27% std::_Rb_tree::_S_right (inline) 43ms 0.22% 51.72% 645ms 3.24% std::map::operator[] (partial-inline) 155ms 0.78% 52.49% 638ms 3.20% __dynamic_cast 636ms 3.19% 55.69% 636ms 3.19% std::operator< (inline) 602ms 3.02% 58.71% 612ms 3.07% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.71% 610ms 3.06% std::_Rb_tree::_M_create_node (inline) 29ms 0.15% 58.86% 598ms 3.00% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.86% 588ms 2.95% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 58.97% 579ms 2.91% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.02% 58.99% 563ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.99% 563ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.03% 59.02% 553ms 2.78% MeshBasedCellPopulation::AcceptCellWriter 18ms 0.09% 59.11% 545ms 2.74% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 59.13% 543ms 2.73% Element::Element 0 0% 59.13% 533ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 59.13% 533ms 2.68% std::map::lower_bound (inline) 2ms 0.01% 59.14% 527ms 2.65% MutableMesh::ReIndex 0 0% 59.14% 522ms 2.62% std::map::find (inline) 76ms 0.38% 59.52% 503ms 2.53% std::ostream::_M_insert 0 0% 59.52% 503ms 2.53% std::ostream::operator<< (inline) 10ms 0.05% 59.57% 502ms 2.52% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.05% 59.62% 486ms 2.44% Element::RegisterWithNodes (inline) 8ms 0.04% 59.66% 475ms 2.39% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.07% 59.73% 473ms 2.38% Node::AddElement 1ms 0.005% 59.74% 465ms 2.34% AbstractCellProperty::IsSubType (inline) 305ms 1.53% 61.27% 447ms 2.24% AbstractCellMutationState::AbstractCellMutationState 154ms 0.77% 62.04% 413ms 2.07% __GI___libc_free 8ms 0.04% 62.08% 374ms 1.88% std::_Rb_tree::erase 2ms 0.01% 62.09% 371ms 1.86% std::set::erase (inline) 20ms 0.1% 62.19% 363ms 1.82% divconqrecurse 14ms 0.07% 62.26% 362ms 1.82% Node::RemoveElement 114ms 0.57% 62.83% 356ms 1.79% std::_Rb_tree::_M_erase 2ms 0.01% 62.84% 353ms 1.77% std::_Vector_base::_M_allocate (inline) 159ms 0.8% 63.64% 346ms 1.74% __cxxabiv1::__si_class_type_info::__do_dyncast 12ms 0.06% 63.70% 344ms 1.73% std::__new_allocator::deallocate (inline) 28ms 0.14% 63.84% 343ms 1.72% Element::ResetIndex 90ms 0.45% 64.30% 338ms 1.70% mergehulls 0 0% 64.30% 338ms 1.70% std::allocator_traits::deallocate (inline) 128ms 0.64% 64.94% 331ms 1.66% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.05% 64.99% 330ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 17ms 0.085% 65.07% 326ms 1.64% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 65.08% 315ms 1.58% NodeLocationWriter::Visit 0 0% 65.08% 311ms 1.56% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 65.10% 302ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 65.11% 301ms 1.51% Cell::GetMutationState 3ms 0.015% 65.12% 299ms 1.50% Cell::GetCellProliferativeType 0 0% 65.12% 295ms 1.48% std::set::~set (inline) 10ms 0.05% 65.18% 288ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 287ms 1.44% 66.62% 287ms 1.44% std::type_info::name (inline) 42ms 0.21% 66.83% 283ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.005% 66.83% 283ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.83% 278ms 1.40% std::_Rb_tree::_M_put_node (inline) 14ms 0.07% 66.90% 275ms 1.38% AbstractTetrahedralElement::CalculateJacobian 18ms 0.09% 66.99% 272ms 1.37% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.1% 67.09% 271ms 1.36% std::num_put::_M_insert_float 208ms 1.04% 68.14% 258ms 1.30% _int_free 248ms 1.25% 69.38% 248ms 1.25% [libchaste_cell_based.so] 0 0% 69.38% 242ms 1.22% std::set::set (inline) 242ms 1.22% 70.60% 242ms 1.22% std::vector::operator[] (inline) 6ms 0.03% 70.63% 242ms 1.22% std::vector::push_back (inline) 9ms 0.045% 70.67% 239ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 70.67% 232ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.05% 70.72% 231ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 80ms 0.4% 71.13% 228ms 1.15% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 61ms 0.31% 71.43% 227ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 16ms 0.08% 71.51% 227ms 1.14% std::vector::_M_realloc_insert 1ms 0.005% 71.52% 225ms 1.13% alternateaxes 208ms 1.04% 72.56% 224ms 1.13% vertexmedian 7ms 0.035% 72.60% 218ms 1.09% std::_Rb_tree::_M_erase_aux (inline) 17ms 0.085% 72.68% 216ms 1.08% std::_Rb_tree::_M_copy (inline) 1ms 0.005% 72.69% 216ms 1.08% std::__cxx11::collate::do_transform 30ms 0.15% 72.84% 214ms 1.07% AbstractTetrahedralElement::RefreshJacobian 4ms 0.02% 72.86% 212ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 72.86% 212ms 1.06% ___vsnprintf 0 0% 72.86% 211ms 1.06% __vsnprintf_internal (inline) 20ms 0.1% 72.96% 207ms 1.04% __printf_buffer 11ms 0.055% 73.02% 204ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 160ms 0.8% 73.82% 202ms 1.01% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 73.83% 200ms 1.00% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.83% 200ms 1.00% MeshBasedCellPopulation::GetDampingConstant 51ms 0.26% 74.08% 194ms 0.97% std::_Rb_tree::_M_clone_node (inline) 136ms 0.68% 74.77% 189ms 0.95% malloc_consolidate 9ms 0.045% 74.81% 181ms 0.91% Element::MarkAsDeleted 0 0% 74.81% 181ms 0.91% OffLatticeSimulation::ApplyBoundaries 40ms 0.2% 75.01% 176ms 0.88% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.04% 75.05% 176ms 0.88% __printf_fp_l_buffer 0 0% 75.05% 176ms 0.88% __printf_fp_spec (inline) 3ms 0.015% 75.07% 175ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 173ms 0.87% 75.94% 173ms 0.87% Node::GetIndex 18ms 0.09% 76.03% 168ms 0.84% TetrahedralMesh::Clear 75ms 0.38% 76.41% 161ms 0.81% __printf_fp_buffer_1 161ms 0.81% 77.21% 161ms 0.81% incircle 6ms 0.03% 77.24% 157ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 115ms 0.58% 77.82% 157ms 0.79% std::_Rb_tree::equal_range (inline) 155ms 0.78% 78.60% 155ms 0.78% std::_Rb_tree_insert_and_rebalance 76ms 0.38% 78.98% 154ms 0.77% AbstractElement::GetNodeLocation 4ms 0.02% 79.00% 150ms 0.75% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 79.03% 149ms 0.75% CellProliferativeTypesWriter::VisitCell 2ms 0.01% 79.04% 142ms 0.71% CellPropertyCollection::HasProperty 2ms 0.01% 79.05% 142ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 141ms 0.71% 79.75% 141ms 0.71% unlink_chunk 0 0% 79.75% 139ms 0.7% Cell::HasCellProperty (inline) 136ms 0.68% 80.44% 136ms 0.68% std::vector::size (inline) 1ms 0.005% 80.44% 135ms 0.68% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 83ms 0.42% 80.86% 134ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 35ms 0.18% 81.04% 131ms 0.66% TetrahedralMesh::EdgesEnd (partial-inline) 40ms 0.2% 81.24% 130ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 11ms 0.055% 81.29% 129ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.29% 127ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 81.29% 126ms 0.63% OutputFileHandler::OpenOutputFile 17ms 0.085% 81.38% 120ms 0.6% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 111ms 0.56% 81.93% 119ms 0.6% vertexsort 0 0% 81.93% 117ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 31ms 0.16% 82.09% 117ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 82.09% 116ms 0.58% Cell::SetCellProliferativeType 5ms 0.025% 82.12% 114ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.065% 82.18% 113ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 82.18% 113ms 0.57% boost::shared_ptr::~shared_ptr (inline) 42ms 0.21% 82.39% 113ms 0.57% std::__ostream_insert 0 0% 82.39% 111ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.02% 82.41% 111ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 110ms 0.55% 82.96% 110ms 0.55% AbstractCellProperty::~AbstractCellProperty 21ms 0.11% 83.07% 105ms 0.53% std::num_put::_M_insert_int 25ms 0.13% 83.20% 103ms 0.52% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline)