File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16566ms, 84.19% of 19677ms total Dropped 760 nodes (cum <= 98.39ms) flat flat% sum% cum cum% 0 0% 0% 19633ms 99.78% __libc_start_call_main 0 0% 0% 19633ms 99.78% __libc_start_main_impl 0 0% 0% 19633ms 99.78% _start 0 0% 0% 19615ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19615ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19615ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19615ms 99.68% main 0 0% 0% 19582ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19582ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19581ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19555ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15212ms 77.31% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.025% 0.025% 10084ms 51.25% AbstractCellBasedSimulation::DoCellBirth 7ms 0.036% 0.061% 9988ms 50.76% Cell::ReadyToDivide 8ms 0.041% 0.1% 9918ms 50.40% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.11% 9770ms 49.65% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.061% 0.17% 9765ms 49.63% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.17% 9749ms 49.55% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.38% 0.55% 9598ms 48.78% AbstractOneStepIvpOdeSolver::InternalSolve 849ms 4.31% 4.87% 8832ms 44.88% RungeKutta4IvpOdeSolver::CalculateNextYValue 3600ms 18.30% 23.16% 7787ms 39.57% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.16% 5023ms 25.53% MeshBasedCellPopulation::Update 192ms 0.98% 24.14% 4237ms 21.53% AbstractCellProperty::IsType (inline) 9ms 0.046% 24.19% 3909ms 19.87% Cylindrical2dMesh::ReMesh 590ms 3.00% 27.18% 2946ms 14.97% AbstractCellProperty::IsSame 0 0% 27.18% 2430ms 12.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 438ms 2.23% 29.41% 2356ms 11.97% std::type_info::operator== (inline) 0 0% 29.41% 2124ms 10.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.41% 2109ms 10.72% MutableMesh::ReMesh 12ms 0.061% 29.47% 2082ms 10.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.47% 1910ms 9.71% AbstractCellPopulation::WriteResultsToFiles 1897ms 9.64% 39.11% 1897ms 9.64% __strcmp_avx2 772ms 3.92% 43.04% 1775ms 9.02% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.8% 43.84% 1656ms 8.42% TetrahedralMesh::EdgeIterator::operator++ 58ms 0.29% 44.13% 1317ms 6.69% std::_Rb_tree::find (inline) 1ms 0.0051% 44.14% 1100ms 5.59% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0051% 44.14% 1078ms 5.48% MeshBasedCellPopulation::UpdateNodePairs 55ms 0.28% 44.42% 1056ms 5.37% operator new 12ms 0.061% 44.48% 1053ms 5.35% TetrahedralMesh::ImportFromMesher 15ms 0.076% 44.56% 1039ms 5.28% std::set::insert (inline) 16ms 0.081% 44.64% 1023ms 5.20% std::_Rb_tree::_M_insert_unique 220ms 1.12% 45.76% 990ms 5.03% __GI___libc_malloc 13ms 0.066% 45.83% 972ms 4.94% MeshBasedCellPopulation::SpringIterator::operator++ 36ms 0.18% 46.01% 928ms 4.72% std::__new_allocator::allocate (inline) 0 0% 46.01% 923ms 4.69% std::allocator_traits::allocate (inline) 0 0% 46.01% 804ms 4.09% triangulate 0 0% 46.01% 768ms 3.90% std::set::count (inline) 4ms 0.02% 46.03% 735ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 46.03% 728ms 3.70% delaunay 0 0% 46.03% 725ms 3.68% divconqdelaunay 1ms 0.0051% 46.03% 700ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 698ms 3.55% 49.58% 698ms 3.55% std::_Rb_tree::_S_right (inline) 6ms 0.03% 49.61% 694ms 3.53% CellPopulationElementWriter::Visit 366ms 1.86% 51.47% 675ms 3.43% _int_malloc 56ms 0.28% 51.76% 668ms 3.39% std::map::operator[] (partial-inline) 29ms 0.15% 51.90% 637ms 3.24% std::_Rb_tree::_M_insert_ (inline) 164ms 0.83% 52.74% 620ms 3.15% __dynamic_cast 0 0% 52.74% 605ms 3.07% std::_Rb_tree::_M_create_node (inline) 1ms 0.0051% 52.74% 591ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 16ms 0.081% 52.82% 589ms 2.99% std::less::operator() (inline) 0 0% 52.82% 583ms 2.96% std::_Rb_tree::_M_get_node (inline) 26ms 0.13% 52.96% 581ms 2.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 567ms 2.88% 55.84% 577ms 2.93% WntCellCycleOdeSystem::CalculateStoppingEvent 573ms 2.91% 58.75% 573ms 2.91% std::operator< (inline) 0 0% 58.75% 559ms 2.84% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 58.77% 553ms 2.81% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.036% 58.80% 541ms 2.75% Element::Element 0 0% 58.80% 540ms 2.74% std::map::find (inline) 0 0% 58.80% 536ms 2.72% std::_Rb_tree::lower_bound (inline) 0 0% 58.80% 536ms 2.72% std::map::lower_bound (inline) 20ms 0.1% 58.91% 530ms 2.69% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.061% 58.97% 509ms 2.59% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.051% 59.02% 509ms 2.59% MutableMesh::ReIndex 2ms 0.01% 59.03% 494ms 2.51% std::ostream::operator<< (inline) 76ms 0.39% 59.41% 492ms 2.50% std::ostream::_M_insert 9ms 0.046% 59.46% 476ms 2.42% Element::RegisterWithNodes (inline) 338ms 1.72% 61.18% 470ms 2.39% AbstractCellMutationState::AbstractCellMutationState 9ms 0.046% 61.22% 468ms 2.38% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.051% 61.27% 464ms 2.36% Node::AddElement 1ms 0.0051% 61.28% 450ms 2.29% AbstractCellProperty::IsSubType (inline) 132ms 0.67% 61.95% 405ms 2.06% __GI___libc_free 138ms 0.7% 62.65% 371ms 1.89% std::_Rb_tree::_M_get_insert_unique_pos 19ms 0.097% 62.75% 360ms 1.83% divconqrecurse 16ms 0.081% 62.83% 347ms 1.76% Node::RemoveElement 109ms 0.55% 63.38% 346ms 1.76% std::_Rb_tree::_M_erase 4ms 0.02% 63.40% 343ms 1.74% std::_Rb_tree::erase 2ms 0.01% 63.41% 342ms 1.74% std::_Vector_base::_M_allocate (inline) 0 0% 63.41% 342ms 1.74% std::set::erase (inline) 158ms 0.8% 64.22% 338ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 104ms 0.53% 64.75% 336ms 1.71% mergehulls 24ms 0.12% 64.87% 335ms 1.70% Element::ResetIndex 15ms 0.076% 64.94% 333ms 1.69% std::__new_allocator::deallocate (inline) 5ms 0.025% 64.97% 332ms 1.69% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.97% 326ms 1.66% std::allocator_traits::deallocate (inline) 7ms 0.036% 65.00% 317ms 1.61% Cell::GetCellProliferativeType 18ms 0.091% 65.10% 314ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 65.11% 303ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 65.12% 300ms 1.52% NodeLocationWriter::Visit 0 0% 65.12% 300ms 1.52% std::_Rb_tree::_M_drop_node (inline) 6ms 0.03% 65.15% 295ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 294ms 1.49% 66.65% 294ms 1.49% std::type_info::name (inline) 0 0% 66.65% 285ms 1.45% std::set::~set (inline) 4ms 0.02% 66.67% 280ms 1.42% Cell::GetMutationState 0 0% 66.67% 279ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.15% 66.81% 275ms 1.40% AbstractCellPopulation::Iterator::IsRealCell 216ms 1.10% 67.91% 273ms 1.39% _int_free 0 0% 67.91% 268ms 1.36% std::_Rb_tree::_M_put_node (inline) 13ms 0.066% 67.98% 261ms 1.33% AbstractTetrahedralElement::CalculateJacobian 22ms 0.11% 68.09% 260ms 1.32% std::num_put::_M_insert_float 250ms 1.27% 69.36% 251ms 1.28% std::vector::operator[] (inline) 17ms 0.086% 69.45% 250ms 1.27% std::vector::push_back (inline) 6ms 0.03% 69.48% 249ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.076% 69.55% 248ms 1.26% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.03% 69.58% 246ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 234ms 1.19% 70.77% 234ms 1.19% [libchaste_cell_based.so] 59ms 0.3% 71.07% 224ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 71.07% 224ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.091% 71.16% 224ms 1.14% std::vector::_M_realloc_insert 3ms 0.015% 71.18% 223ms 1.13% std::set::set (inline) 1ms 0.0051% 71.18% 222ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 71.20% 220ms 1.12% alternateaxes 171ms 0.87% 72.07% 219ms 1.11% AbstractElement::GetNodeGlobalIndex 46ms 0.23% 72.31% 218ms 1.11% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 203ms 1.03% 73.34% 215ms 1.09% vertexmedian 75ms 0.38% 73.72% 214ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 20ms 0.1% 73.82% 211ms 1.07% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 73.83% 207ms 1.05% std::__cxx11::collate::do_transform 148ms 0.75% 74.58% 204ms 1.04% malloc_consolidate 9ms 0.046% 74.63% 204ms 1.04% std::_Rb_tree::_M_erase_aux (inline) 27ms 0.14% 74.77% 199ms 1.01% AbstractTetrahedralElement::RefreshJacobian 5ms 0.025% 74.79% 197ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 74.80% 197ms 1.00% ___vsnprintf 0 0% 74.80% 195ms 0.99% __vsnprintf_internal (inline) 194ms 0.99% 75.79% 194ms 0.99% std::_Rb_tree_insert_and_rebalance 22ms 0.11% 75.90% 191ms 0.97% __printf_buffer 1ms 0.0051% 75.91% 190ms 0.97% MeshBasedCellPopulation::GetDampingConstant 60ms 0.3% 76.21% 190ms 0.97% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 76.22% 188ms 0.96% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 76.22% 185ms 0.94% OffLatticeSimulation::ApplyBoundaries 11ms 0.056% 76.27% 178ms 0.9% Element::MarkAsDeleted 25ms 0.13% 76.40% 174ms 0.88% TetrahedralMesh::Clear 1ms 0.0051% 76.40% 170ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 76.41% 169ms 0.86% CellProliferativeTypesWriter::VisitCell 159ms 0.81% 77.22% 159ms 0.81% Node::GetIndex 59ms 0.3% 77.52% 156ms 0.79% AbstractElement::GetNodeLocation 1ms 0.0051% 77.53% 156ms 0.79% __printf_fp_spec (inline) 12ms 0.061% 77.59% 155ms 0.79% __printf_fp_l_buffer 155ms 0.79% 78.38% 155ms 0.79% std::vector::size (inline) 1ms 0.0051% 78.38% 154ms 0.78% CellPropertyCollection::HasProperty 153ms 0.78% 79.16% 153ms 0.78% unlink_chunk 54ms 0.27% 79.43% 152ms 0.77% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 79.43% 151ms 0.77% Cell::HasCellProperty (inline) 2ms 0.01% 79.44% 147ms 0.75% boost::numeric::ublas::vector_assign (inline) 146ms 0.74% 80.18% 146ms 0.74% incircle 86ms 0.44% 80.62% 141ms 0.72% std::_Rb_tree::equal_range (inline) 8ms 0.041% 80.66% 138ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 54ms 0.27% 80.94% 137ms 0.7% __printf_fp_buffer_1 0 0% 80.94% 136ms 0.69% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 14ms 0.071% 81.01% 135ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 128ms 0.65% 81.66% 135ms 0.69% vertexsort 77ms 0.39% 82.05% 134ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.01% 82.06% 119ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 45ms 0.23% 82.29% 118ms 0.6% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 2ms 0.01% 82.30% 118ms 0.6% Cell::SetCellProliferativeType 10ms 0.051% 82.35% 113ms 0.57% boost::detail::shared_count::~shared_count (inline) 47ms 0.24% 82.59% 113ms 0.57% boost::numeric::ublas::indexing_vector_assign 0 0% 82.59% 113ms 0.57% boost::shared_ptr::~shared_ptr (inline) 9ms 0.046% 82.63% 111ms 0.56% boost::numeric::ublas::c_vector::c_vector (inline) 110ms 0.56% 83.19% 110ms 0.56% AbstractElement::IsDeleted 27ms 0.14% 83.33% 108ms 0.55% TetrahedralMesh::EdgesEnd 107ms 0.54% 83.87% 107ms 0.54% AbstractCellProperty::~AbstractCellProperty 19ms 0.097% 83.97% 105ms 0.53% std::num_put::_M_insert_int 0 0% 83.97% 104ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.025% 84.00% 104ms 0.53% MeshBasedCellPopulation::SpringsEnd (inline) 36ms 0.18% 84.18% 102ms 0.52% std::__ostream_insert 2ms 0.01% 84.19% 99ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath