File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16623ms, 83.50% of 19907ms total Dropped 790 nodes (cum <= 99.53ms) flat flat% sum% cum cum% 0 0% 0% 19862ms 99.77% __libc_start_call_main 0 0% 0% 19862ms 99.77% __libc_start_main_impl 0 0% 0% 19862ms 99.77% _start 0 0% 0% 19843ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19843ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19843ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19843ms 99.68% main 0 0% 0% 19806ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19806ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19806ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19780ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15381ms 77.26% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 10198ms 51.23% AbstractCellBasedSimulation::DoCellBirth 7ms 0.035% 0.045% 10105ms 50.76% Cell::ReadyToDivide 3ms 0.015% 0.06% 10039ms 50.43% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.065% 9884ms 49.65% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.04% 0.11% 9875ms 49.61% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.12% 9864ms 49.55% CellCycleModelOdeHandler::SolveOdeToTime 71ms 0.36% 0.48% 9699ms 48.72% AbstractOneStepIvpOdeSolver::InternalSolve 902ms 4.53% 5.01% 8859ms 44.50% RungeKutta4IvpOdeSolver::CalculateNextYValue 3675ms 18.46% 23.47% 7733ms 38.85% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.47% 5084ms 25.54% MeshBasedCellPopulation::Update 204ms 1.02% 24.49% 4119ms 20.69% AbstractCellProperty::IsType (inline) 7ms 0.035% 24.53% 3961ms 19.90% Cylindrical2dMesh::ReMesh 547ms 2.75% 27.28% 2820ms 14.17% AbstractCellProperty::IsSame 0 0% 27.28% 2468ms 12.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 437ms 2.20% 29.47% 2273ms 11.42% std::type_info::operator== (inline) 0 0% 29.47% 2150ms 10.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.47% 2146ms 10.78% MutableMesh::ReMesh 10ms 0.05% 29.52% 2102ms 10.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.52% 1923ms 9.66% AbstractCellPopulation::WriteResultsToFiles 1812ms 9.10% 38.62% 1812ms 9.10% __strcmp_avx2 765ms 3.84% 42.47% 1783ms 8.96% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.75% 43.22% 1656ms 8.32% TetrahedralMesh::EdgeIterator::operator++ 71ms 0.36% 43.58% 1350ms 6.78% std::_Rb_tree::find (inline) 4ms 0.02% 43.60% 1107ms 5.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.005% 43.60% 1087ms 5.46% MeshBasedCellPopulation::UpdateNodePairs 21ms 0.11% 43.71% 1077ms 5.41% TetrahedralMesh::ImportFromMesher 42ms 0.21% 43.92% 1054ms 5.29% operator new 236ms 1.19% 45.10% 1003ms 5.04% __GI___libc_malloc 12ms 0.06% 45.17% 978ms 4.91% std::set::insert (inline) 10ms 0.05% 45.22% 972ms 4.88% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.065% 45.28% 966ms 4.85% std::_Rb_tree::_M_insert_unique 37ms 0.19% 45.47% 932ms 4.68% std::__new_allocator::allocate (inline) 0 0% 45.47% 927ms 4.66% std::allocator_traits::allocate (inline) 0 0% 45.47% 806ms 4.05% triangulate 0 0% 45.47% 801ms 4.02% std::set::count (inline) 0 0% 45.47% 719ms 3.61% delaunay 3ms 0.015% 45.48% 718ms 3.61% divconqdelaunay 3ms 0.015% 45.50% 715ms 3.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 4ms 0.02% 45.52% 708ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 371ms 1.86% 47.38% 696ms 3.50% _int_malloc 669ms 3.36% 50.74% 669ms 3.36% std::_Rb_tree::_S_right (inline) 649ms 3.26% 54.00% 661ms 3.32% WntCellCycleOdeSystem::CalculateStoppingEvent 7ms 0.035% 54.04% 660ms 3.32% CellPopulationElementWriter::Visit 49ms 0.25% 54.28% 640ms 3.21% std::map::operator[] (partial-inline) 191ms 0.96% 55.24% 639ms 3.21% __dynamic_cast 17ms 0.085% 55.33% 617ms 3.10% std::less::operator() (inline) 0 0% 55.33% 602ms 3.02% std::_Rb_tree::_M_create_node (inline) 20ms 0.1% 55.43% 602ms 3.02% std::_Rb_tree::_M_insert_ (inline) 600ms 3.01% 58.44% 600ms 3.01% std::operator< (inline) 0 0% 58.44% 588ms 2.95% std::_Rb_tree::_M_get_node (inline) 20ms 0.1% 58.54% 584ms 2.93% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.02% 58.56% 574ms 2.88% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.04% 58.60% 571ms 2.87% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.60% 558ms 2.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.60% 539ms 2.71% std::map::find (inline) 7ms 0.035% 58.64% 537ms 2.70% Element::Element 19ms 0.095% 58.73% 526ms 2.64% AbstractCellPopulation::GetCellUsingLocationIndex 347ms 1.74% 60.48% 523ms 2.63% AbstractCellMutationState::AbstractCellMutationState 7ms 0.035% 60.51% 521ms 2.62% MutableMesh::ReIndex 0 0% 60.51% 520ms 2.61% std::_Rb_tree::lower_bound (inline) 0 0% 60.51% 520ms 2.61% std::map::lower_bound (inline) 15ms 0.075% 60.59% 504ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 54ms 0.27% 60.86% 504ms 2.53% std::ostream::_M_insert 0 0% 60.86% 504ms 2.53% std::ostream::operator<< (inline) 15ms 0.075% 60.93% 477ms 2.40% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.01% 60.94% 460ms 2.31% AbstractCellProperty::IsSubType (inline) 10ms 0.05% 60.99% 455ms 2.29% Element::RegisterWithNodes (inline) 13ms 0.065% 61.06% 444ms 2.23% Node::AddElement 154ms 0.77% 61.83% 413ms 2.07% __GI___libc_free 19ms 0.095% 61.93% 400ms 2.01% Node::RemoveElement 4ms 0.02% 61.95% 400ms 2.01% std::_Rb_tree::erase 1ms 0.005% 61.95% 400ms 2.01% std::set::erase (inline) 115ms 0.58% 62.53% 356ms 1.79% std::_Rb_tree::_M_erase 136ms 0.68% 63.21% 351ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 15ms 0.075% 63.29% 347ms 1.74% divconqrecurse 0 0% 63.29% 343ms 1.72% NodeLocationWriter::Visit 14ms 0.07% 63.36% 342ms 1.72% std::__new_allocator::deallocate (inline) 2ms 0.01% 63.37% 341ms 1.71% std::_Vector_base::_M_allocate (inline) 28ms 0.14% 63.51% 339ms 1.70% Element::ResetIndex 0 0% 63.51% 336ms 1.69% std::allocator_traits::deallocate (inline) 163ms 0.82% 64.33% 332ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 85ms 0.43% 64.76% 329ms 1.65% mergehulls 12ms 0.06% 64.82% 326ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 27ms 0.14% 64.95% 323ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 24ms 0.12% 65.07% 310ms 1.56% std::num_put::_M_insert_float 3ms 0.015% 65.09% 309ms 1.55% Cell::GetMutationState 0 0% 65.09% 304ms 1.53% std::set::~set (inline) 0 0% 65.09% 302ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.025% 65.11% 299ms 1.50% Cell::GetCellProliferativeType 0 0% 65.11% 299ms 1.50% std::_Rb_tree::_M_drop_node (inline) 6ms 0.03% 65.14% 296ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 65.15% 287ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 34ms 0.17% 65.32% 279ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 276ms 1.39% 66.71% 276ms 1.39% std::type_info::name (inline) 0 0% 66.71% 269ms 1.35% std::_Rb_tree::_M_put_node (inline) 261ms 1.31% 68.02% 261ms 1.31% std::vector::operator[] (inline) 15ms 0.075% 68.10% 261ms 1.31% std::vector::push_back (inline) 211ms 1.06% 69.16% 259ms 1.30% _int_free 24ms 0.12% 69.28% 254ms 1.28% AbstractTetrahedralElement::CalculateJacobian 253ms 1.27% 70.55% 253ms 1.27% [libchaste_cell_based.so] 8ms 0.04% 70.59% 248ms 1.25% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.065% 70.65% 243ms 1.22% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.035% 70.69% 243ms 1.22% std::__cxx11::collate::do_transform 2ms 0.01% 70.70% 240ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 70.71% 237ms 1.19% alternateaxes 9ms 0.045% 70.76% 237ms 1.19% std::vector::_M_realloc_insert 63ms 0.32% 71.08% 235ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 43ms 0.22% 71.29% 234ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 217ms 1.09% 72.38% 233ms 1.17% vertexmedian 5ms 0.025% 72.41% 232ms 1.17% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.005% 72.41% 231ms 1.16% ___vsnprintf 0 0% 72.41% 230ms 1.16% __vsnprintf_internal (inline) 29ms 0.15% 72.56% 228ms 1.15% __printf_buffer 73ms 0.37% 72.92% 226ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.035% 72.96% 221ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.005% 72.96% 221ms 1.11% std::set::set (inline) 15ms 0.075% 73.04% 217ms 1.09% Element::MarkAsDeleted 2ms 0.01% 73.05% 213ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 31ms 0.16% 73.21% 210ms 1.05% std::_Rb_tree::_M_copy (inline) 1ms 0.005% 73.21% 204ms 1.02% OffLatticeSimulation::ApplyBoundaries 11ms 0.055% 73.27% 203ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 23ms 0.12% 73.38% 199ms 1% AbstractTetrahedralElement::RefreshJacobian 17ms 0.085% 73.47% 195ms 0.98% TetrahedralMesh::Clear 146ms 0.73% 74.20% 195ms 0.98% malloc_consolidate 1ms 0.005% 74.21% 187ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.21% 187ms 0.94% MeshBasedCellPopulation::GetDampingConstant 10ms 0.05% 74.26% 178ms 0.89% __printf_fp_l_buffer 0 0% 74.26% 178ms 0.89% __printf_fp_spec (inline) 144ms 0.72% 74.98% 177ms 0.89% AbstractElement::GetNodeGlobalIndex 5ms 0.025% 75.00% 175ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 48ms 0.24% 75.24% 175ms 0.88% std::_Rb_tree::_M_clone_node (inline) 77ms 0.39% 75.63% 167ms 0.84% AbstractElement::GetNodeLocation 167ms 0.84% 76.47% 167ms 0.84% Node::GetIndex 163ms 0.82% 77.29% 163ms 0.82% std::_Rb_tree_insert_and_rebalance 74ms 0.37% 77.66% 162ms 0.81% __printf_fp_buffer_1 5ms 0.025% 77.69% 159ms 0.8% CellProliferativeTypesWriter::VisitCell 159ms 0.8% 78.48% 159ms 0.8% unlink_chunk 105ms 0.53% 79.01% 158ms 0.79% std::_Rb_tree::equal_range (inline) 3ms 0.015% 79.03% 153ms 0.77% CellPropertyCollection::HasProperty 150ms 0.75% 79.78% 150ms 0.75% incircle 0 0% 79.78% 146ms 0.73% Cell::HasCellProperty (inline) 1ms 0.005% 79.79% 143ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 26ms 0.13% 79.92% 129ms 0.65% TetrahedralMesh::EdgesEnd 56ms 0.28% 80.20% 127ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 80.21% 122ms 0.61% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 45ms 0.23% 80.44% 121ms 0.61% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.025% 80.46% 121ms 0.61% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 73ms 0.37% 80.83% 117ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 106ms 0.53% 81.36% 117ms 0.59% vertexsort 3ms 0.015% 81.38% 116ms 0.58% Cell::SetCellProliferativeType 3ms 0.015% 81.39% 116ms 0.58% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 81.41% 114ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 111ms 0.56% 81.97% 111ms 0.56% AbstractElement::IsDeleted 8ms 0.04% 82.01% 111ms 0.56% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 111ms 0.56% 82.57% 111ms 0.56% std::_Rb_tree_rebalance_for_erase 111ms 0.56% 83.13% 111ms 0.56% std::vector::size (inline) 1ms 0.005% 83.13% 107ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 12ms 0.06% 83.19% 107ms 0.54% Node::~Node 34ms 0.17% 83.36% 106ms 0.53% std::__ostream_insert 7ms 0.035% 83.40% 103ms 0.52% boost::numeric::ublas::c_vector::c_vector (inline) 21ms 0.11% 83.50% 100ms 0.5% std::num_put::_M_insert_int