File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16651ms, 84.53% of 19698ms total Dropped 763 nodes (cum <= 98.49ms) flat flat% sum% cum cum% 0 0% 0% 19655ms 99.78% __libc_start_call_main 0 0% 0% 19655ms 99.78% __libc_start_main_impl 0 0% 0% 19655ms 99.78% _start 0 0% 0% 19637ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19637ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19637ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19637ms 99.69% main 0 0% 0% 19603ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19603ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19603ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19576ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15215ms 77.24% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 10091ms 51.23% AbstractCellBasedSimulation::DoCellBirth 7ms 0.036% 0.046% 9994ms 50.74% Cell::ReadyToDivide 6ms 0.03% 0.076% 9930ms 50.41% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.076% 9808ms 49.79% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.071% 0.15% 9797ms 49.74% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.17% 9780ms 49.65% CellCycleModelOdeHandler::SolveOdeToTime 82ms 0.42% 0.58% 9632ms 48.90% AbstractOneStepIvpOdeSolver::InternalSolve 860ms 4.37% 4.95% 8820ms 44.78% RungeKutta4IvpOdeSolver::CalculateNextYValue 3654ms 18.55% 23.50% 7756ms 39.37% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.50% 5029ms 25.53% MeshBasedCellPopulation::Update 173ms 0.88% 24.38% 4123ms 20.93% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.40% 3922ms 19.91% Cylindrical2dMesh::ReMesh 624ms 3.17% 27.57% 2884ms 14.64% AbstractCellProperty::IsSame 1ms 0.0051% 27.58% 2441ms 12.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 464ms 2.36% 29.93% 2260ms 11.47% std::type_info::operator== (inline) 0 0% 29.93% 2108ms 10.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.93% 2089ms 10.61% MutableMesh::ReMesh 5ms 0.025% 29.96% 2067ms 10.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0051% 29.96% 1913ms 9.71% AbstractCellPopulation::WriteResultsToFiles 804ms 4.08% 34.04% 1855ms 9.42% std::_Rb_tree::_M_lower_bound (inline) 1767ms 8.97% 43.01% 1767ms 8.97% __strcmp_avx2 147ms 0.75% 43.76% 1625ms 8.25% TetrahedralMesh::EdgeIterator::operator++ 73ms 0.37% 44.13% 1326ms 6.73% std::_Rb_tree::find (inline) 5ms 0.025% 44.16% 1097ms 5.57% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0051% 44.16% 1077ms 5.47% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.061% 44.22% 1061ms 5.39% TetrahedralMesh::ImportFromMesher 60ms 0.3% 44.53% 1040ms 5.28% operator new 233ms 1.18% 45.71% 972ms 4.93% __GI___libc_malloc 15ms 0.076% 45.79% 955ms 4.85% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.036% 45.82% 931ms 4.73% std::set::insert (inline) 10ms 0.051% 45.87% 925ms 4.70% std::_Rb_tree::_M_insert_unique 34ms 0.17% 46.05% 898ms 4.56% std::__new_allocator::allocate (inline) 0 0% 46.05% 894ms 4.54% std::allocator_traits::allocate (inline) 0 0% 46.05% 807ms 4.10% std::set::count (inline) 0 0% 46.05% 793ms 4.03% triangulate 61ms 0.31% 46.35% 759ms 3.85% std::map::operator[] (partial-inline) 4ms 0.02% 46.38% 744ms 3.78% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 46.38% 721ms 3.66% delaunay 3ms 0.015% 46.39% 720ms 3.66% divconqdelaunay 701ms 3.56% 49.95% 701ms 3.56% std::_Rb_tree::_S_right (inline) 1ms 0.0051% 49.95% 691ms 3.51% AbstractTwoBodyInteractionForce::AddForceContribution 377ms 1.91% 51.87% 664ms 3.37% _int_malloc 5ms 0.025% 51.89% 654ms 3.32% CellPopulationElementWriter::Visit 628ms 3.19% 55.08% 637ms 3.23% WntCellCycleOdeSystem::CalculateStoppingEvent 188ms 0.95% 56.04% 604ms 3.07% __dynamic_cast 0 0% 56.04% 604ms 3.07% std::_Rb_tree::lower_bound (inline) 0 0% 56.04% 604ms 3.07% std::map::lower_bound (inline) 29ms 0.15% 56.18% 600ms 3.05% AbstractCellPopulation::GetCellUsingLocationIndex 22ms 0.11% 56.30% 600ms 3.05% std::less::operator() (inline) 20ms 0.1% 56.40% 582ms 2.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 27ms 0.14% 56.53% 579ms 2.94% std::_Rb_tree::_M_insert_ (inline) 578ms 2.93% 59.47% 578ms 2.93% std::operator< (inline) 0 0% 59.47% 572ms 2.90% std::_Rb_tree::_M_create_node (inline) 2ms 0.01% 59.48% 569ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.036% 59.51% 551ms 2.80% Element::Element 0 0% 59.51% 550ms 2.79% std::_Rb_tree::_M_get_node (inline) 6ms 0.03% 59.54% 541ms 2.75% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.046% 59.59% 525ms 2.67% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.041% 59.63% 520ms 2.64% MutableMesh::ReIndex 0 0% 59.63% 515ms 2.61% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 59.63% 513ms 2.60% std::map::find (inline) 11ms 0.056% 59.69% 498ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.046% 59.73% 474ms 2.41% Element::RegisterWithNodes (inline) 1ms 0.0051% 59.74% 471ms 2.39% std::ostream::operator<< (inline) 55ms 0.28% 60.02% 470ms 2.39% std::ostream::_M_insert 306ms 1.55% 61.57% 468ms 2.38% AbstractCellMutationState::AbstractCellMutationState 17ms 0.086% 61.66% 461ms 2.34% Node::AddElement 1ms 0.0051% 61.66% 442ms 2.24% AbstractCellProperty::IsSubType (inline) 140ms 0.71% 62.37% 398ms 2.02% __GI___libc_free 2ms 0.01% 62.38% 393ms 2.00% std::set::erase (inline) 11ms 0.056% 62.44% 392ms 1.99% std::_Rb_tree::erase 12ms 0.061% 62.50% 386ms 1.96% Node::RemoveElement 42ms 0.21% 62.71% 362ms 1.84% Element::ResetIndex 15ms 0.076% 62.79% 350ms 1.78% std::__new_allocator::deallocate (inline) 5ms 0.025% 62.81% 348ms 1.77% std::_Vector_base::_M_allocate (inline) 7ms 0.036% 62.85% 347ms 1.76% divconqrecurse 0 0% 62.85% 343ms 1.74% std::allocator_traits::deallocate (inline) 119ms 0.6% 63.45% 338ms 1.72% std::_Rb_tree::_M_get_insert_unique_pos 6ms 0.03% 63.48% 337ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 99ms 0.5% 63.99% 327ms 1.66% mergehulls 98ms 0.5% 64.48% 326ms 1.65% std::_Rb_tree::_M_erase 25ms 0.13% 64.61% 310ms 1.57% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 64.62% 302ms 1.53% NodeLocationWriter::Visit 2ms 0.01% 64.63% 301ms 1.53% Cell::GetCellProliferativeType 4ms 0.02% 64.65% 299ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 140ms 0.71% 65.36% 297ms 1.51% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.36% 296ms 1.50% std::_Rb_tree::_M_drop_node (inline) 288ms 1.46% 66.82% 288ms 1.46% std::type_info::name (inline) 4ms 0.02% 66.84% 285ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 66.85% 283ms 1.44% Cell::GetMutationState 9ms 0.046% 66.90% 283ms 1.44% std::vector::push_back (inline) 0 0% 66.90% 275ms 1.40% std::set::~set (inline) 0 0% 66.90% 270ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.90% 269ms 1.37% std::_Rb_tree::_M_put_node (inline) 30ms 0.15% 67.05% 267ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.056% 67.11% 264ms 1.34% std::vector::_M_realloc_insert 16ms 0.081% 67.19% 261ms 1.33% AbstractTetrahedralElement::CalculateJacobian 18ms 0.091% 67.28% 260ms 1.32% std::num_put::_M_insert_float 208ms 1.06% 68.34% 258ms 1.31% _int_free 81ms 0.41% 68.75% 257ms 1.30% ApcOneHitCellMutationState::ApcOneHitCellMutationState 250ms 1.27% 70.02% 253ms 1.28% std::vector::operator[] (inline) 17ms 0.086% 70.10% 252ms 1.28% std::_Rb_tree::_Rb_tree (partial-inline) 251ms 1.27% 71.38% 251ms 1.27% [libchaste_cell_based.so] 8ms 0.041% 71.42% 240ms 1.22% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 71.45% 232ms 1.18% alternateaxes 0 0% 71.45% 230ms 1.17% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 71.46% 228ms 1.16% std::set::set (inline) 208ms 1.06% 72.51% 222ms 1.13% vertexmedian 4ms 0.02% 72.54% 219ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 78ms 0.4% 72.93% 216ms 1.10% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 72.93% 206ms 1.05% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 72.94% 204ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 72.96% 204ms 1.04% std::__cxx11::collate::do_transform 27ms 0.14% 73.09% 203ms 1.03% AbstractTetrahedralElement::RefreshJacobian 20ms 0.1% 73.20% 202ms 1.03% std::_Rb_tree::_M_copy (inline) 0 0% 73.20% 198ms 1.01% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 73.21% 193ms 0.98% ___vsnprintf 11ms 0.056% 73.27% 192ms 0.97% Element::MarkAsDeleted 1ms 0.0051% 73.27% 190ms 0.96% __vsnprintf_internal (inline) 23ms 0.12% 73.39% 188ms 0.95% __printf_buffer 34ms 0.17% 73.56% 187ms 0.95% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.01% 73.57% 186ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.57% 186ms 0.94% MeshBasedCellPopulation::GetDampingConstant 185ms 0.94% 74.51% 185ms 0.94% Node::GetIndex 150ms 0.76% 75.27% 183ms 0.93% AbstractElement::GetNodeGlobalIndex 132ms 0.67% 75.94% 181ms 0.92% malloc_consolidate 55ms 0.28% 76.22% 180ms 0.91% std::_Rb_tree::_M_clone_node (inline) 6ms 0.03% 76.25% 176ms 0.89% AbstractTetrahedralElement::AbstractTetrahedralElement 174ms 0.88% 77.13% 174ms 0.88% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 77.17% 173ms 0.88% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.03% 77.20% 169ms 0.86% CellProliferativeTypesWriter::VisitCell 70ms 0.36% 77.55% 158ms 0.8% AbstractElement::GetNodeLocation 7ms 0.036% 77.59% 152ms 0.77% __printf_fp_l_buffer 0 0% 77.59% 152ms 0.77% __printf_fp_spec (inline) 104ms 0.53% 78.11% 145ms 0.74% std::_Rb_tree::equal_range (inline) 13ms 0.066% 78.18% 140ms 0.71% TetrahedralMesh::Clear 6ms 0.03% 78.21% 138ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 68ms 0.35% 78.56% 138ms 0.7% __printf_fp_buffer_1 52ms 0.26% 78.82% 135ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 78.82% 134ms 0.68% boost::numeric::ublas::vector_assign (inline) 134ms 0.68% 79.50% 134ms 0.68% incircle 133ms 0.68% 80.18% 133ms 0.68% unlink_chunk 26ms 0.13% 80.31% 129ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 128ms 0.65% 80.96% 128ms 0.65% std::vector::size (inline) 79ms 0.4% 81.36% 127ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 12ms 0.061% 81.42% 126ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.015% 81.43% 126ms 0.64% CellPropertyCollection::HasProperty 11ms 0.056% 81.49% 125ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 109ms 0.55% 82.04% 125ms 0.63% vertexsort 0 0% 82.04% 124ms 0.63% Cell::HasCellProperty (inline) 119ms 0.6% 82.65% 119ms 0.6% AbstractElement::IsDeleted 3ms 0.015% 82.66% 118ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 36ms 0.18% 82.85% 116ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 11ms 0.056% 82.90% 115ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 82.90% 115ms 0.58% boost::shared_ptr::~shared_ptr (inline) 115ms 0.58% 83.49% 115ms 0.58% std::_Rb_tree_rebalance_for_erase 3ms 0.015% 83.50% 113ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 22ms 0.11% 83.61% 113ms 0.57% std::num_put::_M_insert_int 0 0% 83.61% 110ms 0.56% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 42ms 0.21% 83.83% 105ms 0.53% std::__ostream_insert 102ms 0.52% 84.34% 102ms 0.52% boost::detail::sp_counted_base::release 35ms 0.18% 84.52% 101ms 0.51% boost::numeric::ublas::indexing_vector_assign 0 0% 84.52% 100ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 2ms 0.01% 84.53% 99ms 0.5% Cell::SetCellProliferativeType