File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16771ms, 83.80% of 20013ms total Dropped 762 nodes (cum <= 100.06ms) flat flat% sum% cum cum% 0 0% 0% 19969ms 99.78% __libc_start_call_main 0 0% 0% 19969ms 99.78% __libc_start_main_impl 0 0% 0% 19969ms 99.78% _start 0 0% 0% 19950ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19950ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19950ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19950ms 99.69% main 0 0% 0% 19911ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19911ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19911ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19885ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15388ms 76.89% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10182ms 50.88% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 10075ms 50.34% Cell::ReadyToDivide 5ms 0.025% 0.045% 10011ms 50.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.055% 9868ms 49.31% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.085% 0.14% 9857ms 49.25% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.14% 9834ms 49.14% CellCycleModelOdeHandler::SolveOdeToTime 90ms 0.45% 0.59% 9672ms 48.33% AbstractOneStepIvpOdeSolver::InternalSolve 911ms 4.55% 5.14% 8783ms 43.89% RungeKutta4IvpOdeSolver::CalculateNextYValue 3670ms 18.34% 23.48% 7672ms 38.34% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.49% 5083ms 25.40% MeshBasedCellPopulation::Update 204ms 1.02% 24.51% 4076ms 20.37% AbstractCellProperty::IsType (inline) 6ms 0.03% 24.54% 3909ms 19.53% Cylindrical2dMesh::ReMesh 534ms 2.67% 27.21% 2824ms 14.11% AbstractCellProperty::IsSame 0 0% 27.21% 2500ms 12.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 415ms 2.07% 29.28% 2290ms 11.44% std::type_info::operator== (inline) 0 0% 29.28% 2181ms 10.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.065% 29.35% 2133ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.35% 2121ms 10.60% MutableMesh::ReMesh 0 0% 29.35% 1990ms 9.94% AbstractCellPopulation::WriteResultsToFiles 1885ms 9.42% 38.76% 1885ms 9.42% __strcmp_avx2 724ms 3.62% 42.38% 1807ms 9.03% std::_Rb_tree::_M_lower_bound (inline) 176ms 0.88% 43.26% 1688ms 8.43% TetrahedralMesh::EdgeIterator::operator++ 61ms 0.3% 43.57% 1392ms 6.96% std::_Rb_tree::find (inline) 0 0% 43.57% 1136ms 5.68% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.59% 1119ms 5.59% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 52ms 0.26% 43.85% 1070ms 5.35% operator new 16ms 0.08% 43.93% 1062ms 5.31% TetrahedralMesh::ImportFromMesher 9ms 0.045% 43.98% 1014ms 5.07% MeshBasedCellPopulation::SpringIterator::operator++ 239ms 1.19% 45.17% 1012ms 5.06% __GI___libc_malloc 6ms 0.03% 45.20% 988ms 4.94% std::set::insert (inline) 18ms 0.09% 45.29% 982ms 4.91% std::_Rb_tree::_M_insert_unique 46ms 0.23% 45.52% 950ms 4.75% std::__new_allocator::allocate (inline) 0 0% 45.52% 943ms 4.71% std::allocator_traits::allocate (inline) 0 0% 45.52% 834ms 4.17% std::set::count (inline) 0 0% 45.52% 815ms 4.07% triangulate 0 0% 45.52% 736ms 3.68% delaunay 3ms 0.015% 45.54% 735ms 3.67% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.015% 45.55% 735ms 3.67% divconqdelaunay 0 0% 45.55% 720ms 3.60% AbstractTwoBodyInteractionForce::AddForceContribution 386ms 1.93% 47.48% 695ms 3.47% _int_malloc 23ms 0.11% 47.59% 687ms 3.43% std::less::operator() (inline) 6ms 0.03% 47.62% 684ms 3.42% CellPopulationElementWriter::Visit 674ms 3.37% 50.99% 674ms 3.37% std::_Rb_tree::_S_right (inline) 189ms 0.94% 51.94% 672ms 3.36% __dynamic_cast 59ms 0.29% 52.23% 665ms 3.32% std::map::operator[] (partial-inline) 664ms 3.32% 55.55% 664ms 3.32% std::operator< (inline) 641ms 3.20% 58.75% 655ms 3.27% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.75% 614ms 3.07% std::_Rb_tree::_M_create_node (inline) 25ms 0.12% 58.88% 610ms 3.05% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 20ms 0.1% 58.98% 590ms 2.95% std::_Rb_tree::_M_insert_ (inline) 4ms 0.02% 59.00% 589ms 2.94% CellPropertyCollection::GetPropertiesType (inline) 0 0% 59.00% 589ms 2.94% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 59.01% 583ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 25ms 0.12% 59.13% 566ms 2.83% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 59.13% 561ms 2.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 59.13% 553ms 2.76% std::map::find (inline) 1ms 0.005% 59.14% 540ms 2.70% Element::Element 0 0% 59.14% 519ms 2.59% std::_Rb_tree::lower_bound (inline) 0 0% 59.14% 519ms 2.59% std::map::lower_bound (inline) 10ms 0.05% 59.19% 517ms 2.58% Element::RegisterWithNodes (inline) 12ms 0.06% 59.25% 510ms 2.55% Node::AddElement 3ms 0.015% 59.26% 496ms 2.48% AbstractCellProperty::IsSubType (inline) 11ms 0.055% 59.32% 496ms 2.48% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.05% 59.37% 496ms 2.48% MutableMesh::ReIndex 2ms 0.01% 59.38% 495ms 2.47% std::ostream::operator<< (inline) 70ms 0.35% 59.73% 493ms 2.46% std::ostream::_M_insert 311ms 1.55% 61.28% 476ms 2.38% AbstractCellMutationState::AbstractCellMutationState 12ms 0.06% 61.34% 463ms 2.31% Cylindrical2dMesh::CorrectNonPeriodicMesh 127ms 0.63% 61.97% 396ms 1.98% __GI___libc_free 12ms 0.06% 62.03% 377ms 1.88% divconqrecurse 152ms 0.76% 62.79% 374ms 1.87% std::_Rb_tree::_M_get_insert_unique_pos 109ms 0.54% 63.34% 359ms 1.79% mergehulls 10ms 0.05% 63.39% 357ms 1.78% Node::RemoveElement 3ms 0.015% 63.40% 357ms 1.78% std::_Vector_base::_M_allocate (inline) 3ms 0.015% 63.42% 357ms 1.78% std::set::erase (inline) 10ms 0.05% 63.47% 356ms 1.78% std::_Rb_tree::erase 129ms 0.64% 64.11% 355ms 1.77% std::_Rb_tree::_M_erase 156ms 0.78% 64.89% 347ms 1.73% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.11% 65.00% 332ms 1.66% Element::ResetIndex 11ms 0.055% 65.06% 324ms 1.62% std::__new_allocator::deallocate (inline) 2ms 0.01% 65.07% 321ms 1.60% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.085% 65.15% 321ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 0 0% 65.15% 318ms 1.59% std::allocator_traits::deallocate (inline) 5ms 0.025% 65.18% 315ms 1.57% NodeLocationWriter::Visit 3ms 0.015% 65.19% 310ms 1.55% Cell::GetCellProliferativeType 0 0% 65.19% 307ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.19% 307ms 1.53% Cell::GetMutationState 30ms 0.15% 65.34% 300ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.03% 65.37% 298ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 298ms 1.49% 66.86% 298ms 1.49% std::type_info::name (inline) 9ms 0.045% 66.91% 296ms 1.48% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 66.91% 293ms 1.46% std::set::~set (inline) 0 0% 66.91% 292ms 1.46% std::_Rb_tree::_M_drop_node (inline) 24ms 0.12% 67.03% 292ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 222ms 1.11% 68.14% 269ms 1.34% _int_free 4ms 0.02% 68.16% 262ms 1.31% std::set::set (inline) 16ms 0.08% 68.24% 261ms 1.30% std::vector::push_back (inline) 17ms 0.085% 68.32% 257ms 1.28% std::num_put::_M_insert_float 0 0% 68.32% 251ms 1.25% std::_Rb_tree::_M_put_node (inline) 10ms 0.05% 68.37% 249ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 22ms 0.11% 68.48% 248ms 1.24% AbstractTetrahedralElement::CalculateJacobian 4ms 0.02% 68.50% 245ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.005% 68.51% 237ms 1.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.1% 68.61% 236ms 1.18% std::_Rb_tree::_M_copy (inline) 234ms 1.17% 69.77% 234ms 1.17% std::vector::operator[] (inline) 233ms 1.16% 70.94% 233ms 1.16% [libchaste_cell_based.so] 1ms 0.005% 70.94% 232ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 72ms 0.36% 71.30% 231ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 13ms 0.065% 71.37% 229ms 1.14% std::vector::_M_realloc_insert 1ms 0.005% 71.37% 223ms 1.11% alternateaxes 211ms 1.05% 72.43% 222ms 1.11% vertexmedian 43ms 0.21% 72.64% 218ms 1.09% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 73ms 0.36% 73.01% 213ms 1.06% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 66ms 0.33% 73.34% 212ms 1.06% std::_Rb_tree::_M_clone_node (inline) 160ms 0.8% 74.14% 204ms 1.02% malloc_consolidate 6ms 0.03% 74.17% 203ms 1.01% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.1% 74.27% 200ms 1% Element::MarkAsDeleted 5ms 0.025% 74.30% 198ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 74.30% 196ms 0.98% OffLatticeSimulation::ApplyBoundaries 15ms 0.075% 74.37% 195ms 0.97% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 74.39% 189ms 0.94% std::__cxx11::collate::do_transform 17ms 0.085% 74.47% 185ms 0.92% TetrahedralMesh::Clear 1ms 0.005% 74.48% 184ms 0.92% MeshBasedCellPopulation::GetDampingConstant 1ms 0.005% 74.48% 183ms 0.91% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.005% 74.49% 179ms 0.89% ___vsnprintf 0 0% 74.49% 178ms 0.89% __vsnprintf_internal (inline) 176ms 0.88% 75.37% 176ms 0.88% std::_Rb_tree_insert_and_rebalance 24ms 0.12% 75.49% 174ms 0.87% __printf_buffer 129ms 0.64% 76.13% 168ms 0.84% AbstractElement::GetNodeGlobalIndex 166ms 0.83% 76.96% 166ms 0.83% Node::GetIndex 3ms 0.015% 76.97% 161ms 0.8% boost::numeric::ublas::vector_assign (inline) 159ms 0.79% 77.77% 159ms 0.79% incircle 75ms 0.37% 78.14% 158ms 0.79% AbstractElement::GetNodeLocation 3ms 0.015% 78.16% 157ms 0.78% CellProliferativeTypesWriter::VisitCell 2ms 0.01% 78.17% 154ms 0.77% CellPropertyCollection::HasProperty 112ms 0.56% 78.73% 152ms 0.76% std::_Rb_tree::equal_range (inline) 0 0% 78.73% 148ms 0.74% Cell::HasCellProperty (inline) 4ms 0.02% 78.75% 147ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.05% 78.80% 142ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.025% 78.82% 140ms 0.7% __printf_fp_l_buffer 0 0% 78.82% 140ms 0.7% __printf_fp_spec (inline) 11ms 0.055% 78.88% 140ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.015% 78.89% 136ms 0.68% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 46ms 0.23% 79.12% 132ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 67ms 0.33% 79.46% 131ms 0.65% __printf_fp_buffer_1 4ms 0.02% 79.48% 131ms 0.65% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 72ms 0.36% 79.84% 129ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 128ms 0.64% 80.48% 128ms 0.64% unlink_chunk 38ms 0.19% 80.67% 127ms 0.63% boost::numeric::ublas::indexing_vector_assign 0 0% 80.67% 126ms 0.63% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.67% 125ms 0.62% OutputFileHandler::OpenOutputFile 118ms 0.59% 81.26% 123ms 0.61% vertexsort 10ms 0.05% 81.31% 122ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.31% 121ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 121ms 0.6% 81.91% 121ms 0.6% std::vector::size (inline) 10ms 0.05% 81.96% 118ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.96% 118ms 0.59% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 81.98% 115ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.11% 82.09% 115ms 0.57% std::num_put::_M_insert_int 3ms 0.015% 82.10% 114ms 0.57% Cell::SetCellProliferativeType 37ms 0.18% 82.29% 111ms 0.55% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 82.29% 110ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 6ms 0.03% 82.32% 109ms 0.54% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 5ms 0.025% 82.34% 106ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 32ms 0.16% 82.50% 105ms 0.52% TetrahedralMesh::EdgesEnd 0 0% 82.50% 105ms 0.52% std::vector::_M_default_append 0 0% 82.50% 105ms 0.52% std::vector::resize (inline) 102ms 0.51% 83.01% 104ms 0.52% boost::detail::sp_counted_base::release 44ms 0.22% 83.23% 104ms 0.52% std::__ostream_insert 103ms 0.51% 83.75% 103ms 0.51% AbstractElement::IsDeleted 11ms 0.055% 83.80% 101ms 0.5% Node::~Node