File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16888ms, 84.61% of 19959ms total Dropped 802 nodes (cum <= 99.80ms) flat flat% sum% cum cum% 0 0% 0% 19912ms 99.76% __libc_start_call_main 0 0% 0% 19912ms 99.76% __libc_start_main_impl 0 0% 0% 19912ms 99.76% _start 0 0% 0% 19892ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19892ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19892ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19892ms 99.66% main 0 0% 0% 19852ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19852ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19852ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19825ms 99.33% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15339ms 76.85% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.01% 10015ms 50.18% AbstractCellBasedSimulation::DoCellBirth 17ms 0.085% 0.095% 9931ms 49.76% Cell::ReadyToDivide 4ms 0.02% 0.12% 9837ms 49.29% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.13% 9687ms 48.53% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.065% 0.19% 9677ms 48.48% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.21% 9661ms 48.40% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.38% 0.58% 9488ms 47.54% AbstractOneStepIvpOdeSolver::InternalSolve 888ms 4.45% 5.03% 8647ms 43.32% RungeKutta4IvpOdeSolver::CalculateNextYValue 3594ms 18.01% 23.04% 7521ms 37.68% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.05% 5198ms 26.04% MeshBasedCellPopulation::Update 10ms 0.05% 23.10% 4024ms 20.16% Cylindrical2dMesh::ReMesh 91ms 0.46% 23.55% 3997ms 20.03% AbstractCellProperty::IsType (inline) 584ms 2.93% 26.48% 2790ms 13.98% AbstractCellProperty::IsSame 0 0% 26.48% 2443ms 12.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 419ms 2.10% 28.58% 2206ms 11.05% std::type_info::operator== (inline) 1ms 0.005% 28.58% 2179ms 10.92% MutableMesh::ReMesh 1ms 0.005% 28.59% 2151ms 10.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.05% 28.64% 2107ms 10.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.64% 2036ms 10.20% AbstractCellPopulation::WriteResultsToFiles 815ms 4.08% 32.72% 1835ms 9.19% std::_Rb_tree::_M_lower_bound (inline) 1769ms 8.86% 41.59% 1769ms 8.86% __strcmp_avx2 160ms 0.8% 42.39% 1686ms 8.45% TetrahedralMesh::EdgeIterator::operator++ 58ms 0.29% 42.68% 1384ms 6.93% std::_Rb_tree::find (inline) 16ms 0.08% 42.76% 1131ms 5.67% TetrahedralMesh::ImportFromMesher 0 0% 42.76% 1127ms 5.65% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 42.78% 1125ms 5.64% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 50ms 0.25% 43.03% 1046ms 5.24% operator new 9ms 0.045% 43.08% 1007ms 5.05% MeshBasedCellPopulation::SpringIterator::operator++ 246ms 1.23% 44.31% 992ms 4.97% __GI___libc_malloc 11ms 0.055% 44.37% 992ms 4.97% std::set::insert (inline) 17ms 0.085% 44.45% 981ms 4.92% std::_Rb_tree::_M_insert_unique 36ms 0.18% 44.63% 911ms 4.56% std::__new_allocator::allocate (inline) 0 0% 44.63% 907ms 4.54% std::allocator_traits::allocate (inline) 0 0% 44.63% 834ms 4.18% std::set::count (inline) 0 0% 44.63% 779ms 3.90% triangulate 3ms 0.015% 44.65% 759ms 3.80% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.65% 710ms 3.56% delaunay 5ms 0.025% 44.67% 710ms 3.56% divconqdelaunay 1ms 0.005% 44.68% 679ms 3.40% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.03% 44.71% 679ms 3.40% CellPopulationElementWriter::Visit 415ms 2.08% 46.79% 677ms 3.39% _int_malloc 672ms 3.37% 50.15% 672ms 3.37% std::_Rb_tree::_S_right (inline) 46ms 0.23% 50.38% 667ms 3.34% std::map::operator[] (partial-inline) 643ms 3.22% 53.60% 656ms 3.29% WntCellCycleOdeSystem::CalculateStoppingEvent 196ms 0.98% 54.59% 637ms 3.19% __dynamic_cast 5ms 0.025% 54.61% 630ms 3.16% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.11% 54.72% 623ms 3.12% std::less::operator() (inline) 31ms 0.16% 54.87% 621ms 3.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 54.87% 620ms 3.11% std::_Rb_tree::_M_create_node (inline) 3ms 0.015% 54.89% 610ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 602ms 3.02% 57.90% 602ms 3.02% std::operator< (inline) 0 0% 57.90% 587ms 2.94% std::_Rb_tree::_M_get_node (inline) 31ms 0.16% 58.06% 586ms 2.94% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 17ms 0.085% 58.14% 569ms 2.85% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.14% 569ms 2.85% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.14% 543ms 2.72% std::map::find (inline) 9ms 0.045% 58.19% 540ms 2.71% Element::Element 0 0% 58.19% 534ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 58.19% 534ms 2.68% std::map::lower_bound (inline) 14ms 0.07% 58.26% 533ms 2.67% MutableMesh::ReIndex 2ms 0.01% 58.27% 513ms 2.57% std::ostream::operator<< (inline) 66ms 0.33% 58.60% 511ms 2.56% std::ostream::_M_insert 3ms 0.015% 58.62% 489ms 2.45% AbstractCellProperty::IsSubType (inline) 12ms 0.06% 58.68% 485ms 2.43% Cylindrical2dMesh::CorrectNonPeriodicMesh 5ms 0.025% 58.70% 485ms 2.43% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.055% 58.76% 472ms 2.36% Element::RegisterWithNodes (inline) 9ms 0.045% 58.80% 458ms 2.29% Node::AddElement 176ms 0.88% 59.68% 454ms 2.27% __GI___libc_free 309ms 1.55% 61.23% 451ms 2.26% AbstractCellMutationState::AbstractCellMutationState 14ms 0.07% 61.30% 377ms 1.89% Node::RemoveElement 5ms 0.025% 61.33% 377ms 1.89% std::_Rb_tree::erase 0 0% 61.33% 375ms 1.88% std::set::erase (inline) 18ms 0.09% 61.42% 365ms 1.83% divconqrecurse 27ms 0.14% 61.55% 362ms 1.81% Element::ResetIndex 12ms 0.06% 61.61% 345ms 1.73% std::__new_allocator::deallocate (inline) 9ms 0.045% 61.66% 344ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 122ms 0.61% 62.27% 343ms 1.72% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 62.27% 342ms 1.71% std::allocator_traits::deallocate (inline) 93ms 0.47% 62.73% 341ms 1.71% std::_Rb_tree::_M_erase 5ms 0.025% 62.76% 337ms 1.69% Cell::GetCellProliferativeType 136ms 0.68% 63.44% 336ms 1.68% __cxxabiv1::__si_class_type_info::__do_dyncast 94ms 0.47% 63.91% 335ms 1.68% mergehulls 0 0% 63.91% 330ms 1.65% NodeLocationWriter::Visit 7ms 0.035% 63.95% 323ms 1.62% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 63.96% 323ms 1.62% std::_Vector_base::_M_allocate (inline) 323ms 1.62% 65.58% 323ms 1.62% std::type_info::name (inline) 3ms 0.015% 65.59% 314ms 1.57% Cell::GetMutationState 0 0% 65.59% 307ms 1.54% std::_Rb_tree::_M_drop_node (inline) 15ms 0.075% 65.67% 307ms 1.54% std::_Rb_tree::~_Rb_tree (inline) 294ms 1.47% 67.14% 295ms 1.48% std::vector::operator[] (inline) 4ms 0.02% 67.16% 292ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.11% 67.27% 289ms 1.45% std::num_put::_M_insert_float 15ms 0.075% 67.34% 285ms 1.43% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.34% 284ms 1.42% std::set::~set (inline) 1ms 0.005% 67.35% 278ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 220ms 1.10% 68.45% 276ms 1.38% _int_free 34ms 0.17% 68.62% 273ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.62% 272ms 1.36% std::_Rb_tree::_M_put_node (inline) 5ms 0.025% 68.65% 269ms 1.35% std::set::set (inline) 26ms 0.13% 68.78% 252ms 1.26% AbstractTetrahedralElement::CalculateJacobian 10ms 0.05% 68.83% 243ms 1.22% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 68.84% 241ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 28ms 0.14% 68.98% 240ms 1.20% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 69.00% 237ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.03% 69.03% 231ms 1.16% std::vector::push_back (inline) 7ms 0.035% 69.07% 229ms 1.15% std::__cxx11::collate::do_transform 11ms 0.055% 69.12% 227ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 69.12% 227ms 1.14% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 69.13% 226ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 57ms 0.29% 69.42% 224ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 24ms 0.12% 69.54% 223ms 1.12% TetrahedralMesh::Clear 4ms 0.02% 69.56% 223ms 1.12% alternateaxes 12ms 0.06% 69.62% 220ms 1.10% std::vector::_M_realloc_insert 203ms 1.02% 70.63% 218ms 1.09% vertexmedian 1ms 0.005% 70.64% 215ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 70.64% 215ms 1.08% ___vsnprintf 0 0% 70.64% 214ms 1.07% __vsnprintf_internal (inline) 40ms 0.2% 70.85% 208ms 1.04% __printf_buffer 153ms 0.77% 71.61% 206ms 1.03% AbstractElement::GetNodeGlobalIndex 71ms 0.36% 71.97% 205ms 1.03% std::_Rb_tree::_M_clone_node (inline) 7ms 0.035% 72.00% 195ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 37ms 0.19% 72.19% 194ms 0.97% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 34ms 0.17% 72.36% 194ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 18ms 0.09% 72.45% 191ms 0.96% Element::MarkAsDeleted 23ms 0.12% 72.56% 187ms 0.94% AbstractTetrahedralElement::RefreshJacobian 4ms 0.02% 72.58% 185ms 0.93% CellProliferativeTypesWriter::VisitCell 4ms 0.02% 72.60% 184ms 0.92% CellPropertyCollection::HasProperty 0 0% 72.60% 184ms 0.92% OffLatticeSimulation::ApplyBoundaries 181ms 0.91% 73.51% 181ms 0.91% [libchaste_cell_based.so] 0 0% 73.51% 180ms 0.9% Cell::HasCellProperty (inline) 174ms 0.87% 74.38% 174ms 0.87% std::_Rb_tree_insert_and_rebalance 3ms 0.015% 74.40% 172ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 166ms 0.83% 75.23% 166ms 0.83% Node::GetIndex 10ms 0.05% 75.28% 161ms 0.81% __printf_fp_l_buffer 0 0% 75.28% 161ms 0.81% __printf_fp_spec (inline) 113ms 0.57% 75.85% 159ms 0.8% malloc_consolidate 157ms 0.79% 76.63% 157ms 0.79% std::vector::size (inline) 156ms 0.78% 77.41% 156ms 0.78% incircle 8ms 0.04% 77.45% 148ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 76ms 0.38% 77.83% 146ms 0.73% __printf_fp_buffer_1 3ms 0.015% 77.85% 142ms 0.71% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 77.87% 141ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 63ms 0.32% 78.19% 139ms 0.7% AbstractElement::GetNodeLocation 0 0% 78.19% 138ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 12ms 0.06% 78.25% 138ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 91ms 0.46% 78.70% 138ms 0.69% std::_Rb_tree::equal_range (inline) 138ms 0.69% 79.39% 138ms 0.69% unlink_chunk 0 0% 79.39% 136ms 0.68% OutputFileHandler::OpenOutputFile 12ms 0.06% 79.45% 136ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 7ms 0.035% 79.49% 135ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 79ms 0.4% 79.88% 131ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 129ms 0.65% 80.53% 129ms 0.65% AbstractElement::IsDeleted 49ms 0.25% 80.78% 127ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 46ms 0.23% 81.01% 126ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 30ms 0.15% 81.16% 126ms 0.63% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 81.16% 125ms 0.63% Cell::SetCellProliferativeType 0 0% 81.16% 124ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 47ms 0.24% 81.39% 123ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.01% 81.40% 122ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 5ms 0.025% 81.43% 120ms 0.6% Node::~Node 24ms 0.12% 81.55% 120ms 0.6% std::num_put::_M_insert_int 0 0% 81.55% 119ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 119ms 0.6% 82.14% 119ms 0.6% AbstractCellProperty::~AbstractCellProperty 117ms 0.59% 82.73% 117ms 0.59% std::_Rb_tree_rebalance_for_erase 15ms 0.075% 82.80% 115ms 0.58% boost::detail::shared_count::~shared_count (inline) 35ms 0.18% 82.98% 115ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 82.98% 115ms 0.58% boost::shared_ptr::~shared_ptr (inline) 109ms 0.55% 83.53% 109ms 0.55% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.53% 105ms 0.53% std::vector::resize (inline) 8ms 0.04% 83.57% 104ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.005% 83.57% 104ms 0.52% std::vector::_M_default_append 99ms 0.5% 84.07% 104ms 0.52% vertexsort 102ms 0.51% 84.58% 102ms 0.51% [libchaste_crypt.so] 5ms 0.025% 84.60% 100ms 0.5% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 2ms 0.01% 84.61% 100ms 0.5% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 0 0% 84.61% 100ms 0.5% NodeMap::NodeMap