File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16703ms, 85.44% of 19549ms total Dropped 829 nodes (cum <= 97.75ms) flat flat% sum% cum cum% 0 0% 0% 19503ms 99.76% __libc_start_call_main 0 0% 0% 19503ms 99.76% __libc_start_main_impl 0 0% 0% 19503ms 99.76% _start 0 0% 0% 19482ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19482ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19482ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19482ms 99.66% main 0 0% 0% 19436ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19436ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19436ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19408ms 99.28% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 14770ms 75.55% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.031% 0.036% 9315ms 47.65% AbstractCellBasedSimulation::DoCellBirth 9ms 0.046% 0.082% 9208ms 47.10% Cell::ReadyToDivide 9ms 0.046% 0.13% 9115ms 46.63% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.13% 8957ms 45.82% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.21% 8951ms 45.79% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.22% 8934ms 45.70% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.31% 0.53% 8726ms 44.64% AbstractOneStepIvpOdeSolver::InternalSolve 962ms 4.92% 5.45% 7803ms 39.92% RungeKutta4IvpOdeSolver::CalculateNextYValue 2747ms 14.05% 19.50% 6642ms 33.98% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.50% 5355ms 27.39% MeshBasedCellPopulation::Update 4ms 0.02% 19.53% 4142ms 21.19% Cylindrical2dMesh::ReMesh 70ms 0.36% 19.88% 3908ms 19.99% AbstractCellProperty::IsType (inline) 2ms 0.01% 19.89% 2571ms 13.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 319ms 1.63% 21.53% 2527ms 12.93% AbstractCellProperty::IsSame 1ms 0.0051% 21.53% 2271ms 11.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 21.53% 2269ms 11.61% MutableMesh::ReMesh 8ms 0.041% 21.57% 2230ms 11.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 238ms 1.22% 22.79% 2208ms 11.29% std::type_info::operator== (inline) 2152ms 11.01% 33.80% 2152ms 11.01% __strcmp_avx2 2ms 0.01% 33.81% 2062ms 10.55% AbstractCellPopulation::WriteResultsToFiles 759ms 3.88% 37.69% 1831ms 9.37% std::_Rb_tree::_M_lower_bound (inline) 156ms 0.8% 38.49% 1676ms 8.57% TetrahedralMesh::EdgeIterator::operator++ 75ms 0.38% 38.87% 1376ms 7.04% std::_Rb_tree::find (inline) 2ms 0.01% 38.88% 1185ms 6.06% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 38.93% 1160ms 5.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.061% 38.99% 1123ms 5.74% TetrahedralMesh::ImportFromMesher 18ms 0.092% 39.08% 1051ms 5.38% MeshBasedCellPopulation::SpringIterator::operator++ 44ms 0.23% 39.31% 1046ms 5.35% operator new 7ms 0.036% 39.34% 1006ms 5.15% std::set::insert (inline) 15ms 0.077% 39.42% 999ms 5.11% std::_Rb_tree::_M_insert_unique 233ms 1.19% 40.61% 979ms 5.01% __GI___libc_malloc 29ms 0.15% 40.76% 927ms 4.74% std::__new_allocator::allocate (inline) 0 0% 40.76% 920ms 4.71% std::allocator_traits::allocate (inline) 1ms 0.0051% 40.76% 890ms 4.55% triangulate 0 0% 40.76% 840ms 4.30% std::set::count (inline) 0 0% 40.76% 804ms 4.11% delaunay 8ms 0.041% 40.81% 803ms 4.11% divconqdelaunay 5ms 0.026% 40.83% 781ms 4.00% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.0051% 40.84% 778ms 3.98% AbstractTwoBodyInteractionForce::AddForceContribution 726ms 3.71% 44.55% 726ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 84ms 0.43% 44.98% 718ms 3.67% std::map::operator[] (partial-inline) 716ms 3.66% 48.64% 716ms 3.66% std::_Rb_tree::_S_right (inline) 9ms 0.046% 48.69% 712ms 3.64% CellPopulationElementWriter::Visit 26ms 0.13% 48.82% 685ms 3.50% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 175ms 0.9% 49.72% 674ms 3.45% __dynamic_cast 346ms 1.77% 51.49% 656ms 3.36% _int_malloc 30ms 0.15% 51.64% 635ms 3.25% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.056% 51.70% 631ms 3.23% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.097% 51.79% 627ms 3.21% std::less::operator() (inline) 5ms 0.026% 51.82% 612ms 3.13% MeshBasedCellPopulation::AcceptCellWriter 608ms 3.11% 54.93% 608ms 3.11% std::operator< (inline) 35ms 0.18% 55.11% 604ms 3.09% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.11% 601ms 3.07% std::_Rb_tree::_M_create_node (inline) 7ms 0.036% 55.14% 581ms 2.97% Element::Element 0 0% 55.14% 573ms 2.93% std::_Rb_tree::_M_get_node (inline) 8ms 0.041% 55.18% 554ms 2.83% MutableMesh::ReIndex 0 0% 55.18% 546ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 55.18% 546ms 2.79% std::map::lower_bound (inline) 0 0% 55.18% 544ms 2.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.18% 534ms 2.73% std::map::find (inline) 12ms 0.061% 55.25% 518ms 2.65% Element::RegisterWithNodes (inline) 20ms 0.1% 55.35% 503ms 2.57% Node::AddElement 2ms 0.01% 55.36% 492ms 2.52% std::ostream::operator<< (inline) 11ms 0.056% 55.41% 488ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 78ms 0.4% 55.81% 487ms 2.49% std::ostream::_M_insert 1ms 0.0051% 55.82% 486ms 2.49% AbstractCellProperty::IsSubType (inline) 7ms 0.036% 55.85% 481ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 133ms 0.68% 56.53% 417ms 2.13% __GI___libc_free 21ms 0.11% 56.64% 407ms 2.08% Node::RemoveElement 270ms 1.38% 58.02% 406ms 2.08% AbstractCellMutationState::AbstractCellMutationState 125ms 0.64% 58.66% 402ms 2.06% std::_Rb_tree::_M_erase 1ms 0.0051% 58.67% 402ms 2.06% std::set::erase (inline) 10ms 0.051% 58.72% 401ms 2.05% std::_Rb_tree::erase 144ms 0.74% 59.46% 380ms 1.94% std::_Rb_tree::_M_get_insert_unique_pos 34ms 0.17% 59.63% 363ms 1.86% Element::ResetIndex 10ms 0.051% 59.68% 363ms 1.86% std::__new_allocator::deallocate (inline) 17ms 0.087% 59.77% 360ms 1.84% std::_Rb_tree::~_Rb_tree (inline) 0 0% 59.77% 359ms 1.84% std::allocator_traits::deallocate (inline) 15ms 0.077% 59.84% 358ms 1.83% divconqrecurse 2ms 0.01% 59.85% 349ms 1.79% std::_Vector_base::_M_allocate (inline) 0 0% 59.85% 347ms 1.78% std::_Rb_tree::_M_drop_node (inline) 160ms 0.82% 60.67% 345ms 1.76% __cxxabiv1::__si_class_type_info::__do_dyncast 340ms 1.74% 62.41% 340ms 1.74% [libchaste_cell_based.so] 2ms 0.01% 62.42% 339ms 1.73% Cell::GetCellProliferativeType 0 0% 62.42% 339ms 1.73% std::set::~set (inline) 95ms 0.49% 62.91% 336ms 1.72% mergehulls 8ms 0.041% 62.95% 328ms 1.68% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 62.96% 320ms 1.64% Cell::GetMutationState 0 0% 62.96% 311ms 1.59% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 62.99% 306ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 295ms 1.51% 64.49% 299ms 1.53% std::vector::operator[] (inline) 5ms 0.026% 64.52% 293ms 1.50% alternateaxes 269ms 1.38% 65.90% 286ms 1.46% vertexmedian 248ms 1.27% 67.16% 284ms 1.45% _int_free 9ms 0.046% 67.21% 275ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.11% 67.32% 270ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0051% 67.32% 269ms 1.38% NodeLocationWriter::Visit 34ms 0.17% 67.50% 262ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0051% 67.50% 262ms 1.34% AbstractCellPopulation::Iterator::operator++ (inline) 14ms 0.072% 67.57% 259ms 1.32% std::vector::push_back (inline) 14ms 0.072% 67.65% 250ms 1.28% AbstractTetrahedralElement::CalculateJacobian 15ms 0.077% 67.72% 247ms 1.26% std::num_put::_M_insert_float 1ms 0.0051% 67.73% 247ms 1.26% std::set::set (inline) 12ms 0.061% 67.79% 244ms 1.25% std::_Rb_tree::_M_erase_aux (inline) 97ms 0.5% 68.28% 241ms 1.23% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 104ms 0.53% 68.82% 235ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 68.82% 235ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.036% 68.85% 235ms 1.20% std::vector::_M_realloc_insert 6ms 0.031% 68.88% 232ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 56ms 0.29% 69.17% 226ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 15ms 0.077% 69.25% 222ms 1.14% Element::MarkAsDeleted 25ms 0.13% 69.37% 220ms 1.13% std::_Rb_tree::_M_copy (inline) 11ms 0.056% 69.43% 212ms 1.08% TetrahedralMesh::Clear 7ms 0.036% 69.47% 211ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 9ms 0.046% 69.51% 211ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.015% 69.53% 203ms 1.04% std::__cxx11::collate::do_transform 128ms 0.65% 70.18% 200ms 1.02% AbstractElement::GetNodeGlobalIndex 3ms 0.015% 70.20% 196ms 1.00% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.21% 196ms 1.00% ___vsnprintf 42ms 0.21% 70.42% 195ms 1% TetrahedralMesh::EdgesEnd (partial-inline) 32ms 0.16% 70.59% 194ms 0.99% __printf_buffer 0 0% 70.59% 194ms 0.99% __vsnprintf_internal (inline) 4ms 0.02% 70.61% 193ms 0.99% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.62% 192ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 132ms 0.68% 71.29% 192ms 0.98% malloc_consolidate 1ms 0.0051% 71.30% 190ms 0.97% OffLatticeSimulation::ApplyBoundaries 60ms 0.31% 71.60% 188ms 0.96% std::_Rb_tree::_M_clone_node (inline) 25ms 0.13% 71.73% 186ms 0.95% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 71.75% 186ms 0.95% CellProliferativeTypesWriter::VisitCell 181ms 0.93% 72.67% 181ms 0.93% Node::GetIndex 10ms 0.051% 72.72% 179ms 0.92% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 5ms 0.026% 72.75% 175ms 0.9% AbstractTetrahedralElement::AbstractTetrahedralElement 174ms 0.89% 73.64% 174ms 0.89% std::vector::size (inline) 7ms 0.036% 73.68% 171ms 0.87% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 2ms 0.01% 73.69% 168ms 0.86% CellPropertyCollection::HasProperty 168ms 0.86% 74.55% 168ms 0.86% std::_Rb_tree_insert_and_rebalance 0 0% 74.55% 166ms 0.85% Cell::HasCellProperty (inline) 159ms 0.81% 75.36% 159ms 0.81% unlink_chunk 108ms 0.55% 75.91% 157ms 0.8% std::_Rb_tree::equal_range (inline) 6ms 0.031% 75.94% 153ms 0.78% __printf_fp_l_buffer 0 0% 75.94% 153ms 0.78% __printf_fp_spec (inline) 3ms 0.015% 75.96% 152ms 0.78% boost::numeric::ublas::vector_assign (inline) 86ms 0.44% 76.40% 149ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 57ms 0.29% 76.69% 147ms 0.75% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 146ms 0.75% 77.44% 146ms 0.75% [libchaste_crypt.so] 4ms 0.02% 77.46% 143ms 0.73% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 61ms 0.31% 77.77% 143ms 0.73% __printf_fp_buffer_1 47ms 0.24% 78.01% 141ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.02% 78.03% 141ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 53ms 0.27% 78.30% 140ms 0.72% AbstractElement::GetNodeLocation 47ms 0.24% 78.54% 139ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 139ms 0.71% 79.25% 139ms 0.71% incircle 5ms 0.026% 79.28% 138ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.02% 79.30% 136ms 0.7% Node::~Node 123ms 0.63% 79.93% 135ms 0.69% vertexsort 86ms 0.44% 80.37% 132ms 0.68% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 80.37% 131ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.37% 129ms 0.66% OutputFileHandler::OpenOutputFile 127ms 0.65% 81.02% 127ms 0.65% AbstractCellMutationState::~AbstractCellMutationState 34ms 0.17% 81.19% 122ms 0.62% boost::numeric::ublas::indexing_vector_assign 3ms 0.015% 81.21% 118ms 0.6% Cell::SetCellProliferativeType 29ms 0.15% 81.35% 118ms 0.6% std::__ostream_insert 0 0% 81.35% 115ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 68ms 0.35% 81.70% 113ms 0.58% TimeStepper::AdvanceOneTimeStep 113ms 0.58% 82.28% 113ms 0.58% std::type_info::name (inline) 112ms 0.57% 82.85% 112ms 0.57% std::_Rb_tree_increment 6ms 0.031% 82.88% 111ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 25ms 0.13% 83.01% 111ms 0.57% std::num_put::_M_insert_int 109ms 0.56% 83.57% 109ms 0.56% [libchaste_mesh.so] 14ms 0.072% 83.64% 106ms 0.54% boost::detail::shared_count::~shared_count (inline) 0 0% 83.64% 106ms 0.54% boost::shared_ptr::~shared_ptr (inline) 48ms 0.25% 83.89% 104ms 0.53% std::basic_filebuf::xsputn 103ms 0.53% 84.41% 103ms 0.53% std::_Rb_tree_rebalance_for_erase 101ms 0.52% 84.93% 101ms 0.52% counterclockwise 100ms 0.51% 85.44% 100ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 85.44% 99ms 0.51% AbstractCellBasedSimulation::DoCellRemoval (inline)