File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16946ms, 86.38% of 19618ms total Dropped 777 nodes (cum <= 98.09ms) flat flat% sum% cum cum% 0 0% 0% 19572ms 99.77% __libc_start_call_main 0 0% 0% 19572ms 99.77% __libc_start_main_impl 0 0% 0% 19572ms 99.77% _start 0 0% 0% 19550ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19550ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19550ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19550ms 99.65% main 0 0% 0% 19511ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19511ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19511ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19484ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14871ms 75.80% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0051% 9391ms 47.87% AbstractCellBasedSimulation::DoCellBirth 6ms 0.031% 0.036% 9306ms 47.44% Cell::ReadyToDivide 4ms 0.02% 0.056% 9225ms 47.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.061% 9078ms 46.27% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.087% 0.15% 9069ms 46.23% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.031% 0.18% 9046ms 46.11% CellCycleModelOdeHandler::SolveOdeToTime 59ms 0.3% 0.48% 8870ms 45.21% AbstractOneStepIvpOdeSolver::InternalSolve 1001ms 5.10% 5.58% 7964ms 40.60% RungeKutta4IvpOdeSolver::CalculateNextYValue 2810ms 14.32% 19.91% 6765ms 34.48% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.91% 5373ms 27.39% MeshBasedCellPopulation::Update 6ms 0.031% 19.94% 4193ms 21.37% Cylindrical2dMesh::ReMesh 56ms 0.29% 20.23% 3941ms 20.09% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.23% 2600ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 364ms 1.86% 22.09% 2501ms 12.75% AbstractCellProperty::IsSame 0 0% 22.09% 2301ms 11.73% MutableMesh::ReMesh 1ms 0.0051% 22.09% 2273ms 11.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.041% 22.13% 2230ms 11.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 234ms 1.19% 23.33% 2137ms 10.89% std::type_info::operator== (inline) 2025ms 10.32% 33.65% 2025ms 10.32% __strcmp_avx2 0 0% 33.65% 2011ms 10.25% AbstractCellPopulation::WriteResultsToFiles 807ms 4.11% 37.76% 1875ms 9.56% std::_Rb_tree::_M_lower_bound (inline) 172ms 0.88% 38.64% 1717ms 8.75% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.33% 38.97% 1386ms 7.06% std::_Rb_tree::find (inline) 0 0% 38.97% 1150ms 5.86% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 38.99% 1142ms 5.82% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.066% 39.06% 1141ms 5.82% TetrahedralMesh::ImportFromMesher 39ms 0.2% 39.26% 1072ms 5.46% operator new 9ms 0.046% 39.31% 1022ms 5.21% std::set::insert (inline) 242ms 1.23% 40.54% 1017ms 5.18% __GI___libc_malloc 12ms 0.061% 40.60% 1016ms 5.18% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.061% 40.66% 1013ms 5.16% std::_Rb_tree::_M_insert_unique 32ms 0.16% 40.82% 937ms 4.78% std::__new_allocator::allocate (inline) 0 0% 40.82% 935ms 4.77% std::allocator_traits::allocate (inline) 1ms 0.0051% 40.83% 907ms 4.62% triangulate 0 0% 40.83% 838ms 4.27% std::set::count (inline) 0 0% 40.83% 830ms 4.23% delaunay 3ms 0.015% 40.85% 830ms 4.23% divconqdelaunay 0 0% 40.85% 773ms 3.94% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.036% 40.88% 767ms 3.91% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 5ms 0.025% 40.91% 732ms 3.73% CellPopulationElementWriter::Visit 56ms 0.29% 41.19% 725ms 3.70% std::map::operator[] (partial-inline) 721ms 3.68% 44.87% 721ms 3.68% WntCellCycleOdeSystem::CalculateStoppingEvent 386ms 1.97% 46.83% 692ms 3.53% _int_malloc 680ms 3.47% 50.30% 680ms 3.47% std::_Rb_tree::_S_right (inline) 19ms 0.097% 50.40% 673ms 3.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 22ms 0.11% 50.51% 671ms 3.42% std::less::operator() (inline) 213ms 1.09% 51.60% 655ms 3.34% __dynamic_cast 649ms 3.31% 54.90% 649ms 3.31% std::operator< (inline) 0 0% 54.90% 638ms 3.25% std::_Rb_tree::_M_create_node (inline) 25ms 0.13% 55.03% 634ms 3.23% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.061% 55.09% 616ms 3.14% CellPropertyCollection::GetPropertiesType (inline) 31ms 0.16% 55.25% 614ms 3.13% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.25% 604ms 3.08% std::_Rb_tree::_M_get_node (inline) 6ms 0.031% 55.28% 592ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.041% 55.32% 576ms 2.94% Element::Element 0 0% 55.32% 574ms 2.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.32% 572ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 55.32% 572ms 2.92% std::map::lower_bound (inline) 5ms 0.025% 55.35% 541ms 2.76% MutableMesh::ReIndex 0 0% 55.35% 541ms 2.76% std::map::find (inline) 12ms 0.061% 55.41% 532ms 2.71% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.051% 55.46% 507ms 2.58% Element::RegisterWithNodes (inline) 12ms 0.061% 55.52% 494ms 2.52% Node::AddElement 14ms 0.071% 55.59% 478ms 2.44% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 55.60% 472ms 2.41% AbstractCellProperty::IsSubType (inline) 295ms 1.50% 57.10% 465ms 2.37% AbstractCellMutationState::AbstractCellMutationState 0 0% 57.10% 464ms 2.37% std::ostream::operator<< (inline) 74ms 0.38% 57.48% 463ms 2.36% std::ostream::_M_insert 143ms 0.73% 58.21% 443ms 2.26% __GI___libc_free 145ms 0.74% 58.95% 388ms 1.98% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.071% 59.02% 383ms 1.95% divconqrecurse 10ms 0.051% 59.07% 376ms 1.92% std::_Rb_tree::erase 2ms 0.01% 59.08% 376ms 1.92% std::set::erase (inline) 14ms 0.071% 59.15% 373ms 1.90% Node::RemoveElement 16ms 0.082% 59.23% 363ms 1.85% std::__new_allocator::deallocate (inline) 0 0% 59.23% 360ms 1.84% std::allocator_traits::deallocate (inline) 98ms 0.5% 59.73% 359ms 1.83% mergehulls 27ms 0.14% 59.87% 353ms 1.80% Element::ResetIndex 7ms 0.036% 59.90% 352ms 1.79% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 351ms 1.79% 61.69% 351ms 1.79% [libchaste_cell_based.so] 106ms 0.54% 62.23% 350ms 1.78% std::_Rb_tree::_M_erase 3ms 0.015% 62.25% 334ms 1.70% std::_Vector_base::_M_allocate (inline) 3ms 0.015% 62.26% 333ms 1.70% Cell::GetMutationState 145ms 0.74% 63.00% 331ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.14% 63.14% 317ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 0 0% 63.14% 316ms 1.61% std::_Rb_tree::_M_drop_node (inline) 4ms 0.02% 63.16% 313ms 1.60% Cell::GetCellProliferativeType 246ms 1.25% 64.42% 298ms 1.52% _int_free 0 0% 64.42% 298ms 1.52% std::set::~set (inline) 5ms 0.025% 64.44% 292ms 1.49% alternateaxes 10ms 0.051% 64.49% 288ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 274ms 1.40% 65.89% 286ms 1.46% vertexmedian 282ms 1.44% 67.33% 284ms 1.45% std::vector::operator[] (inline) 0 0% 67.33% 283ms 1.44% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 67.35% 282ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 33ms 0.17% 67.51% 272ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.51% 271ms 1.38% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.02% 67.53% 268ms 1.37% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.02% 67.56% 267ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.56% 267ms 1.36% NodeLocationWriter::Visit 59ms 0.3% 67.86% 264ms 1.35% ApcOneHitCellMutationState::ApcOneHitCellMutationState 14ms 0.071% 67.93% 264ms 1.35% std::vector::push_back (inline) 23ms 0.12% 68.04% 257ms 1.31% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 68.05% 256ms 1.30% std::set::set (inline) 109ms 0.56% 68.61% 251ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 89ms 0.45% 69.06% 249ms 1.27% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 28ms 0.14% 69.21% 246ms 1.25% std::_Rb_tree::_M_copy (inline) 20ms 0.1% 69.31% 241ms 1.23% std::num_put::_M_insert_float 16ms 0.082% 69.39% 239ms 1.22% std::vector::_M_realloc_insert 1ms 0.0051% 69.40% 225ms 1.15% MeshBasedCellPopulation::GetDampingConstant 0 0% 69.40% 224ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.40% 224ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.056% 69.45% 214ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 66ms 0.34% 69.79% 214ms 1.09% std::_Rb_tree::_M_clone_node (inline) 11ms 0.056% 69.84% 212ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 141ms 0.72% 70.56% 211ms 1.08% AbstractElement::GetNodeGlobalIndex 17ms 0.087% 70.65% 209ms 1.07% Element::MarkAsDeleted 0 0% 70.65% 202ms 1.03% OffLatticeSimulation::ApplyBoundaries 18ms 0.092% 70.74% 200ms 1.02% TetrahedralMesh::Clear 7ms 0.036% 70.78% 199ms 1.01% std::__cxx11::collate::do_transform 26ms 0.13% 70.91% 197ms 1.00% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 70.92% 195ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.031% 70.96% 192ms 0.98% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.056% 71.01% 192ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0051% 71.02% 192ms 0.98% CellProliferativeTypesWriter::VisitCell 0 0% 71.02% 187ms 0.95% __vsnprintf_internal (inline) 134ms 0.68% 71.70% 187ms 0.95% malloc_consolidate 0 0% 71.70% 186ms 0.95% ___vsnprintf 30ms 0.15% 71.85% 182ms 0.93% __printf_buffer 181ms 0.92% 72.78% 181ms 0.92% std::vector::size (inline) 63ms 0.32% 73.10% 179ms 0.91% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 166ms 0.85% 73.94% 166ms 0.85% std::_Rb_tree_insert_and_rebalance 165ms 0.84% 74.78% 165ms 0.84% incircle 108ms 0.55% 75.33% 162ms 0.83% std::_Rb_tree::equal_range (inline) 156ms 0.8% 76.13% 156ms 0.8% unlink_chunk 153ms 0.78% 76.91% 153ms 0.78% [libchaste_crypt.so] 60ms 0.31% 77.21% 150ms 0.76% AbstractElement::GetNodeLocation 149ms 0.76% 77.97% 149ms 0.76% AbstractCellMutationState::~AbstractCellMutationState 27ms 0.14% 78.11% 148ms 0.75% TetrahedralMesh::EdgesEnd (partial-inline) 146ms 0.74% 78.86% 146ms 0.74% Node::GetIndex 8ms 0.041% 78.90% 145ms 0.74% __printf_fp_l_buffer 0 0% 78.90% 145ms 0.74% __printf_fp_spec (inline) 47ms 0.24% 79.14% 144ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.02% 79.16% 144ms 0.73% CellPropertyCollection::HasProperty 86ms 0.44% 79.60% 143ms 0.73% Cylindrical2dMesh::GetVectorFromAtoB 131ms 0.67% 80.26% 143ms 0.73% vertexsort 4ms 0.02% 80.28% 141ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.28% 138ms 0.7% Cell::HasCellProperty (inline) 1ms 0.0051% 80.29% 137ms 0.7% boost::numeric::ublas::vector_assign (inline) 3ms 0.015% 80.30% 136ms 0.69% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 135ms 0.69% 80.99% 135ms 0.69% std::type_info::name (inline) 59ms 0.3% 81.29% 133ms 0.68% __printf_fp_buffer_1 14ms 0.071% 81.36% 130ms 0.66% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.65% 82.02% 128ms 0.65% std::_Rb_tree_increment 7ms 0.036% 82.05% 126ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 17ms 0.087% 82.14% 123ms 0.63% boost::detail::shared_count::~shared_count (inline) 0 0% 82.14% 123ms 0.63% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 82.15% 122ms 0.62% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 120ms 0.61% 82.77% 120ms 0.61% boost::shared_ptr::operator-> (inline) 40ms 0.2% 82.97% 119ms 0.61% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.031% 83.00% 115ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 84ms 0.43% 83.43% 114ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 38ms 0.19% 83.62% 114ms 0.58% boost::numeric::ublas::indexing_vector_assign 40ms 0.2% 83.83% 114ms 0.58% boost::shared_ptr::shared_ptr (inline) 112ms 0.57% 84.40% 112ms 0.57% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 5ms 0.025% 84.42% 111ms 0.57% Node::~Node 30ms 0.15% 84.58% 107ms 0.55% std::_Vector_base::_M_deallocate (inline) 17ms 0.087% 84.66% 107ms 0.55% std::num_put::_M_insert_int 0 0% 84.66% 106ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 84.67% 103ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 33ms 0.17% 84.84% 103ms 0.53% std::__ostream_insert 102ms 0.52% 85.36% 102ms 0.52% AbstractCellProperty::AbstractCellProperty 4ms 0.02% 85.38% 101ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 85.38% 100ms 0.51% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 85.38% 100ms 0.51% OutputFileHandler::OpenOutputFile 100ms 0.51% 85.89% 100ms 0.51% [libchaste_mesh.so] 96ms 0.49% 86.38% 100ms 0.51% boost::detail::sp_counted_base::release 0 0% 86.38% 99ms 0.5% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 86.38% 99ms 0.5% std::basic_ofstream::basic_ofstream (inline)