File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16694ms, 86.09% of 19392ms total Dropped 804 nodes (cum <= 96.96ms) flat flat% sum% cum cum% 0 0% 0% 19350ms 99.78% __libc_start_call_main 0 0% 0% 19350ms 99.78% __libc_start_main_impl 0 0% 0% 19350ms 99.78% _start 0 0% 0% 19330ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19330ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19330ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19330ms 99.68% main 0 0% 0% 19294ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19294ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19294ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19269ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 14229ms 73.38% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 8472ms 43.69% AbstractCellBasedSimulation::DoCellBirth 8ms 0.041% 0.041% 8369ms 43.16% Cell::ReadyToDivide 0 0% 0.041% 8233ms 42.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0052% 0.046% 8071ms 41.62% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 18ms 0.093% 0.14% 8067ms 41.60% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0052% 0.14% 8043ms 41.48% CellCycleModelOdeHandler::SolveOdeToTime 64ms 0.33% 0.47% 7814ms 40.29% AbstractOneStepIvpOdeSolver::InternalSolve 939ms 4.84% 5.32% 7046ms 36.33% RungeKutta4IvpOdeSolver::CalculateNextYValue 2984ms 15.39% 20.70% 5931ms 30.58% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 20.71% 5638ms 29.07% MeshBasedCellPopulation::Update 5ms 0.026% 20.74% 4455ms 22.97% Cylindrical2dMesh::ReMesh 278ms 1.43% 22.17% 3127ms 16.13% AbstractCellProperty::IsType (inline) 1ms 0.0052% 22.18% 2776ms 14.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.18% 2512ms 12.95% MutableMesh::ReMesh 1ms 0.0052% 22.18% 2487ms 12.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.021% 22.21% 2455ms 12.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 22.21% 2254ms 11.62% AbstractCellPopulation::WriteResultsToFiles 751ms 3.87% 26.08% 1810ms 9.33% std::_Rb_tree::_M_lower_bound (inline) 140ms 0.72% 26.80% 1718ms 8.86% TetrahedralMesh::EdgeIterator::operator++ 49ms 0.25% 27.05% 1448ms 7.47% operator new 241ms 1.24% 28.30% 1407ms 7.26% AbstractCellProperty::IsSame 13ms 0.067% 28.36% 1397ms 7.20% TetrahedralMesh::ImportFromMesher 526ms 2.71% 31.07% 1375ms 7.09% __GI___libc_malloc 53ms 0.27% 31.35% 1365ms 7.04% std::_Rb_tree::find (inline) 13ms 0.067% 31.42% 1188ms 6.13% std::set::insert (inline) 16ms 0.083% 31.50% 1175ms 6.06% std::_Rb_tree::_M_insert_unique 36ms 0.19% 31.68% 1169ms 6.03% std::__new_allocator::allocate (inline) 173ms 0.89% 32.58% 1166ms 6.01% std::type_info::operator== (inline) 0 0% 32.58% 1160ms 5.98% std::allocator_traits::allocate (inline) 0 0% 32.58% 1133ms 5.84% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 32.59% 1115ms 5.75% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1093ms 5.64% 38.23% 1093ms 5.64% __strcmp_evex 7ms 0.036% 38.26% 1013ms 5.22% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.031% 38.29% 968ms 4.99% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 16ms 0.083% 38.38% 910ms 4.69% CellPropertyCollection::GetPropertiesType (inline) 864ms 4.46% 42.83% 864ms 4.46% [libchaste_cell_based.so] 0 0% 42.83% 853ms 4.40% std::set::count (inline) 314ms 1.62% 44.45% 850ms 4.38% __dynamic_cast 0 0% 44.45% 844ms 4.35% std::_Rb_tree::_M_create_node (inline) 8ms 0.041% 44.49% 833ms 4.30% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 44.49% 820ms 4.23% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 44.50% 819ms 4.22% triangulate 12ms 0.062% 44.56% 773ms 3.99% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.15% 44.72% 769ms 3.97% std::_Rb_tree::_M_insert_ (inline) 4ms 0.021% 44.74% 758ms 3.91% CellPopulationElementWriter::Visit 0 0% 44.74% 746ms 3.85% std::_Rb_tree::_Alloc_node::operator() (inline) 87ms 0.45% 45.19% 746ms 3.85% std::map::operator[] (partial-inline) 34ms 0.18% 45.36% 731ms 3.77% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 45.36% 721ms 3.72% delaunay 3ms 0.015% 45.38% 721ms 3.72% divconqdelaunay 426ms 2.20% 47.58% 709ms 3.66% _int_malloc 19ms 0.098% 47.67% 671ms 3.46% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.031% 47.71% 640ms 3.30% AbstractCellProperty::IsSubType (inline) 636ms 3.28% 50.98% 636ms 3.28% std::_Rb_tree::_S_right (inline) 6ms 0.031% 51.02% 629ms 3.24% Element::Element 141ms 0.73% 51.74% 615ms 3.17% __GI___libc_free 6ms 0.031% 51.77% 601ms 3.10% Element::RegisterWithNodes (inline) 10ms 0.052% 51.83% 591ms 3.05% Node::AddElement 574ms 2.96% 54.79% 574ms 2.96% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.026% 54.81% 540ms 2.78% Cell::GetMutationState 6ms 0.031% 54.84% 539ms 2.78% std::less::operator() (inline) 533ms 2.75% 57.59% 533ms 2.75% std::operator< (inline) 24ms 0.12% 57.71% 525ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 57.71% 517ms 2.67% std::_Rb_tree::lower_bound (inline) 0 0% 57.71% 517ms 2.67% std::map::lower_bound (inline) 0 0% 57.71% 508ms 2.62% std::map::find (inline) 6ms 0.031% 57.75% 506ms 2.61% MutableMesh::ReIndex 231ms 1.19% 58.94% 483ms 2.49% AbstractCellMutationState::AbstractCellMutationState 0 0% 58.94% 479ms 2.47% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0052% 58.94% 475ms 2.45% std::ostream::operator<< (inline) 83ms 0.43% 59.37% 474ms 2.44% std::_Rb_tree::_M_erase 74ms 0.38% 59.75% 473ms 2.44% std::ostream::_M_insert 396ms 2.04% 61.79% 466ms 2.40% _int_free 44ms 0.23% 62.02% 463ms 2.39% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.067% 62.09% 456ms 2.35% std::__new_allocator::deallocate (inline) 14ms 0.072% 62.16% 455ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 62.16% 444ms 2.29% std::allocator_traits::deallocate (inline) 0 0% 62.16% 439ms 2.26% std::set::~set (inline) 3ms 0.015% 62.18% 437ms 2.25% Cell::GetCellProliferativeType 4ms 0.021% 62.20% 419ms 2.16% std::_Rb_tree::erase 0 0% 62.20% 417ms 2.15% std::set::erase (inline) 5ms 0.026% 62.22% 407ms 2.10% Node::RemoveElement 402ms 2.07% 64.29% 402ms 2.07% [libchaste_crypt.so] 170ms 0.88% 65.17% 396ms 2.04% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.17% 393ms 2.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 65.17% 393ms 2.03% MeshBasedCellPopulation::GetDampingConstant 147ms 0.76% 65.93% 390ms 2.01% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 65.93% 380ms 1.96% std::_Rb_tree::_M_put_node (inline) 19ms 0.098% 66.03% 377ms 1.94% divconqrecurse 1ms 0.0052% 66.03% 367ms 1.89% LegacyCellProliferativeTypesWriter::VisitCell 30ms 0.15% 66.19% 349ms 1.80% Element::ResetIndex 2ms 0.01% 66.20% 342ms 1.76% std::_Vector_base::_M_allocate (inline) 97ms 0.5% 66.70% 341ms 1.76% mergehulls 18ms 0.093% 66.79% 337ms 1.74% TetrahedralMesh::Clear 12ms 0.062% 66.85% 328ms 1.69% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0052% 66.86% 311ms 1.60% std::set::set (inline) 32ms 0.17% 67.02% 297ms 1.53% std::_Rb_tree::_M_copy (inline) 17ms 0.088% 67.11% 295ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 12ms 0.062% 67.17% 281ms 1.45% boost::detail::shared_count::~shared_count (inline) 0 0% 67.17% 281ms 1.45% boost::shared_ptr::~shared_ptr (inline) 18ms 0.093% 67.26% 278ms 1.43% AbstractTetrahedralElement::CalculateJacobian 14ms 0.072% 67.34% 278ms 1.43% std::vector::push_back (inline) 6ms 0.031% 67.37% 274ms 1.41% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.046% 67.41% 269ms 1.39% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 67.41% 266ms 1.37% CellProliferativeTypesWriter::VisitCell 0 0% 67.41% 265ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 67.42% 264ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 120ms 0.62% 68.04% 261ms 1.35% std::_Rb_tree::_M_clone_node (inline) 29ms 0.15% 68.19% 260ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 253ms 1.30% 69.50% 260ms 1.34% boost::detail::sp_counted_base::release 8ms 0.041% 69.54% 259ms 1.34% std::_Rb_tree::_M_erase_aux (inline) 0 0% 69.54% 252ms 1.30% NodeLocationWriter::Visit 14ms 0.072% 69.61% 247ms 1.27% std::vector::_M_realloc_insert 8ms 0.041% 69.65% 241ms 1.24% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0052% 69.66% 240ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 235ms 1.21% 70.87% 235ms 1.21% [libchaste_mesh.so] 7ms 0.036% 70.91% 234ms 1.21% Element::MarkAsDeleted 5ms 0.026% 70.93% 224ms 1.16% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0052% 70.94% 224ms 1.16% Cylindrical2dMesh::CreateMirrorNodes 4ms 0.021% 70.96% 223ms 1.15% alternateaxes 13ms 0.067% 71.02% 223ms 1.15% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.062% 71.09% 223ms 1.15% std::num_put::_M_insert_float 9ms 0.046% 71.13% 220ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 198ms 1.02% 72.15% 219ms 1.13% vertexmedian 18ms 0.093% 72.25% 218ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.026% 72.27% 210ms 1.08% CellPropertyCollection::HasProperty 210ms 1.08% 73.35% 210ms 1.08% std::_Rb_tree_increment 0 0% 73.35% 207ms 1.07% Cell::HasCellProperty (inline) 30ms 0.15% 73.51% 205ms 1.06% AbstractTetrahedralElement::RefreshJacobian 195ms 1.01% 74.52% 195ms 1.01% std::_Rb_tree::_S_left (inline) 2ms 0.01% 74.53% 194ms 1.00% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.021% 74.55% 191ms 0.98% Node::~Node 10ms 0.052% 74.60% 189ms 0.97% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.015% 74.61% 186ms 0.96% std::__cxx11::collate::do_transform 1ms 0.0052% 74.62% 178ms 0.92% ___vsnprintf 0 0% 74.62% 177ms 0.91% OffLatticeSimulation::ApplyBoundaries 0 0% 74.62% 177ms 0.91% __vsnprintf_internal (inline) 175ms 0.9% 75.52% 176ms 0.91% std::vector::operator[] (inline) 136ms 0.7% 76.22% 175ms 0.9% malloc_consolidate 17ms 0.088% 76.31% 174ms 0.9% __printf_buffer 6ms 0.031% 76.34% 170ms 0.88% boost::numeric::ublas::vector_assign (inline) 104ms 0.54% 76.88% 165ms 0.85% AbstractElement::GetNodeGlobalIndex 1ms 0.0052% 76.88% 161ms 0.83% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 96ms 0.5% 77.38% 161ms 0.83% std::_Rb_tree::equal_range (inline) 2ms 0.01% 77.39% 156ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 155ms 0.8% 78.19% 155ms 0.8% incircle 151ms 0.78% 78.97% 151ms 0.78% std::_Rb_tree_insert_and_rebalance 98ms 0.51% 79.47% 150ms 0.77% AbstractElement::GetNodeLocation 3ms 0.015% 79.49% 148ms 0.76% __printf_fp_spec (inline) 35ms 0.18% 79.67% 147ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 146ms 0.75% 80.42% 146ms 0.75% unlink_chunk 6ms 0.031% 80.45% 145ms 0.75% __printf_fp_l_buffer 2ms 0.01% 80.46% 142ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 65ms 0.34% 80.80% 140ms 0.72% std::__ostream_insert 139ms 0.72% 81.51% 139ms 0.72% AbstractCellProperty::AbstractCellProperty 36ms 0.19% 81.70% 139ms 0.72% std::num_put::_M_insert_int 137ms 0.71% 82.41% 137ms 0.71% std::type_info::name (inline) 51ms 0.26% 82.67% 135ms 0.7% __printf_fp_buffer_1 5ms 0.026% 82.69% 135ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.021% 82.71% 133ms 0.69% Cell::SetCellProliferativeType 4ms 0.021% 82.74% 131ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.021% 82.76% 126ms 0.65% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 82.76% 122ms 0.63% tcache_get (inline) 122ms 0.63% 83.38% 122ms 0.63% tcache_get_n (inline) 62ms 0.32% 83.70% 119ms 0.61% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 83.70% 118ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0052% 83.71% 117ms 0.6% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0052% 83.71% 116ms 0.6% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0052% 83.72% 115ms 0.59% OutputFileHandler::OpenOutputFile 6ms 0.031% 83.75% 113ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 40ms 0.21% 83.96% 113ms 0.58% boost::numeric::ublas::indexing_vector_assign 111ms 0.57% 84.53% 111ms 0.57% Node::GetIndex 96ms 0.5% 85.02% 108ms 0.56% vertexsort 0 0% 85.02% 105ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 3ms 0.015% 85.04% 105ms 0.54% MeshBasedCellPopulation::SpringsEnd (inline) 19ms 0.098% 85.14% 103ms 0.53% TetrahedralMesh::EdgesEnd 0 0% 85.14% 102ms 0.53% std::operator<< (inline) 102ms 0.53% 85.66% 102ms 0.53% std::vector::size (inline) 4ms 0.021% 85.68% 101ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 85.68% 101ms 0.52% std::__new_allocator::destroy (inline) 0 0% 85.68% 101ms 0.52% std::allocator_traits::destroy (inline) 0 0% 85.68% 100ms 0.52% std::_Rb_tree::_M_destroy_node (inline) 0 0% 85.68% 98ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 35ms 0.18% 85.87% 98ms 0.51% std::_Vector_base::_M_deallocate (inline) 43ms 0.22% 86.09% 98ms 0.51% std::basic_filebuf::xsputn