File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16613ms, 85.26% of 19486ms total Dropped 780 nodes (cum <= 97.43ms) flat flat% sum% cum cum% 0 0% 0% 19441ms 99.77% __libc_start_call_main 0 0% 0% 19441ms 99.77% __libc_start_main_impl 0 0% 0% 19441ms 99.77% _start 0 0% 0% 19420ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19420ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19420ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19420ms 99.66% main 0 0% 0% 19382ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19382ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19382ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19355ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 14766ms 75.78% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9302ms 47.74% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.01% 9215ms 47.29% Cell::ReadyToDivide 7ms 0.036% 0.046% 9151ms 46.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.051% 9013ms 46.25% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.092% 9006ms 46.22% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.13% 8995ms 46.16% CellCycleModelOdeHandler::SolveOdeToTime 76ms 0.39% 0.52% 8837ms 45.35% AbstractOneStepIvpOdeSolver::InternalSolve 1041ms 5.34% 5.86% 7932ms 40.71% RungeKutta4IvpOdeSolver::CalculateNextYValue 2755ms 14.14% 20.00% 6706ms 34.41% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 20.00% 5343ms 27.42% MeshBasedCellPopulation::Update 3ms 0.015% 20.02% 4095ms 21.02% Cylindrical2dMesh::ReMesh 61ms 0.31% 20.33% 3952ms 20.28% AbstractCellProperty::IsType (inline) 339ms 1.74% 22.07% 2579ms 13.24% AbstractCellProperty::IsSame 1ms 0.0051% 22.08% 2569ms 13.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.08% 2246ms 11.53% MutableMesh::ReMesh 0 0% 22.08% 2241ms 11.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 225ms 1.15% 23.23% 2240ms 11.50% std::type_info::operator== (inline) 10ms 0.051% 23.28% 2192ms 11.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 2185ms 11.21% 34.50% 2185ms 11.21% __strcmp_avx2 0 0% 34.50% 2012ms 10.33% AbstractCellPopulation::WriteResultsToFiles 805ms 4.13% 38.63% 1913ms 9.82% std::_Rb_tree::_M_lower_bound (inline) 142ms 0.73% 39.36% 1734ms 8.90% TetrahedralMesh::EdgeIterator::operator++ 85ms 0.44% 39.79% 1418ms 7.28% std::_Rb_tree::find (inline) 0 0% 39.79% 1211ms 6.21% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.036% 39.83% 1158ms 5.94% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 24ms 0.12% 39.95% 1113ms 5.71% TetrahedralMesh::ImportFromMesher 21ms 0.11% 40.06% 1039ms 5.33% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.21% 40.26% 1038ms 5.33% operator new 12ms 0.062% 40.33% 1029ms 5.28% std::set::insert (inline) 12ms 0.062% 40.39% 1017ms 5.22% std::_Rb_tree::_M_insert_unique 233ms 1.20% 41.58% 984ms 5.05% __GI___libc_malloc 45ms 0.23% 41.81% 932ms 4.78% std::__new_allocator::allocate (inline) 0 0% 41.81% 930ms 4.77% std::allocator_traits::allocate (inline) 0 0% 41.81% 879ms 4.51% triangulate 0 0% 41.81% 866ms 4.44% std::set::count (inline) 0 0% 41.81% 793ms 4.07% delaunay 2ms 0.01% 41.82% 793ms 4.07% divconqdelaunay 756ms 3.88% 45.70% 756ms 3.88% std::_Rb_tree::_S_right (inline) 0 0% 45.70% 752ms 3.86% AbstractTwoBodyInteractionForce::AddForceContribution 40ms 0.21% 45.91% 748ms 3.84% std::map::operator[] (partial-inline) 4ms 0.021% 45.93% 741ms 3.80% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 716ms 3.67% 49.60% 716ms 3.67% WntCellCycleOdeSystem::CalculateStoppingEvent 11ms 0.056% 49.66% 711ms 3.65% CellPopulationElementWriter::Visit 370ms 1.90% 51.56% 684ms 3.51% _int_malloc 186ms 0.95% 52.51% 662ms 3.40% __dynamic_cast 18ms 0.092% 52.61% 660ms 3.39% std::less::operator() (inline) 17ms 0.087% 52.69% 650ms 3.34% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 642ms 3.29% 55.99% 642ms 3.29% std::operator< (inline) 11ms 0.056% 56.05% 619ms 3.18% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.05% 618ms 3.17% std::_Rb_tree::_M_create_node (inline) 0 0% 56.05% 605ms 3.10% std::_Rb_tree::lower_bound (inline) 0 0% 56.05% 605ms 3.10% std::map::lower_bound (inline) 9ms 0.046% 56.09% 594ms 3.05% CellPropertyCollection::GetPropertiesType (inline) 35ms 0.18% 56.27% 594ms 3.05% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.27% 590ms 3.03% std::_Rb_tree::_M_get_node (inline) 6ms 0.031% 56.30% 580ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.021% 56.32% 558ms 2.86% Element::Element 0 0% 56.32% 558ms 2.86% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 56.32% 550ms 2.82% std::map::find (inline) 13ms 0.067% 56.39% 527ms 2.70% MutableMesh::ReIndex 10ms 0.051% 56.44% 497ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 16ms 0.082% 56.52% 488ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 56.52% 483ms 2.48% AbstractCellProperty::IsSubType (inline) 9ms 0.046% 56.57% 475ms 2.44% Element::RegisterWithNodes (inline) 69ms 0.35% 56.92% 473ms 2.43% std::ostream::_M_insert 0 0% 56.92% 473ms 2.43% std::ostream::operator<< (inline) 11ms 0.056% 56.98% 464ms 2.38% Node::AddElement 297ms 1.52% 58.50% 449ms 2.30% AbstractCellMutationState::AbstractCellMutationState 126ms 0.65% 59.15% 445ms 2.28% __GI___libc_free 139ms 0.71% 59.86% 411ms 2.11% std::_Rb_tree::_M_get_insert_unique_pos 128ms 0.66% 60.52% 403ms 2.07% std::_Rb_tree::_M_erase 17ms 0.087% 60.61% 380ms 1.95% divconqrecurse 40ms 0.21% 60.81% 379ms 1.94% std::_Rb_tree::~_Rb_tree (inline) 14ms 0.072% 60.88% 369ms 1.89% std::__new_allocator::deallocate (inline) 4ms 0.021% 60.91% 366ms 1.88% std::set::erase (inline) 12ms 0.062% 60.97% 365ms 1.87% Node::RemoveElement 0 0% 60.97% 365ms 1.87% std::allocator_traits::deallocate (inline) 9ms 0.046% 61.01% 364ms 1.87% std::_Rb_tree::erase 0 0% 61.01% 362ms 1.86% std::_Rb_tree::_M_drop_node (inline) 95ms 0.49% 61.50% 353ms 1.81% mergehulls 0 0% 61.50% 348ms 1.79% std::set::~set (inline) 170ms 0.87% 62.37% 347ms 1.78% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 62.38% 342ms 1.76% std::_Vector_base::_M_allocate (inline) 23ms 0.12% 62.50% 330ms 1.69% Element::ResetIndex 266ms 1.37% 63.87% 316ms 1.62% _int_free 1ms 0.0051% 63.87% 315ms 1.62% Cell::GetMutationState 5ms 0.026% 63.90% 314ms 1.61% Cell::GetCellProliferativeType 10ms 0.051% 63.95% 313ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 63.95% 304ms 1.56% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 63.96% 297ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 63.97% 295ms 1.51% NodeLocationWriter::Visit 292ms 1.50% 65.47% 292ms 1.50% [libchaste_cell_based.so] 3ms 0.015% 65.48% 289ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 281ms 1.44% 66.92% 283ms 1.45% std::vector::operator[] (inline) 12ms 0.062% 66.99% 279ms 1.43% std::vector::push_back (inline) 6ms 0.031% 67.02% 278ms 1.43% alternateaxes 11ms 0.056% 67.07% 277ms 1.42% std::_Rb_tree::_Rb_tree (partial-inline) 34ms 0.17% 67.25% 272ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.25% 271ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 254ms 1.30% 68.55% 271ms 1.39% vertexmedian 6ms 0.031% 68.58% 270ms 1.39% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.082% 68.66% 262ms 1.34% std::num_put::_M_insert_float 20ms 0.1% 68.77% 257ms 1.32% AbstractTetrahedralElement::CalculateJacobian 4ms 0.021% 68.79% 255ms 1.31% std::set::set (inline) 15ms 0.077% 68.86% 254ms 1.30% std::vector::_M_realloc_insert 97ms 0.5% 69.36% 250ms 1.28% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 61ms 0.31% 69.68% 239ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 84ms 0.43% 70.11% 236ms 1.21% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 5ms 0.026% 70.13% 233ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 25ms 0.13% 70.26% 233ms 1.20% std::_Rb_tree::_M_copy (inline) 11ms 0.056% 70.32% 232ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.32% 225ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 70.33% 210ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 70.34% 210ms 1.08% std::__cxx11::collate::do_transform 157ms 0.81% 71.15% 206ms 1.06% AbstractElement::GetNodeGlobalIndex 72ms 0.37% 71.52% 205ms 1.05% std::_Rb_tree::_M_clone_node (inline) 16ms 0.082% 71.60% 204ms 1.05% TetrahedralMesh::Clear 0 0% 71.60% 202ms 1.04% ___vsnprintf 0 0% 71.60% 202ms 1.04% __vsnprintf_internal (inline) 1ms 0.0051% 71.61% 201ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.61% 201ms 1.03% MeshBasedCellPopulation::GetDampingConstant 13ms 0.067% 71.67% 201ms 1.03% __printf_buffer 0 0% 71.67% 197ms 1.01% OffLatticeSimulation::ApplyBoundaries 9ms 0.046% 71.72% 196ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.021% 71.74% 191ms 0.98% AbstractTetrahedralElement::AbstractTetrahedralElement 26ms 0.13% 71.87% 191ms 0.98% AbstractTetrahedralElement::RefreshJacobian 10ms 0.051% 71.92% 186ms 0.95% Element::MarkAsDeleted 117ms 0.6% 72.52% 181ms 0.93% malloc_consolidate 38ms 0.2% 72.72% 178ms 0.91% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0051% 72.72% 176ms 0.9% __printf_fp_l_buffer 0 0% 72.72% 176ms 0.9% __printf_fp_spec (inline) 1ms 0.0051% 72.73% 175ms 0.9% CellProliferativeTypesWriter::VisitCell 8ms 0.041% 72.77% 173ms 0.89% MeshBasedCellPopulation::SpringsEnd (inline) 170ms 0.87% 73.64% 170ms 0.87% unlink_chunk 81ms 0.42% 74.06% 169ms 0.87% __printf_fp_buffer_1 159ms 0.82% 74.87% 159ms 0.82% [libchaste_crypt.so] 157ms 0.81% 75.68% 157ms 0.81% incircle 148ms 0.76% 76.44% 148ms 0.76% std::_Rb_tree_insert_and_rebalance 55ms 0.28% 76.72% 144ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 144ms 0.74% 77.46% 144ms 0.74% Node::GetIndex 143ms 0.73% 78.19% 143ms 0.73% AbstractCellMutationState::~AbstractCellMutationState 3ms 0.015% 78.21% 143ms 0.73% CellPropertyCollection::HasProperty 0 0% 78.21% 141ms 0.72% Cell::HasCellProperty (inline) 56ms 0.29% 78.50% 140ms 0.72% AbstractElement::GetNodeLocation 10ms 0.051% 78.55% 140ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 36ms 0.18% 78.73% 139ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 22ms 0.11% 78.85% 138ms 0.71% boost::detail::shared_count::~shared_count (inline) 0 0% 78.85% 138ms 0.71% boost::shared_ptr::~shared_ptr (inline) 4ms 0.021% 78.87% 134ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 81ms 0.42% 79.28% 134ms 0.69% std::_Rb_tree::equal_range (inline) 1ms 0.0051% 79.29% 132ms 0.68% boost::numeric::ublas::vector_assign (inline) 0 0% 79.29% 131ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 72ms 0.37% 79.66% 130ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 48ms 0.25% 79.90% 127ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 118ms 0.61% 80.51% 122ms 0.63% vertexsort 0 0% 80.51% 120ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 11ms 0.056% 80.57% 120ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 120ms 0.62% 81.18% 120ms 0.62% std::vector::size (inline) 0 0% 81.18% 119ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.18% 118ms 0.61% OutputFileHandler::OpenOutputFile 5ms 0.026% 81.21% 116ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0051% 81.21% 115ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 66ms 0.34% 81.55% 113ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 81.55% 112ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 10ms 0.051% 81.60% 112ms 0.57% Node::~Node 2ms 0.01% 81.61% 110ms 0.56% Cell::SetCellProliferativeType 110ms 0.56% 82.18% 110ms 0.56% [libchaste_mesh.so] 103ms 0.53% 82.71% 109ms 0.56% boost::detail::sp_counted_base::release 109ms 0.56% 83.26% 109ms 0.56% std::type_info::name (inline) 108ms 0.55% 83.82% 108ms 0.55% AbstractElement::IsDeleted 20ms 0.1% 83.92% 105ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 28ms 0.14% 84.07% 105ms 0.54% boost::numeric::ublas::indexing_vector_assign 18ms 0.092% 84.16% 104ms 0.53% std::num_put::_M_insert_int 7ms 0.036% 84.19% 103ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 102ms 0.52% 84.72% 102ms 0.52% AbstractCellProperty::AbstractCellProperty 5ms 0.026% 84.74% 101ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 100ms 0.51% 85.26% 100ms 0.51% std::_Rb_tree_increment