File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16336ms, 84.66% of 19297ms total Dropped 786 nodes (cum <= 96.48ms) flat flat% sum% cum cum% 0 0% 0% 19249ms 99.75% __libc_start_call_main 0 0% 0% 19249ms 99.75% __libc_start_main_impl 0 0% 0% 19249ms 99.75% _start 0 0% 0% 19225ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19225ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19225ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19225ms 99.63% main 0 0% 0% 19185ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19185ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19185ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0052% 0.0052% 19159ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0.0052% 14583ms 75.57% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0052% 0.01% 9259ms 47.98% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.031% 9164ms 47.49% Cell::ReadyToDivide 4ms 0.021% 0.052% 9079ms 47.05% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.052% 8928ms 46.27% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.093% 8920ms 46.22% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.13% 8904ms 46.14% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.37% 0.5% 8736ms 45.27% AbstractOneStepIvpOdeSolver::InternalSolve 1000ms 5.18% 5.68% 7820ms 40.52% RungeKutta4IvpOdeSolver::CalculateNextYValue 2731ms 14.15% 19.84% 6628ms 34.35% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.84% 5216ms 27.03% MeshBasedCellPopulation::Update 3ms 0.016% 19.85% 4037ms 20.92% Cylindrical2dMesh::ReMesh 68ms 0.35% 20.21% 3916ms 20.29% AbstractCellProperty::IsType (inline) 346ms 1.79% 22.00% 2583ms 13.39% AbstractCellProperty::IsSame 1ms 0.0052% 22.00% 2557ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 224ms 1.16% 23.16% 2237ms 11.59% std::type_info::operator== (inline) 0 0% 23.16% 2233ms 11.57% MutableMesh::ReMesh 1ms 0.0052% 23.17% 2222ms 11.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.062% 23.23% 2176ms 11.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 2107ms 10.92% 34.15% 2107ms 10.92% __strcmp_avx2 0 0% 34.15% 2015ms 10.44% AbstractCellPopulation::WriteResultsToFiles 844ms 4.37% 38.52% 1915ms 9.92% std::_Rb_tree::_M_lower_bound (inline) 189ms 0.98% 39.50% 1720ms 8.91% TetrahedralMesh::EdgeIterator::operator++ 87ms 0.45% 39.95% 1430ms 7.41% std::_Rb_tree::find (inline) 0 0% 39.95% 1144ms 5.93% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.062% 40.02% 1125ms 5.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 5ms 0.026% 40.04% 1078ms 5.59% TetrahedralMesh::ImportFromMesher 38ms 0.2% 40.24% 1046ms 5.42% operator new 10ms 0.052% 40.29% 1036ms 5.37% MeshBasedCellPopulation::SpringIterator::operator++ 253ms 1.31% 41.60% 986ms 5.11% __GI___libc_malloc 9ms 0.047% 41.65% 979ms 5.07% std::set::insert (inline) 12ms 0.062% 41.71% 970ms 5.03% std::_Rb_tree::_M_insert_unique 36ms 0.19% 41.90% 911ms 4.72% std::__new_allocator::allocate (inline) 0 0% 41.90% 906ms 4.70% std::allocator_traits::allocate (inline) 1ms 0.0052% 41.90% 885ms 4.59% triangulate 0 0% 41.90% 849ms 4.40% std::set::count (inline) 0 0% 41.90% 787ms 4.08% delaunay 6ms 0.031% 41.93% 787ms 4.08% divconqdelaunay 1ms 0.0052% 41.94% 762ms 3.95% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.016% 41.95% 757ms 3.92% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 55ms 0.29% 42.24% 725ms 3.76% std::map::operator[] (partial-inline) 724ms 3.75% 45.99% 724ms 3.75% std::_Rb_tree::_S_right (inline) 706ms 3.66% 49.65% 706ms 3.66% WntCellCycleOdeSystem::CalculateStoppingEvent 12ms 0.062% 49.71% 703ms 3.64% CellPopulationElementWriter::Visit 23ms 0.12% 49.83% 668ms 3.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 371ms 1.92% 51.75% 658ms 3.41% _int_malloc 205ms 1.06% 52.82% 657ms 3.40% __dynamic_cast 19ms 0.098% 52.91% 636ms 3.30% std::less::operator() (inline) 25ms 0.13% 53.04% 626ms 3.24% AbstractCellPopulation::GetCellUsingLocationIndex 617ms 3.20% 56.24% 617ms 3.20% std::operator< (inline) 13ms 0.067% 56.31% 602ms 3.12% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.036% 56.35% 597ms 3.09% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.35% 589ms 3.05% std::_Rb_tree::lower_bound (inline) 0 0% 56.35% 589ms 3.05% std::map::lower_bound (inline) 0 0% 56.35% 582ms 3.02% std::_Rb_tree::_M_create_node (inline) 0 0% 56.35% 575ms 2.98% std::map::find (inline) 32ms 0.17% 56.51% 572ms 2.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.51% 555ms 2.88% std::_Rb_tree::_M_get_node (inline) 13ms 0.067% 56.58% 544ms 2.82% Element::Element 0 0% 56.58% 527ms 2.73% std::_Rb_tree::_Alloc_node::operator() (inline) 22ms 0.11% 56.69% 522ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 6ms 0.031% 56.72% 495ms 2.57% MutableMesh::ReIndex 2ms 0.01% 56.73% 477ms 2.47% AbstractCellProperty::IsSubType (inline) 13ms 0.067% 56.80% 472ms 2.45% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.057% 56.86% 468ms 2.43% Element::RegisterWithNodes (inline) 4ms 0.021% 56.88% 452ms 2.34% Node::AddElement 68ms 0.35% 57.23% 450ms 2.33% std::ostream::_M_insert 0 0% 57.23% 450ms 2.33% std::ostream::operator<< (inline) 119ms 0.62% 57.85% 418ms 2.17% __GI___libc_free 266ms 1.38% 59.23% 411ms 2.13% AbstractCellMutationState::AbstractCellMutationState 2ms 0.01% 59.24% 404ms 2.09% std::set::erase (inline) 10ms 0.052% 59.29% 403ms 2.09% std::_Rb_tree::erase 16ms 0.083% 59.37% 402ms 2.08% Node::RemoveElement 12ms 0.062% 59.43% 386ms 2.00% divconqrecurse 156ms 0.81% 60.24% 386ms 2.00% std::_Rb_tree::_M_get_insert_unique_pos 112ms 0.58% 60.82% 383ms 1.98% std::_Rb_tree::_M_erase 11ms 0.057% 60.88% 378ms 1.96% std::__new_allocator::deallocate (inline) 0 0% 60.88% 375ms 1.94% std::allocator_traits::deallocate (inline) 106ms 0.55% 61.43% 371ms 1.92% mergehulls 19ms 0.098% 61.53% 354ms 1.83% std::_Rb_tree::~_Rb_tree (inline) 0 0% 61.53% 353ms 1.83% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 61.54% 353ms 1.83% std::_Vector_base::_M_allocate (inline) 170ms 0.88% 62.42% 340ms 1.76% __cxxabiv1::__si_class_type_info::__do_dyncast 17ms 0.088% 62.51% 338ms 1.75% Element::ResetIndex 2ms 0.01% 62.52% 327ms 1.69% Cell::GetCellProliferativeType 0 0% 62.52% 326ms 1.69% std::set::~set (inline) 318ms 1.65% 64.17% 318ms 1.65% [libchaste_cell_based.so] 0 0% 64.17% 313ms 1.62% std::_Rb_tree::_M_put_node (inline) 1ms 0.0052% 64.17% 311ms 1.61% Cell::GetMutationState 14ms 0.073% 64.24% 304ms 1.58% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0052% 64.25% 302ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 10ms 0.052% 64.30% 300ms 1.55% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 259ms 1.34% 65.64% 299ms 1.55% _int_free 279ms 1.45% 67.09% 285ms 1.48% std::vector::operator[] (inline) 0 0% 67.09% 276ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.093% 67.18% 276ms 1.43% std::_Rb_tree::_Rb_tree (partial-inline) 28ms 0.15% 67.33% 274ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0052% 67.33% 270ms 1.40% NodeLocationWriter::Visit 6ms 0.031% 67.36% 259ms 1.34% alternateaxes 3ms 0.016% 67.38% 258ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.083% 67.46% 255ms 1.32% AbstractTetrahedralElement::CalculateJacobian 243ms 1.26% 68.72% 253ms 1.31% vertexmedian 3ms 0.016% 68.74% 252ms 1.31% std::set::set (inline) 8ms 0.041% 68.78% 252ms 1.31% std::vector::push_back (inline) 23ms 0.12% 68.90% 243ms 1.26% std::num_put::_M_insert_float 0 0% 68.90% 241ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.067% 68.96% 240ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 18ms 0.093% 69.06% 236ms 1.22% std::vector::_M_realloc_insert 95ms 0.49% 69.55% 233ms 1.21% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 91ms 0.47% 70.02% 224ms 1.16% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 19ms 0.098% 70.12% 223ms 1.16% std::_Rb_tree::_M_copy (inline) 51ms 0.26% 70.38% 222ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.026% 70.41% 219ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 9ms 0.047% 70.46% 215ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0052% 70.46% 211ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 13ms 0.067% 70.53% 208ms 1.08% Element::MarkAsDeleted 0 0% 70.53% 208ms 1.08% OffLatticeSimulation::ApplyBoundaries 1ms 0.0052% 70.53% 202ms 1.05% std::__cxx11::collate::do_transform 21ms 0.11% 70.64% 197ms 1.02% __printf_buffer 66ms 0.34% 70.99% 197ms 1.02% std::_Rb_tree::_M_clone_node (inline) 3ms 0.016% 71.00% 196ms 1.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.00% 196ms 1.02% MeshBasedCellPopulation::GetDampingConstant 0 0% 71.00% 196ms 1.02% ___vsnprintf 0 0% 71.00% 196ms 1.02% __vsnprintf_internal (inline) 144ms 0.75% 71.75% 194ms 1.01% AbstractElement::GetNodeGlobalIndex 29ms 0.15% 71.90% 186ms 0.96% AbstractTetrahedralElement::RefreshJacobian 13ms 0.067% 71.96% 182ms 0.94% TetrahedralMesh::Clear 125ms 0.65% 72.61% 180ms 0.93% malloc_consolidate 179ms 0.93% 73.54% 179ms 0.93% incircle 4ms 0.021% 73.56% 170ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.016% 73.58% 167ms 0.87% __printf_fp_l_buffer 0 0% 73.58% 167ms 0.87% __printf_fp_spec (inline) 0 0% 73.58% 165ms 0.86% CellProliferativeTypesWriter::VisitCell 5ms 0.026% 73.60% 165ms 0.86% CellPropertyCollection::HasProperty 88ms 0.46% 74.06% 160ms 0.83% __printf_fp_buffer_1 0 0% 74.06% 158ms 0.82% Cell::HasCellProperty (inline) 98ms 0.51% 74.57% 158ms 0.82% std::_Rb_tree::equal_range (inline) 155ms 0.8% 75.37% 155ms 0.8% std::type_info::name (inline) 152ms 0.79% 76.16% 152ms 0.79% [libchaste_crypt.so] 152ms 0.79% 76.94% 152ms 0.79% std::_Rb_tree_insert_and_rebalance 6ms 0.031% 76.98% 148ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 147ms 0.76% 77.74% 147ms 0.76% unlink_chunk 146ms 0.76% 78.49% 146ms 0.76% std::vector::size (inline) 50ms 0.26% 78.75% 144ms 0.75% AbstractElement::GetNodeLocation 143ms 0.74% 79.49% 143ms 0.74% Node::GetIndex 142ms 0.74% 80.23% 142ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 54ms 0.28% 80.51% 142ms 0.74% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 50ms 0.26% 80.77% 141ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 15ms 0.078% 80.85% 140ms 0.73% boost::detail::shared_count::~shared_count (inline) 0 0% 80.85% 140ms 0.73% boost::shared_ptr::~shared_ptr (inline) 2ms 0.01% 80.86% 138ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.86% 135ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 94ms 0.49% 81.34% 135ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 81.34% 135ms 0.7% OutputFileHandler::OpenOutputFile 5ms 0.026% 81.37% 133ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 48ms 0.25% 81.62% 130ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0052% 81.62% 129ms 0.67% boost::numeric::ublas::vector_assign (inline) 122ms 0.63% 82.26% 126ms 0.65% vertexsort 3ms 0.016% 82.27% 120ms 0.62% Cell::SetCellProliferativeType 1ms 0.0052% 82.28% 119ms 0.62% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 113ms 0.59% 82.86% 117ms 0.61% boost::detail::sp_counted_base::release 7ms 0.036% 82.90% 112ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.01% 82.91% 110ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.026% 82.94% 110ms 0.57% Node::~Node 1ms 0.0052% 82.94% 109ms 0.56% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 82.94% 108ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.073% 83.01% 107ms 0.55% TetrahedralMesh::EdgesEnd (partial-inline) 63ms 0.33% 83.34% 104ms 0.54% TimeStepper::AdvanceOneTimeStep 27ms 0.14% 83.48% 103ms 0.53% std::__ostream_insert 1ms 0.0052% 83.48% 102ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 28ms 0.15% 83.63% 102ms 0.53% boost::numeric::ublas::indexing_vector_assign 101ms 0.52% 84.15% 101ms 0.52% std::_Rb_tree_increment 0 0% 84.15% 99ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 97ms 0.5% 84.66% 97ms 0.5% [libchaste_mesh.so]