File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16213ms, 83.49% of 19419ms total Dropped 784 nodes (cum <= 97.09ms) flat flat% sum% cum cum% 0 0% 0% 19376ms 99.78% __libc_start_call_main 0 0% 0% 19376ms 99.78% __libc_start_main_impl 0 0% 0% 19376ms 99.78% _start 0 0% 0% 19355ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19355ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19355ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19355ms 99.67% main 0 0% 0% 19315ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19315ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19315ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19289ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14709ms 75.75% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0051% 9277ms 47.77% AbstractCellBasedSimulation::DoCellBirth 5ms 0.026% 0.031% 9173ms 47.24% Cell::ReadyToDivide 2ms 0.01% 0.041% 9092ms 46.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.051% 8952ms 46.10% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.046% 0.098% 8944ms 46.06% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.11% 8931ms 45.99% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.35% 0.46% 8769ms 45.16% AbstractOneStepIvpOdeSolver::InternalSolve 1044ms 5.38% 5.83% 7895ms 40.66% RungeKutta4IvpOdeSolver::CalculateNextYValue 2775ms 14.29% 20.12% 6663ms 34.31% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.12% 5313ms 27.36% MeshBasedCellPopulation::Update 1ms 0.0051% 20.13% 4088ms 21.05% Cylindrical2dMesh::ReMesh 66ms 0.34% 20.47% 3907ms 20.12% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.47% 2548ms 13.12% OffLatticeSimulation::UpdateCellLocationsAndTopology 312ms 1.61% 22.08% 2525ms 13.00% AbstractCellProperty::IsSame 0 0% 22.08% 2251ms 11.59% MutableMesh::ReMesh 0 0% 22.08% 2234ms 11.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 216ms 1.11% 23.19% 2213ms 11.40% std::type_info::operator== (inline) 9ms 0.046% 23.24% 2190ms 11.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 2146ms 11.05% 34.29% 2146ms 11.05% __strcmp_avx2 0 0% 34.29% 2023ms 10.42% AbstractCellPopulation::WriteResultsToFiles 779ms 4.01% 38.30% 1876ms 9.66% std::_Rb_tree::_M_lower_bound (inline) 153ms 0.79% 39.09% 1674ms 8.62% TetrahedralMesh::EdgeIterator::operator++ 69ms 0.36% 39.45% 1390ms 7.16% std::_Rb_tree::find (inline) 0 0% 39.45% 1191ms 6.13% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.026% 39.47% 1150ms 5.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.093% 39.56% 1117ms 5.75% TetrahedralMesh::ImportFromMesher 48ms 0.25% 39.81% 1099ms 5.66% operator new 12ms 0.062% 39.87% 1046ms 5.39% MeshBasedCellPopulation::SpringIterator::operator++ 283ms 1.46% 41.33% 1032ms 5.31% __GI___libc_malloc 41ms 0.21% 41.54% 986ms 5.08% std::__new_allocator::allocate (inline) 3ms 0.015% 41.56% 979ms 5.04% std::set::insert (inline) 0 0% 41.56% 977ms 5.03% std::allocator_traits::allocate (inline) 14ms 0.072% 41.63% 976ms 5.03% std::_Rb_tree::_M_insert_unique 1ms 0.0051% 41.63% 882ms 4.54% triangulate 0 0% 41.63% 842ms 4.34% std::set::count (inline) 0 0% 41.63% 791ms 4.07% delaunay 5ms 0.026% 41.66% 791ms 4.07% divconqdelaunay 3ms 0.015% 41.68% 758ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 53ms 0.27% 41.95% 736ms 3.79% std::map::operator[] (partial-inline) 734ms 3.78% 45.73% 734ms 3.78% std::_Rb_tree::_S_right (inline) 0 0% 45.73% 725ms 3.73% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.026% 45.75% 705ms 3.63% CellPopulationElementWriter::Visit 684ms 3.52% 49.28% 684ms 3.52% WntCellCycleOdeSystem::CalculateStoppingEvent 212ms 1.09% 50.37% 667ms 3.43% __dynamic_cast 13ms 0.067% 50.44% 665ms 3.42% std::less::operator() (inline) 18ms 0.093% 50.53% 660ms 3.40% AbstractCellPopulation::GetCellUsingLocationIndex 652ms 3.36% 53.89% 652ms 3.36% std::operator< (inline) 334ms 1.72% 55.61% 648ms 3.34% _int_malloc 34ms 0.18% 55.78% 637ms 3.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 55.78% 619ms 3.19% std::_Rb_tree::_M_create_node (inline) 7ms 0.036% 55.82% 601ms 3.09% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.82% 597ms 3.07% std::_Rb_tree::_M_get_node (inline) 0 0% 55.82% 593ms 3.05% std::_Rb_tree::lower_bound (inline) 0 0% 55.82% 593ms 3.05% std::map::lower_bound (inline) 5ms 0.026% 55.84% 591ms 3.04% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.15% 56.00% 576ms 2.97% std::_Rb_tree::_M_insert_ (inline) 7ms 0.036% 56.03% 561ms 2.89% Element::Element 0 0% 56.03% 561ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 56.03% 541ms 2.79% std::map::find (inline) 9ms 0.046% 56.08% 537ms 2.77% MutableMesh::ReIndex 2ms 0.01% 56.09% 501ms 2.58% AbstractCellProperty::IsSubType (inline) 14ms 0.072% 56.16% 493ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.067% 56.23% 485ms 2.50% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 56.24% 463ms 2.38% std::ostream::operator<< (inline) 138ms 0.71% 56.95% 461ms 2.37% __GI___libc_free 58ms 0.3% 57.25% 460ms 2.37% std::ostream::_M_insert 12ms 0.062% 57.32% 459ms 2.36% Element::RegisterWithNodes (inline) 5ms 0.026% 57.34% 446ms 2.30% Node::AddElement 295ms 1.52% 58.86% 444ms 2.29% AbstractCellMutationState::AbstractCellMutationState 114ms 0.59% 59.45% 387ms 1.99% std::_Rb_tree::_M_erase 140ms 0.72% 60.17% 386ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0051% 60.17% 381ms 1.96% std::_Vector_base::_M_allocate (inline) 10ms 0.051% 60.22% 380ms 1.96% std::__new_allocator::deallocate (inline) 0 0% 60.22% 378ms 1.95% std::allocator_traits::deallocate (inline) 9ms 0.046% 60.27% 377ms 1.94% std::_Rb_tree::erase 0 0% 60.27% 376ms 1.94% std::set::erase (inline) 19ms 0.098% 60.37% 371ms 1.91% divconqrecurse 7ms 0.036% 60.40% 367ms 1.89% Node::RemoveElement 23ms 0.12% 60.52% 353ms 1.82% std::_Rb_tree::~_Rb_tree (inline) 347ms 1.79% 62.31% 347ms 1.79% [libchaste_cell_based.so] 0 0% 62.31% 347ms 1.79% std::_Rb_tree::_M_drop_node (inline) 89ms 0.46% 62.77% 341ms 1.76% mergehulls 20ms 0.1% 62.87% 332ms 1.71% Element::ResetIndex 0 0% 62.87% 329ms 1.69% std::set::~set (inline) 156ms 0.8% 63.67% 325ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.046% 63.72% 322ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 244ms 1.26% 64.98% 322ms 1.66% _int_free 4ms 0.021% 65.00% 318ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 25ms 0.13% 65.13% 317ms 1.63% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.01% 65.14% 316ms 1.63% Cell::GetCellProliferativeType 0 0% 65.14% 311ms 1.60% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 65.15% 310ms 1.60% Cell::GetMutationState 16ms 0.082% 65.23% 298ms 1.53% AbstractTetrahedralElement::CalculateJacobian 13ms 0.067% 65.30% 298ms 1.53% std::vector::push_back (inline) 0 0% 65.30% 296ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 65.31% 292ms 1.50% std::set::set (inline) 37ms 0.19% 65.50% 291ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 7ms 0.036% 65.54% 282ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 276ms 1.42% 66.96% 280ms 1.44% std::vector::operator[] (inline) 4ms 0.021% 66.98% 278ms 1.43% alternateaxes 12ms 0.062% 67.04% 276ms 1.42% std::vector::_M_realloc_insert 0 0% 67.04% 272ms 1.40% NodeLocationWriter::Visit 260ms 1.34% 68.38% 272ms 1.40% vertexmedian 108ms 0.56% 68.94% 266ms 1.37% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 68.95% 262ms 1.35% AbstractCellPopulation::IsCellAttachedToLocationIndex 27ms 0.14% 69.09% 259ms 1.33% std::_Rb_tree::_M_copy (inline) 67ms 0.35% 69.44% 250ms 1.29% AbstractTetrahedralElement::RefreshJacobian 8ms 0.041% 69.48% 242ms 1.25% std::num_put::_M_insert_float 66ms 0.34% 69.82% 239ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 8ms 0.041% 69.86% 238ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 88ms 0.45% 70.31% 236ms 1.22% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 15ms 0.077% 70.39% 230ms 1.18% std::_Rb_tree::_M_erase_aux (inline) 75ms 0.39% 70.78% 229ms 1.18% std::_Rb_tree::_M_clone_node (inline) 0 0% 70.78% 222ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 70.79% 216ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 70.79% 216ms 1.11% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.80% 215ms 1.11% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.015% 70.82% 212ms 1.09% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.026% 70.84% 205ms 1.06% std::__cxx11::collate::do_transform 143ms 0.74% 71.58% 202ms 1.04% malloc_consolidate 15ms 0.077% 71.66% 200ms 1.03% TetrahedralMesh::Clear 5ms 0.026% 71.68% 198ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 141ms 0.73% 72.41% 195ms 1.00% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 72.42% 195ms 1.00% ___vsnprintf 13ms 0.067% 72.49% 193ms 0.99% Element::MarkAsDeleted 0 0% 72.49% 193ms 0.99% __vsnprintf_internal (inline) 12ms 0.062% 72.55% 190ms 0.98% __printf_buffer 0 0% 72.55% 187ms 0.96% OffLatticeSimulation::ApplyBoundaries 4ms 0.021% 72.57% 186ms 0.96% CellPropertyCollection::HasProperty 2ms 0.01% 72.58% 180ms 0.93% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 72.59% 178ms 0.92% CellProliferativeTypesWriter::VisitCell 0 0% 72.59% 177ms 0.91% Cell::HasCellProperty (inline) 29ms 0.15% 72.74% 174ms 0.9% TetrahedralMesh::EdgesEnd (partial-inline) 170ms 0.88% 73.62% 170ms 0.88% incircle 2ms 0.01% 73.63% 168ms 0.87% __printf_fp_l_buffer 0 0% 73.63% 168ms 0.87% __printf_fp_spec (inline) 108ms 0.56% 74.19% 161ms 0.83% AbstractElement::GetNodeLocation 85ms 0.44% 74.62% 161ms 0.83% __printf_fp_buffer_1 158ms 0.81% 75.44% 158ms 0.81% unlink_chunk 157ms 0.81% 76.24% 157ms 0.81% Node::GetIndex 3ms 0.015% 76.26% 157ms 0.81% boost::numeric::ublas::vector_assign (inline) 151ms 0.78% 77.04% 151ms 0.78% std::vector::size (inline) 3ms 0.015% 77.05% 149ms 0.77% MeshBasedCellPopulation::SpringsEnd (inline) 146ms 0.75% 77.81% 146ms 0.75% std::_Rb_tree_insert_and_rebalance 94ms 0.48% 78.29% 144ms 0.74% std::_Rb_tree::equal_range (inline) 143ms 0.74% 79.03% 143ms 0.74% [libchaste_crypt.so] 5ms 0.026% 79.05% 142ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 50ms 0.26% 79.31% 139ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 47ms 0.24% 79.55% 135ms 0.7% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 77ms 0.4% 79.95% 135ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 90ms 0.46% 80.41% 135ms 0.7% TetrahedralMesh::EdgeIterator::EdgeIterator 2ms 0.01% 80.42% 135ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.42% 133ms 0.68% AbstractCellBasedWriter::OpenOutputFileForAppend 12ms 0.062% 80.48% 132ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 43ms 0.22% 80.70% 129ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 113ms 0.58% 81.29% 129ms 0.66% vertexsort 0 0% 81.29% 128ms 0.66% OutputFileHandler::OpenOutputFile 126ms 0.65% 81.94% 126ms 0.65% std::type_info::name (inline) 119ms 0.61% 82.55% 119ms 0.61% AbstractCellMutationState::~AbstractCellMutationState 0 0% 82.55% 119ms 0.61% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 41ms 0.21% 82.76% 118ms 0.61% boost::numeric::ublas::indexing_vector_assign 0 0% 82.76% 117ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 82.77% 116ms 0.6% Cell::SetCellProliferativeType 8ms 0.041% 82.82% 116ms 0.6% Node::~Node 29ms 0.15% 82.97% 115ms 0.59% std::__ostream_insert 0 0% 82.97% 113ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 17ms 0.088% 83.05% 113ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 83.05% 113ms 0.58% boost::shared_ptr::~shared_ptr (inline) 16ms 0.082% 83.14% 106ms 0.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 69ms 0.36% 83.49% 99ms 0.51% TimeStepper::AdvanceOneTimeStep