File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16715ms, 85.79% of 19484ms total Dropped 781 nodes (cum <= 97.42ms) flat flat% sum% cum cum% 0 0% 0% 19440ms 99.77% __libc_start_call_main 0 0% 0% 19440ms 99.77% __libc_start_main_impl 0 0% 0% 19440ms 99.77% _start 0 0% 0% 19418ms 99.66% main 0 0% 0% 19417ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19417ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19417ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19379ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19379ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19379ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19352ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14782ms 75.87% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 9306ms 47.76% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.026% 9197ms 47.20% Cell::ReadyToDivide 5ms 0.026% 0.051% 9127ms 46.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.021% 0.072% 8974ms 46.06% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.15% 8964ms 46.01% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.16% 8942ms 45.89% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.34% 0.5% 8778ms 45.05% AbstractOneStepIvpOdeSolver::InternalSolve 1009ms 5.18% 5.68% 7850ms 40.29% RungeKutta4IvpOdeSolver::CalculateNextYValue 2741ms 14.07% 19.75% 6650ms 34.13% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.75% 5343ms 27.42% MeshBasedCellPopulation::Update 2ms 0.01% 19.76% 4125ms 21.17% Cylindrical2dMesh::ReMesh 71ms 0.36% 20.13% 3889ms 19.96% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.13% 2581ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 371ms 1.90% 22.04% 2497ms 12.82% AbstractCellProperty::IsSame 1ms 0.0051% 22.04% 2257ms 11.58% MutableMesh::ReMesh 1ms 0.0051% 22.05% 2244ms 11.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 22.10% 2179ms 11.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 216ms 1.11% 23.21% 2126ms 10.91% std::type_info::operator== (inline) 2023ms 10.38% 33.59% 2023ms 10.38% __strcmp_avx2 0 0% 33.59% 1978ms 10.15% AbstractCellPopulation::WriteResultsToFiles 780ms 4.00% 37.59% 1902ms 9.76% std::_Rb_tree::_M_lower_bound (inline) 168ms 0.86% 38.46% 1719ms 8.82% TetrahedralMesh::EdgeIterator::operator++ 69ms 0.35% 38.81% 1397ms 7.17% std::_Rb_tree::find (inline) 2ms 0.01% 38.82% 1180ms 6.06% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.026% 38.85% 1156ms 5.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.046% 38.89% 1127ms 5.78% TetrahedralMesh::ImportFromMesher 36ms 0.18% 39.08% 1058ms 5.43% operator new 9ms 0.046% 39.12% 1042ms 5.35% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.067% 39.19% 1025ms 5.26% std::set::insert (inline) 253ms 1.30% 40.49% 1014ms 5.20% __GI___libc_malloc 15ms 0.077% 40.57% 1012ms 5.19% std::_Rb_tree::_M_insert_unique 33ms 0.17% 40.74% 937ms 4.81% std::__new_allocator::allocate (inline) 0 0% 40.74% 928ms 4.76% std::allocator_traits::allocate (inline) 2ms 0.01% 40.75% 878ms 4.51% triangulate 0 0% 40.75% 840ms 4.31% std::set::count (inline) 0 0% 40.75% 799ms 4.10% delaunay 2ms 0.01% 40.76% 798ms 4.10% divconqdelaunay 771ms 3.96% 44.71% 771ms 3.96% std::_Rb_tree::_S_right (inline) 736ms 3.78% 48.49% 737ms 3.78% WntCellCycleOdeSystem::CalculateStoppingEvent 51ms 0.26% 48.75% 736ms 3.78% std::map::operator[] (partial-inline) 3ms 0.015% 48.77% 699ms 3.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 6ms 0.031% 48.80% 695ms 3.57% CellPopulationElementWriter::Visit 0 0% 48.80% 693ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 350ms 1.80% 50.60% 671ms 3.44% _int_malloc 14ms 0.072% 50.67% 666ms 3.42% std::less::operator() (inline) 652ms 3.35% 54.01% 652ms 3.35% std::operator< (inline) 177ms 0.91% 54.92% 640ms 3.28% __dynamic_cast 0 0% 54.92% 605ms 3.11% std::_Rb_tree::_M_create_node (inline) 14ms 0.072% 54.99% 600ms 3.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 54.99% 590ms 3.03% std::_Rb_tree::lower_bound (inline) 0 0% 54.99% 590ms 3.03% std::map::lower_bound (inline) 22ms 0.11% 55.11% 584ms 3.00% AbstractCellPopulation::GetCellUsingLocationIndex 28ms 0.14% 55.25% 582ms 2.99% std::_Rb_tree::_M_insert_ (inline) 4ms 0.021% 55.27% 581ms 2.98% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.27% 571ms 2.93% std::_Rb_tree::_M_get_node (inline) 9ms 0.046% 55.32% 567ms 2.91% Element::Element 7ms 0.036% 55.35% 556ms 2.85% MutableMesh::ReIndex 0 0% 55.35% 551ms 2.83% std::map::find (inline) 0 0% 55.35% 544ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.01% 55.36% 541ms 2.78% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.051% 55.41% 507ms 2.60% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.077% 55.49% 493ms 2.53% Element::RegisterWithNodes (inline) 2ms 0.01% 55.50% 483ms 2.48% std::ostream::operator<< (inline) 82ms 0.42% 55.92% 481ms 2.47% std::ostream::_M_insert 12ms 0.062% 55.98% 479ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.062% 56.05% 474ms 2.43% Node::AddElement 2ms 0.01% 56.06% 471ms 2.42% AbstractCellProperty::IsSubType (inline) 13ms 0.067% 56.12% 433ms 2.22% std::_Rb_tree::erase 17ms 0.087% 56.21% 432ms 2.22% Node::RemoveElement 0 0% 56.21% 432ms 2.22% std::set::erase (inline) 258ms 1.32% 57.53% 419ms 2.15% AbstractCellMutationState::AbstractCellMutationState 147ms 0.75% 58.29% 415ms 2.13% std::_Rb_tree::_M_get_insert_unique_pos 123ms 0.63% 58.92% 399ms 2.05% __GI___libc_free 27ms 0.14% 59.06% 384ms 1.97% Element::ResetIndex 125ms 0.64% 59.70% 373ms 1.91% std::_Rb_tree::_M_erase 10ms 0.051% 59.75% 364ms 1.87% divconqrecurse 29ms 0.15% 59.90% 362ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.021% 59.92% 361ms 1.85% std::_Vector_base::_M_allocate (inline) 354ms 1.82% 61.74% 354ms 1.82% [libchaste_cell_based.so] 13ms 0.067% 61.80% 345ms 1.77% std::__new_allocator::deallocate (inline) 98ms 0.5% 62.31% 344ms 1.77% mergehulls 9ms 0.046% 62.35% 343ms 1.76% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 62.35% 342ms 1.76% std::allocator_traits::deallocate (inline) 172ms 0.88% 63.24% 340ms 1.75% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.24% 333ms 1.71% std::set::~set (inline) 2ms 0.01% 63.25% 325ms 1.67% NodeLocationWriter::Visit 0 0% 63.25% 317ms 1.63% std::_Rb_tree::_M_drop_node (inline) 42ms 0.22% 63.46% 313ms 1.61% AbstractCellPopulation::Iterator::IsRealCell 0 0% 63.46% 313ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.026% 63.49% 304ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 63.50% 298ms 1.53% Cell::GetMutationState 8ms 0.041% 63.54% 298ms 1.53% alternateaxes 3ms 0.015% 63.55% 297ms 1.52% Cell::GetCellProliferativeType 275ms 1.41% 64.97% 290ms 1.49% vertexmedian 286ms 1.47% 66.43% 287ms 1.47% std::vector::operator[] (inline) 20ms 0.1% 66.54% 284ms 1.46% std::vector::push_back (inline) 234ms 1.20% 67.74% 276ms 1.42% _int_free 10ms 0.051% 67.79% 272ms 1.40% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 67.79% 272ms 1.40% std::_Rb_tree::_M_put_node (inline) 16ms 0.082% 67.87% 271ms 1.39% std::num_put::_M_insert_float 21ms 0.11% 67.98% 270ms 1.39% AbstractTetrahedralElement::CalculateJacobian 16ms 0.082% 68.06% 270ms 1.39% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.026% 68.09% 257ms 1.32% LegacyCellProliferativeTypesWriter::VisitCell 98ms 0.5% 68.59% 255ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.082% 68.67% 255ms 1.31% std::vector::_M_realloc_insert 12ms 0.062% 68.73% 247ms 1.27% std::_Rb_tree::_M_erase_aux (inline) 9ms 0.046% 68.78% 239ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 68.79% 237ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 68.81% 234ms 1.20% std::set::set (inline) 17ms 0.087% 68.89% 227ms 1.17% Element::MarkAsDeleted 1ms 0.0051% 68.90% 227ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 26ms 0.13% 69.03% 227ms 1.17% std::_Rb_tree::_M_copy (inline) 90ms 0.46% 69.49% 226ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.01% 69.50% 223ms 1.14% std::__cxx11::collate::do_transform 1ms 0.0051% 69.51% 222ms 1.14% MeshBasedCellPopulation::GetDampingConstant 4ms 0.021% 69.53% 220ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 54ms 0.28% 69.81% 217ms 1.11% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0051% 69.81% 214ms 1.10% ___vsnprintf 28ms 0.14% 69.95% 213ms 1.09% AbstractTetrahedralElement::RefreshJacobian 14ms 0.072% 70.03% 213ms 1.09% TetrahedralMesh::Clear 34ms 0.17% 70.20% 213ms 1.09% __printf_buffer 0 0% 70.20% 213ms 1.09% __vsnprintf_internal (inline) 142ms 0.73% 70.93% 206ms 1.06% malloc_consolidate 9ms 0.046% 70.98% 202ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 70.98% 202ms 1.04% OffLatticeSimulation::ApplyBoundaries 64ms 0.33% 71.30% 196ms 1.01% std::_Rb_tree::_M_clone_node (inline) 138ms 0.71% 72.01% 195ms 1.00% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 72.02% 187ms 0.96% AbstractTetrahedralElement::AbstractTetrahedralElement 125ms 0.64% 72.66% 181ms 0.93% std::_Rb_tree::equal_range (inline) 5ms 0.026% 72.69% 170ms 0.87% __printf_fp_l_buffer 0 0% 72.69% 170ms 0.87% __printf_fp_spec (inline) 170ms 0.87% 73.56% 170ms 0.87% incircle 1ms 0.0051% 73.57% 168ms 0.86% boost::numeric::ublas::vector_assign (inline) 72ms 0.37% 73.94% 167ms 0.86% AbstractElement::GetNodeLocation 163ms 0.84% 74.77% 163ms 0.84% AbstractCellMutationState::~AbstractCellMutationState 4ms 0.021% 74.79% 162ms 0.83% CellProliferativeTypesWriter::VisitCell 72ms 0.37% 75.16% 162ms 0.83% __printf_fp_buffer_1 51ms 0.26% 75.43% 161ms 0.83% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 156ms 0.8% 76.23% 156ms 0.8% std::_Rb_tree_insert_and_rebalance 37ms 0.19% 76.42% 154ms 0.79% TetrahedralMesh::EdgesEnd (partial-inline) 154ms 0.79% 77.21% 154ms 0.79% std::vector::size (inline) 3ms 0.015% 77.22% 153ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 151ms 0.77% 78.00% 151ms 0.77% unlink_chunk 37ms 0.19% 78.19% 150ms 0.77% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0051% 78.19% 146ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 9ms 0.046% 78.24% 146ms 0.75% boost::numeric::ublas::c_vector::c_vector (inline) 145ms 0.74% 78.98% 145ms 0.74% [libchaste_crypt.so] 2ms 0.01% 78.99% 144ms 0.74% CellPropertyCollection::HasProperty 0 0% 78.99% 142ms 0.73% Cell::HasCellProperty (inline) 141ms 0.72% 79.72% 141ms 0.72% std::type_info::name (inline) 12ms 0.062% 79.78% 140ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 137ms 0.7% 80.48% 137ms 0.7% Node::GetIndex 38ms 0.2% 80.68% 136ms 0.7% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 17ms 0.087% 80.76% 136ms 0.7% boost::detail::shared_count::~shared_count (inline) 0 0% 80.76% 136ms 0.7% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.76% 131ms 0.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.021% 80.78% 130ms 0.67% Node::~Node 31ms 0.16% 80.94% 130ms 0.67% boost::numeric::ublas::indexing_vector_assign 0 0% 80.94% 129ms 0.66% Cell::SetCellProliferativeType 119ms 0.61% 81.55% 129ms 0.66% vertexsort 3ms 0.015% 81.57% 127ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.015% 81.58% 125ms 0.64% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0051% 81.59% 121ms 0.62% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 64ms 0.33% 81.92% 116ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 81.92% 114ms 0.59% AbstractCellBasedWriter::OpenOutputFileForAppend 112ms 0.57% 82.49% 112ms 0.57% std::_Rb_tree_rebalance_for_erase 0 0% 82.49% 111ms 0.57% OutputFileHandler::OpenOutputFile 77ms 0.4% 82.89% 111ms 0.57% TetrahedralMesh::EdgeIterator::EdgeIterator 105ms 0.54% 83.43% 110ms 0.56% boost::detail::sp_counted_base::release 110ms 0.56% 83.99% 110ms 0.56% std::_Rb_tree_increment 57ms 0.29% 84.28% 105ms 0.54% TimeStepper::AdvanceOneTimeStep 105ms 0.54% 84.82% 105ms 0.54% boost::shared_ptr::operator-> (inline) 1ms 0.0051% 84.83% 104ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 104ms 0.53% 85.36% 104ms 0.53% AbstractCellProperty::AbstractCellProperty 39ms 0.2% 85.56% 103ms 0.53% boost::shared_ptr::shared_ptr (inline) 5ms 0.026% 85.59% 102ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 31ms 0.16% 85.75% 102ms 0.52% std::__ostream_insert 8ms 0.041% 85.79% 99ms 0.51% Cylindrical2dMesh::CreateMirrorNodes