File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16457ms, 84.59% of 19456ms total Dropped 763 nodes (cum <= 97.28ms) flat flat% sum% cum cum% 0 0% 0% 19408ms 99.75% __libc_start_call_main 0 0% 0% 19408ms 99.75% __libc_start_main_impl 0 0% 0% 19408ms 99.75% _start 0 0% 0% 19383ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19383ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19383ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19383ms 99.62% main 0 0% 0% 19341ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19341ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19341ms 99.41% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19314ms 99.27% AbstractCellBasedSimulation::Solve 0 0% 0% 14714ms 75.63% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9283ms 47.71% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.021% 9188ms 47.22% Cell::ReadyToDivide 3ms 0.015% 0.036% 9099ms 46.77% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.051% 8949ms 46.00% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.13% 8937ms 45.93% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.14% 8916ms 45.83% CellCycleModelOdeHandler::SolveOdeToTime 81ms 0.42% 0.56% 8762ms 45.03% AbstractOneStepIvpOdeSolver::InternalSolve 1019ms 5.24% 5.80% 7855ms 40.37% RungeKutta4IvpOdeSolver::CalculateNextYValue 2830ms 14.55% 20.34% 6623ms 34.04% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.34% 5290ms 27.19% MeshBasedCellPopulation::Update 5ms 0.026% 20.37% 4094ms 21.04% Cylindrical2dMesh::ReMesh 52ms 0.27% 20.64% 3821ms 19.64% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.64% 2584ms 13.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 320ms 1.64% 22.29% 2461ms 12.65% AbstractCellProperty::IsSame 0 0% 22.29% 2273ms 11.68% MutableMesh::ReMesh 0 0% 22.29% 2224ms 11.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.041% 22.33% 2169ms 11.15% AbstractNumericalMethod::ComputeForcesIncludingDamping 188ms 0.97% 23.29% 2141ms 11.00% std::type_info::operator== (inline) 2070ms 10.64% 33.93% 2070ms 10.64% __strcmp_avx2 0 0% 33.93% 2010ms 10.33% AbstractCellPopulation::WriteResultsToFiles 799ms 4.11% 38.04% 1929ms 9.91% std::_Rb_tree::_M_lower_bound (inline) 173ms 0.89% 38.93% 1685ms 8.66% TetrahedralMesh::EdgeIterator::operator++ 55ms 0.28% 39.21% 1425ms 7.32% std::_Rb_tree::find (inline) 0 0% 39.21% 1154ms 5.93% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.026% 39.24% 1139ms 5.85% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.051% 39.29% 1104ms 5.67% TetrahedralMesh::ImportFromMesher 44ms 0.23% 39.51% 1062ms 5.46% operator new 14ms 0.072% 39.59% 1005ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 252ms 1.30% 40.88% 999ms 5.13% __GI___libc_malloc 21ms 0.11% 40.99% 966ms 4.97% std::set::insert (inline) 14ms 0.072% 41.06% 945ms 4.86% std::_Rb_tree::_M_insert_unique 28ms 0.14% 41.21% 924ms 4.75% std::__new_allocator::allocate (inline) 0 0% 41.21% 924ms 4.75% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.21% 914ms 4.70% triangulate 0 0% 41.21% 861ms 4.43% std::set::count (inline) 0 0% 41.21% 817ms 4.20% delaunay 2ms 0.01% 41.22% 816ms 4.19% divconqdelaunay 760ms 3.91% 45.13% 760ms 3.91% std::_Rb_tree::_S_right (inline) 8ms 0.041% 45.17% 745ms 3.83% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 722ms 3.71% 48.88% 722ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 2ms 0.01% 48.89% 719ms 3.70% AbstractTwoBodyInteractionForce::AddForceContribution 59ms 0.3% 49.19% 716ms 3.68% std::map::operator[] (partial-inline) 203ms 1.04% 50.24% 678ms 3.48% __dynamic_cast 6ms 0.031% 50.27% 668ms 3.43% CellPopulationElementWriter::Visit 380ms 1.95% 52.22% 660ms 3.39% _int_malloc 20ms 0.1% 52.32% 653ms 3.36% std::less::operator() (inline) 633ms 3.25% 55.58% 633ms 3.25% std::operator< (inline) 25ms 0.13% 55.71% 624ms 3.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.026% 55.73% 618ms 3.18% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.73% 616ms 3.17% std::_Rb_tree::_M_create_node (inline) 8ms 0.041% 55.77% 593ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.77% 586ms 3.01% std::_Rb_tree::_M_get_node (inline) 17ms 0.087% 55.86% 584ms 3.00% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.86% 574ms 2.95% std::_Rb_tree::lower_bound (inline) 0 0% 55.86% 574ms 2.95% std::map::lower_bound (inline) 37ms 0.19% 56.05% 566ms 2.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.05% 562ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 56.05% 562ms 2.89% std::map::find (inline) 5ms 0.026% 56.08% 541ms 2.78% Element::Element 9ms 0.046% 56.12% 527ms 2.71% MutableMesh::ReIndex 12ms 0.062% 56.18% 525ms 2.70% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.026% 56.21% 510ms 2.62% AbstractCellProperty::IsSubType (inline) 15ms 0.077% 56.29% 491ms 2.52% Cylindrical2dMesh::CorrectNonPeriodicMesh 14ms 0.072% 56.36% 483ms 2.48% Element::RegisterWithNodes (inline) 11ms 0.057% 56.41% 472ms 2.43% Node::AddElement 1ms 0.0051% 56.42% 460ms 2.36% std::ostream::operator<< (inline) 74ms 0.38% 56.80% 458ms 2.35% std::ostream::_M_insert 124ms 0.64% 57.44% 429ms 2.20% __GI___libc_free 276ms 1.42% 58.86% 419ms 2.15% AbstractCellMutationState::AbstractCellMutationState 16ms 0.082% 58.94% 406ms 2.09% divconqrecurse 12ms 0.062% 59.00% 390ms 2.00% std::_Rb_tree::erase 1ms 0.0051% 59.00% 390ms 2.00% std::set::erase (inline) 105ms 0.54% 59.54% 383ms 1.97% mergehulls 14ms 0.072% 59.62% 378ms 1.94% Node::RemoveElement 118ms 0.61% 60.22% 369ms 1.90% std::_Rb_tree::_M_erase 139ms 0.71% 60.94% 366ms 1.88% std::_Rb_tree::_M_get_insert_unique_pos 26ms 0.13% 61.07% 357ms 1.83% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.087% 61.16% 343ms 1.76% Element::ResetIndex 6ms 0.031% 61.19% 343ms 1.76% std::__new_allocator::deallocate (inline) 163ms 0.84% 62.03% 342ms 1.76% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 62.04% 341ms 1.75% std::_Vector_base::_M_allocate (inline) 0 0% 62.04% 339ms 1.74% std::allocator_traits::deallocate (inline) 1ms 0.0051% 62.05% 333ms 1.71% Cell::GetCellProliferativeType 1ms 0.0051% 62.05% 332ms 1.71% Cell::GetMutationState 0 0% 62.05% 330ms 1.70% std::set::~set (inline) 329ms 1.69% 63.74% 329ms 1.69% [libchaste_cell_based.so] 5ms 0.026% 63.77% 313ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.021% 63.79% 310ms 1.59% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 63.79% 305ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.036% 63.83% 305ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 63.83% 305ms 1.57% std::_Rb_tree::_M_drop_node (inline) 237ms 1.22% 65.04% 304ms 1.56% _int_free 303ms 1.56% 66.60% 303ms 1.56% std::vector::operator[] (inline) 35ms 0.18% 66.78% 301ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.78% 300ms 1.54% NodeLocationWriter::Visit 18ms 0.093% 66.87% 291ms 1.50% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.021% 66.89% 275ms 1.41% alternateaxes 0 0% 66.89% 271ms 1.39% std::_Rb_tree::_M_put_node (inline) 245ms 1.26% 68.15% 270ms 1.39% vertexmedian 6ms 0.031% 68.18% 268ms 1.38% std::vector::push_back (inline) 111ms 0.57% 68.76% 263ms 1.35% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.072% 68.83% 261ms 1.34% std::num_put::_M_insert_float 23ms 0.12% 68.95% 259ms 1.33% AbstractTetrahedralElement::CalculateJacobian 10ms 0.051% 69.00% 255ms 1.31% std::vector::_M_realloc_insert 3ms 0.015% 69.01% 251ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0051% 69.02% 250ms 1.28% std::set::set (inline) 8ms 0.041% 69.06% 244ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 28ms 0.14% 69.20% 241ms 1.24% std::_Rb_tree::_M_copy (inline) 3ms 0.015% 69.22% 232ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 55ms 0.28% 69.50% 229ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 69.51% 227ms 1.17% MeshBasedCellPopulation::GetDampingConstant 8ms 0.041% 69.55% 226ms 1.16% std::__cxx11::collate::do_transform 108ms 0.56% 70.11% 224ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0051% 70.11% 223ms 1.15% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0051% 70.12% 223ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 161ms 0.83% 70.94% 219ms 1.13% AbstractElement::GetNodeGlobalIndex 13ms 0.067% 71.01% 219ms 1.13% std::_Rb_tree::_M_erase_aux (inline) 0 0% 71.01% 218ms 1.12% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 71.02% 213ms 1.09% ___vsnprintf 0 0% 71.02% 211ms 1.08% __vsnprintf_internal (inline) 61ms 0.31% 71.34% 209ms 1.07% std::_Rb_tree::_M_clone_node (inline) 22ms 0.11% 71.45% 207ms 1.06% __printf_buffer 11ms 0.057% 71.50% 202ms 1.04% Element::MarkAsDeleted 9ms 0.046% 71.55% 198ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.098% 71.65% 194ms 1% TetrahedralMesh::Clear 7ms 0.036% 71.68% 181ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 27ms 0.14% 71.82% 181ms 0.93% AbstractTetrahedralElement::RefreshJacobian 8ms 0.041% 71.86% 177ms 0.91% __printf_fp_l_buffer 0 0% 71.86% 177ms 0.91% __printf_fp_spec (inline) 2ms 0.01% 71.88% 173ms 0.89% CellProliferativeTypesWriter::VisitCell 171ms 0.88% 72.75% 171ms 0.88% incircle 3ms 0.015% 72.77% 169ms 0.87% CellPropertyCollection::HasProperty 121ms 0.62% 73.39% 168ms 0.86% malloc_consolidate 0 0% 73.39% 167ms 0.86% Cell::HasCellProperty (inline) 82ms 0.42% 73.81% 166ms 0.85% __printf_fp_buffer_1 94ms 0.48% 74.30% 165ms 0.85% std::_Rb_tree::equal_range (inline) 160ms 0.82% 75.12% 160ms 0.82% unlink_chunk 156ms 0.8% 75.92% 156ms 0.8% std::type_info::name (inline) 49ms 0.25% 76.17% 155ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 76.17% 148ms 0.76% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.026% 76.20% 148ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 52ms 0.27% 76.46% 147ms 0.76% AbstractElement::GetNodeLocation 0 0% 76.46% 145ms 0.75% OutputFileHandler::OpenOutputFile 145ms 0.75% 77.21% 145ms 0.75% [libchaste_crypt.so] 3ms 0.015% 77.23% 144ms 0.74% boost::numeric::ublas::vector_assign (inline) 142ms 0.73% 77.96% 142ms 0.73% std::vector::size (inline) 1ms 0.0051% 77.96% 141ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 77.96% 139ms 0.71% AbstractCellBasedSimulation::DoCellRemoval (inline) 139ms 0.71% 78.67% 139ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 52ms 0.27% 78.94% 135ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 135ms 0.69% 79.64% 135ms 0.69% Node::GetIndex 0 0% 79.64% 132ms 0.68% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.01% 79.65% 131ms 0.67% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 40ms 0.21% 79.85% 130ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 5ms 0.026% 79.88% 129ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.1% 79.98% 126ms 0.65% TetrahedralMesh::EdgesEnd 122ms 0.63% 80.61% 126ms 0.65% vertexsort 2ms 0.01% 80.62% 125ms 0.64% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 125ms 0.64% 81.26% 125ms 0.64% std::_Rb_tree_insert_and_rebalance 34ms 0.17% 81.44% 124ms 0.64% std::__ostream_insert 7ms 0.036% 81.47% 123ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.47% 121ms 0.62% Cell::SetCellProliferativeType 5ms 0.026% 81.50% 118ms 0.61% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 71ms 0.36% 81.86% 117ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 34ms 0.17% 82.04% 116ms 0.6% boost::numeric::ublas::indexing_vector_assign 8ms 0.041% 82.08% 113ms 0.58% Node::~Node 13ms 0.067% 82.14% 112ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 82.14% 112ms 0.58% boost::shared_ptr::~shared_ptr (inline) 8ms 0.041% 82.19% 111ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 111ms 0.57% 82.76% 111ms 0.57% std::_Rb_tree_increment 105ms 0.54% 83.30% 105ms 0.54% counterclockwise 0 0% 83.30% 104ms 0.53% std::operator<< (inline) 40ms 0.21% 83.50% 103ms 0.53% boost::shared_ptr::shared_ptr (inline) 101ms 0.52% 84.02% 101ms 0.52% std::_Rb_tree_rebalance_for_erase 1ms 0.0051% 84.03% 100ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 11ms 0.057% 84.08% 99ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 98ms 0.5% 84.59% 98ms 0.5% TetrahedralMesh::EdgeIterator::operator!= (partial-inline)