File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16676ms, 83.90% of 19875ms total Dropped 806 nodes (cum <= 99.38ms) flat flat% sum% cum cum% 0 0% 0% 19825ms 99.75% __libc_start_call_main 0 0% 0% 19825ms 99.75% __libc_start_main_impl 0 0% 0% 19825ms 99.75% _start 0 0% 0% 19801ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19801ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19801ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19801ms 99.63% main 0 0% 0% 19758ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19758ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19758ms 99.41% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 19731ms 99.28% AbstractCellBasedSimulation::Solve 2ms 0.01% 0.015% 15070ms 75.82% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.02% 0.035% 9545ms 48.03% AbstractCellBasedSimulation::DoCellBirth 13ms 0.065% 0.1% 9444ms 47.52% Cell::ReadyToDivide 7ms 0.035% 0.14% 9339ms 46.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.15% 9182ms 46.20% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.065% 0.22% 9171ms 46.14% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.23% 9154ms 46.06% CellCycleModelOdeHandler::SolveOdeToTime 59ms 0.3% 0.53% 8986ms 45.21% AbstractOneStepIvpOdeSolver::InternalSolve 1048ms 5.27% 5.80% 8139ms 40.95% RungeKutta4IvpOdeSolver::CalculateNextYValue 2808ms 14.13% 19.93% 6922ms 34.83% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 19.93% 5416ms 27.25% MeshBasedCellPopulation::Update 6ms 0.03% 19.96% 4186ms 21.06% Cylindrical2dMesh::ReMesh 68ms 0.34% 20.31% 4139ms 20.83% AbstractCellProperty::IsType (inline) 429ms 2.16% 22.47% 2735ms 13.76% AbstractCellProperty::IsSame 1ms 0.005% 22.47% 2568ms 12.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 282ms 1.42% 23.89% 2306ms 11.60% std::type_info::operator== (inline) 0 0% 23.89% 2293ms 11.54% MutableMesh::ReMesh 0 0% 23.89% 2249ms 11.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 17ms 0.086% 23.97% 2198ms 11.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 2119ms 10.66% 34.64% 2119ms 10.66% __strcmp_avx2 0 0% 34.64% 2084ms 10.49% AbstractCellPopulation::WriteResultsToFiles 789ms 3.97% 38.61% 1866ms 9.39% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.85% 39.46% 1724ms 8.67% TetrahedralMesh::EdgeIterator::operator++ 70ms 0.35% 39.81% 1391ms 7.00% std::_Rb_tree::find (inline) 2ms 0.01% 39.82% 1188ms 5.98% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.05% 39.87% 1159ms 5.83% TetrahedralMesh::ImportFromMesher 3ms 0.015% 39.88% 1126ms 5.67% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 32ms 0.16% 40.05% 1106ms 5.56% operator new 11ms 0.055% 40.10% 1076ms 5.41% MeshBasedCellPopulation::SpringIterator::operator++ 243ms 1.22% 41.32% 1051ms 5.29% __GI___libc_malloc 13ms 0.065% 41.39% 991ms 4.99% std::set::insert (inline) 16ms 0.081% 41.47% 978ms 4.92% std::_Rb_tree::_M_insert_unique 30ms 0.15% 41.62% 959ms 4.83% std::__new_allocator::allocate (inline) 0 0% 41.62% 955ms 4.81% std::allocator_traits::allocate (inline) 0 0% 41.62% 838ms 4.22% std::set::count (inline) 0 0% 41.62% 831ms 4.18% triangulate 6ms 0.03% 41.65% 770ms 3.87% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.005% 41.66% 754ms 3.79% delaunay 2ms 0.01% 41.67% 752ms 3.78% divconqdelaunay 66ms 0.33% 42.00% 728ms 3.66% std::map::operator[] (partial-inline) 1ms 0.005% 42.00% 720ms 3.62% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.03% 42.03% 720ms 3.62% CellPopulationElementWriter::Visit 382ms 1.92% 43.95% 720ms 3.62% _int_malloc 707ms 3.56% 47.51% 707ms 3.56% std::_Rb_tree::_S_right (inline) 681ms 3.43% 50.94% 681ms 3.43% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.065% 51.00% 675ms 3.40% std::less::operator() (inline) 662ms 3.33% 54.33% 662ms 3.33% std::operator< (inline) 224ms 1.13% 55.46% 652ms 3.28% __dynamic_cast 38ms 0.19% 55.65% 637ms 3.21% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 3ms 0.015% 55.67% 632ms 3.18% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.025% 55.69% 609ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.69% 608ms 3.06% std::_Rb_tree::_M_create_node (inline) 0 0% 55.69% 580ms 2.92% std::_Rb_tree::_M_get_node (inline) 31ms 0.16% 55.85% 577ms 2.90% std::_Rb_tree::_M_insert_ (inline) 25ms 0.13% 55.97% 567ms 2.85% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.97% 565ms 2.84% std::_Rb_tree::lower_bound (inline) 0 0% 55.97% 565ms 2.84% std::map::lower_bound (inline) 9ms 0.045% 56.02% 550ms 2.77% Element::Element 0 0% 56.02% 546ms 2.75% std::map::find (inline) 0 0% 56.02% 538ms 2.71% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.04% 56.06% 523ms 2.63% MutableMesh::ReIndex 7ms 0.035% 56.10% 502ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.005% 56.10% 500ms 2.52% std::ostream::operator<< (inline) 61ms 0.31% 56.41% 497ms 2.50% std::ostream::_M_insert 11ms 0.055% 56.46% 480ms 2.42% Cylindrical2dMesh::CorrectNonPeriodicMesh 146ms 0.73% 57.20% 479ms 2.41% __GI___libc_free 1ms 0.005% 57.20% 475ms 2.39% AbstractCellProperty::IsSubType (inline) 322ms 1.62% 58.82% 452ms 2.27% AbstractCellMutationState::AbstractCellMutationState 7ms 0.035% 58.86% 443ms 2.23% Element::RegisterWithNodes (inline) 6ms 0.03% 58.89% 433ms 2.18% Node::AddElement 115ms 0.58% 59.47% 391ms 1.97% std::_Rb_tree::_M_erase 125ms 0.63% 60.10% 385ms 1.94% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.05% 60.15% 375ms 1.89% std::_Rb_tree::erase 12ms 0.06% 60.21% 374ms 1.88% Node::RemoveElement 0 0% 60.21% 374ms 1.88% std::_Vector_base::_M_allocate (inline) 1ms 0.005% 60.21% 373ms 1.88% std::set::erase (inline) 372ms 1.87% 62.08% 372ms 1.87% [libchaste_cell_based.so] 13ms 0.065% 62.15% 371ms 1.87% std::__new_allocator::deallocate (inline) 0 0% 62.15% 367ms 1.85% std::allocator_traits::deallocate (inline) 15ms 0.075% 62.22% 362ms 1.82% divconqrecurse 18ms 0.091% 62.31% 359ms 1.81% std::_Rb_tree::~_Rb_tree (inline) 0 0% 62.31% 345ms 1.74% std::_Rb_tree::_M_drop_node (inline) 5ms 0.025% 62.34% 341ms 1.72% Cell::GetMutationState 100ms 0.5% 62.84% 339ms 1.71% mergehulls 0 0% 62.84% 337ms 1.70% std::set::~set (inline) 264ms 1.33% 64.17% 331ms 1.67% _int_free 27ms 0.14% 64.31% 328ms 1.65% Element::ResetIndex 6ms 0.03% 64.34% 317ms 1.59% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.086% 64.42% 315ms 1.58% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.42% 314ms 1.58% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 64.44% 312ms 1.57% Cell::GetCellProliferativeType 23ms 0.12% 64.56% 311ms 1.56% AbstractTetrahedralElement::CalculateJacobian 1ms 0.005% 64.56% 311ms 1.56% NodeLocationWriter::Visit 5ms 0.025% 64.59% 302ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 145ms 0.73% 65.32% 302ms 1.52% __cxxabiv1::__si_class_type_info::__do_dyncast 40ms 0.2% 65.52% 291ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.52% 288ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.05% 65.57% 274ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.04% 65.61% 270ms 1.36% AbstractCellPopulation::IsCellAttachedToLocationIndex 265ms 1.33% 66.94% 270ms 1.36% std::vector::operator[] (inline) 25ms 0.13% 67.07% 269ms 1.35% TetrahedralMesh::Clear 0 0% 67.07% 268ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 24ms 0.12% 67.19% 263ms 1.32% std::num_put::_M_insert_float 4ms 0.02% 67.21% 262ms 1.32% std::vector::push_back (inline) 91ms 0.46% 67.67% 256ms 1.29% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 8ms 0.04% 67.71% 255ms 1.28% alternateaxes 6ms 0.03% 67.74% 252ms 1.27% std::set::set (inline) 27ms 0.14% 67.87% 250ms 1.26% std::vector::_M_realloc_insert 10ms 0.05% 67.92% 247ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 233ms 1.17% 69.10% 247ms 1.24% vertexmedian 93ms 0.47% 69.56% 246ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 26ms 0.13% 69.70% 239ms 1.20% AbstractTetrahedralElement::RefreshJacobian 11ms 0.055% 69.75% 231ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 34ms 0.17% 69.92% 227ms 1.14% std::_Rb_tree::_M_copy (inline) 0 0% 69.92% 225ms 1.13% MeshBasedCellPopulation::GetDampingConstant 0 0% 69.92% 224ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 53ms 0.27% 70.19% 223ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 165ms 0.83% 71.02% 222ms 1.12% malloc_consolidate 16ms 0.081% 71.10% 222ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.02% 71.12% 220ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 71.13% 211ms 1.06% std::__cxx11::collate::do_transform 9ms 0.045% 71.17% 209ms 1.05% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.015% 71.19% 205ms 1.03% ___vsnprintf 0 0% 71.19% 204ms 1.03% OffLatticeSimulation::ApplyBoundaries 0 0% 71.19% 202ms 1.02% __vsnprintf_internal (inline) 139ms 0.7% 71.89% 200ms 1.01% AbstractElement::GetNodeGlobalIndex 22ms 0.11% 72.00% 200ms 1.01% __printf_buffer 3ms 0.015% 72.02% 198ms 1% CellPropertyCollection::HasProperty 9ms 0.045% 72.06% 195ms 0.98% Element::MarkAsDeleted 85ms 0.43% 72.49% 194ms 0.98% AbstractElement::GetNodeLocation 0 0% 72.49% 190ms 0.96% Cell::HasCellProperty (inline) 190ms 0.96% 73.44% 190ms 0.96% [libchaste_crypt.so] 53ms 0.27% 73.71% 187ms 0.94% std::_Rb_tree::_M_clone_node (inline) 6ms 0.03% 73.74% 180ms 0.91% CellProliferativeTypesWriter::VisitCell 169ms 0.85% 74.59% 169ms 0.85% Node::GetIndex 169ms 0.85% 75.44% 169ms 0.85% incircle 168ms 0.85% 76.29% 168ms 0.85% unlink_chunk 4ms 0.02% 76.31% 163ms 0.82% __printf_fp_l_buffer 0 0% 76.31% 163ms 0.82% __printf_fp_spec (inline) 12ms 0.06% 76.37% 162ms 0.82% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 12ms 0.06% 76.43% 161ms 0.81% Node::~Node 64ms 0.32% 76.75% 155ms 0.78% __printf_fp_buffer_1 155ms 0.78% 77.53% 155ms 0.78% std::type_info::name (inline) 19ms 0.096% 77.63% 151ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 150ms 0.75% 78.38% 150ms 0.75% std::_Rb_tree_insert_and_rebalance 98ms 0.49% 78.87% 149ms 0.75% std::_Rb_tree::equal_range (inline) 148ms 0.74% 79.62% 148ms 0.74% std::vector::size (inline) 51ms 0.26% 79.87% 146ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.015% 79.89% 146ms 0.73% boost::numeric::ublas::vector_assign (inline) 1ms 0.005% 79.89% 145ms 0.73% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.025% 79.92% 139ms 0.7% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.04% 79.96% 134ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 11ms 0.055% 80.02% 131ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.02% 130ms 0.65% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.02% 129ms 0.65% OutputFileHandler::OpenOutputFile 128ms 0.64% 80.66% 128ms 0.64% std::_Rb_tree_increment 7ms 0.035% 80.69% 127ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 40ms 0.2% 80.90% 125ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 82ms 0.41% 81.31% 125ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 109ms 0.55% 81.86% 125ms 0.63% vertexsort 34ms 0.17% 82.03% 124ms 0.62% std::__ostream_insert 29ms 0.15% 82.17% 123ms 0.62% TetrahedralMesh::EdgesEnd 1ms 0.005% 82.18% 120ms 0.6% Cell::SetCellProliferativeType 0 0% 82.18% 114ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 21ms 0.11% 82.28% 113ms 0.57% std::num_put::_M_insert_int 7ms 0.035% 82.32% 112ms 0.56% Cylindrical2dMesh::CreateMirrorNodes 6ms 0.03% 82.35% 110ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 31ms 0.16% 82.51% 109ms 0.55% boost::numeric::ublas::indexing_vector_assign 0 0% 82.51% 107ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.04% 82.55% 106ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 82.55% 106ms 0.53% boost::shared_ptr::~shared_ptr (inline) 16ms 0.081% 82.63% 104ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 104ms 0.52% 83.15% 104ms 0.52% Node::rGetLocation 47ms 0.24% 83.39% 103ms 0.52% std::basic_filebuf::xsputn 1ms 0.005% 83.39% 102ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.51% 83.90% 101ms 0.51% boost::shared_ptr::operator-> (inline) 1ms 0.005% 83.90% 101ms 0.51% std::vector::_M_default_append 0 0% 83.90% 101ms 0.51% std::vector::resize (inline)