File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13552ms, 85.46% of 15857ms total Dropped 781 nodes (cum <= 79.28ms) flat flat% sum% cum cum% 0 0% 0% 15811ms 99.71% __libc_start_call_main 0 0% 0% 15811ms 99.71% __libc_start_main_impl 0 0% 0% 15811ms 99.71% _start 0 0% 0% 15793ms 99.60% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15793ms 99.60% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15793ms 99.60% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15793ms 99.60% main 0 0% 0% 15756ms 99.36% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15756ms 99.36% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15756ms 99.36% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15729ms 99.19% AbstractCellBasedSimulation::Solve 1ms 0.0063% 0.0063% 11370ms 71.70% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.013% 0.019% 6153ms 38.80% AbstractCellBasedSimulation::DoCellBirth 7ms 0.044% 0.063% 6058ms 38.20% Cell::ReadyToDivide 2ms 0.013% 0.076% 5978ms 37.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0063% 0.082% 5829ms 36.76% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.11% 0.19% 5819ms 36.70% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.019% 0.21% 5799ms 36.57% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.45% 0.66% 5593ms 35.27% AbstractOneStepIvpOdeSolver::InternalSolve 1ms 0.0063% 0.67% 5110ms 32.23% MeshBasedCellPopulation::Update 914ms 5.76% 6.43% 4781ms 30.15% RungeKutta4IvpOdeSolver::CalculateNextYValue 2ms 0.013% 6.45% 3947ms 24.89% Cylindrical2dMesh::ReMesh 3241ms 20.44% 26.88% 3628ms 22.88% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 26.88% 2276ms 14.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 26.88% 2151ms 13.56% MutableMesh::ReMesh 0 0% 26.88% 2075ms 13.09% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0063% 26.89% 2006ms 12.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.063% 26.95% 1952ms 12.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 800ms 5.05% 32.00% 1791ms 11.29% std::_Rb_tree::_M_lower_bound (inline) 190ms 1.20% 33.20% 1691ms 10.66% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.42% 33.61% 1364ms 8.60% std::_Rb_tree::find (inline) 0 0% 33.61% 1121ms 7.07% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.05% 33.66% 1118ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.082% 33.75% 1077ms 6.79% TetrahedralMesh::ImportFromMesher 40ms 0.25% 34.00% 994ms 6.27% operator new 14ms 0.088% 34.09% 991ms 6.25% MeshBasedCellPopulation::SpringIterator::operator++ 208ms 1.31% 35.40% 940ms 5.93% __GI___libc_malloc 11ms 0.069% 35.47% 940ms 5.93% std::set::insert (inline) 14ms 0.088% 35.56% 929ms 5.86% std::_Rb_tree::_M_insert_unique 0 0% 35.56% 858ms 5.41% std::set::count (inline) 37ms 0.23% 35.79% 857ms 5.40% std::__new_allocator::allocate (inline) 0 0% 35.79% 850ms 5.36% std::allocator_traits::allocate (inline) 3ms 0.019% 35.81% 804ms 5.07% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.013% 35.82% 804ms 5.07% triangulate 7ms 0.044% 35.86% 727ms 4.58% CellPopulationElementWriter::Visit 0 0% 35.86% 718ms 4.53% delaunay 5ms 0.032% 35.90% 718ms 4.53% divconqdelaunay 2ms 0.013% 35.91% 703ms 4.43% CellPropertyCollection::GetPropertiesType (inline) 55ms 0.35% 36.26% 660ms 4.16% std::map::operator[] (partial-inline) 2ms 0.013% 36.27% 654ms 4.12% MeshBasedCellPopulation::AcceptCellWriter 369ms 2.33% 38.59% 653ms 4.12% _int_malloc 622ms 3.92% 42.52% 637ms 4.02% WntCellCycleOdeSystem::CalculateStoppingEvent 18ms 0.11% 42.63% 633ms 3.99% std::less::operator() (inline) 630ms 3.97% 46.60% 630ms 3.97% std::_Rb_tree::_S_right (inline) 615ms 3.88% 50.48% 615ms 3.88% std::operator< (inline) 3ms 0.019% 50.50% 605ms 3.82% AbstractCellProperty::IsSubType (inline) 169ms 1.07% 51.57% 605ms 3.82% __dynamic_cast 0 0% 51.57% 580ms 3.66% std::_Rb_tree::_M_create_node (inline) 27ms 0.17% 51.74% 568ms 3.58% std::_Rb_tree::_M_insert_ (inline) 22ms 0.14% 51.88% 561ms 3.54% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.019% 51.90% 554ms 3.49% Element::Element 0 0% 51.90% 549ms 3.46% std::_Rb_tree::_M_get_node (inline) 17ms 0.11% 52.00% 521ms 3.29% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 52.00% 519ms 3.27% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 52.00% 519ms 3.27% std::_Rb_tree::lower_bound (inline) 0 0% 52.00% 519ms 3.27% std::map::lower_bound (inline) 3ms 0.019% 52.02% 518ms 3.27% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.05% 52.07% 499ms 3.15% MutableMesh::ReIndex 0 0% 52.07% 497ms 3.13% std::map::find (inline) 1ms 0.0063% 52.08% 485ms 3.06% std::ostream::operator<< (inline) 67ms 0.42% 52.50% 484ms 3.05% std::ostream::_M_insert 14ms 0.088% 52.59% 477ms 3.01% Element::RegisterWithNodes (inline) 8ms 0.05% 52.64% 464ms 2.93% Cylindrical2dMesh::CorrectNonPeriodicMesh 14ms 0.088% 52.73% 461ms 2.91% Node::AddElement 145ms 0.91% 53.64% 447ms 2.82% __GI___libc_free 17ms 0.11% 53.75% 419ms 2.64% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 10ms 0.063% 53.81% 390ms 2.46% std::_Rb_tree::erase 3ms 0.019% 53.83% 390ms 2.46% std::set::erase (inline) 3ms 0.019% 53.85% 388ms 2.45% Cell::GetCellProliferativeType 12ms 0.076% 53.93% 385ms 2.43% divconqrecurse 12ms 0.076% 54.00% 384ms 2.42% Node::RemoveElement 2ms 0.013% 54.01% 380ms 2.40% Cell::GetMutationState 52ms 0.33% 54.34% 368ms 2.32% AbstractCellProperty::IsType (inline) 114ms 0.72% 55.06% 368ms 2.32% mergehulls 106ms 0.67% 55.73% 366ms 2.31% std::_Rb_tree::_M_erase 10ms 0.063% 55.79% 357ms 2.25% std::__new_allocator::deallocate (inline) 0 0% 55.79% 350ms 2.21% std::allocator_traits::deallocate (inline) 124ms 0.78% 56.57% 347ms 2.19% std::_Rb_tree::_M_get_insert_unique_pos 32ms 0.2% 56.78% 343ms 2.16% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.025% 56.80% 337ms 2.13% LegacyCellProliferativeTypesWriter::VisitCell 151ms 0.95% 57.75% 329ms 2.07% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.18% 57.93% 326ms 2.06% Element::ResetIndex 0 0% 57.93% 324ms 2.04% std::_Rb_tree::_M_drop_node (inline) 0 0% 57.93% 321ms 2.02% std::set::~set (inline) 316ms 1.99% 59.92% 316ms 1.99% CellProperty::GetTypeId 5ms 0.032% 59.95% 306ms 1.93% std::_Vector_base::_M_allocate (inline) 4ms 0.025% 59.98% 303ms 1.91% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 252ms 1.59% 61.57% 302ms 1.90% _int_free 0 0% 61.57% 287ms 1.81% std::_Rb_tree::_M_put_node (inline) 286ms 1.80% 63.37% 286ms 1.80% __strcmp_avx2 1ms 0.0063% 63.38% 284ms 1.79% NodeLocationWriter::Visit 18ms 0.11% 63.49% 282ms 1.78% AbstractTetrahedralElement::CalculateJacobian 13ms 0.082% 63.57% 282ms 1.78% std::_Rb_tree::_Rb_tree (partial-inline) 277ms 1.75% 65.32% 278ms 1.75% std::vector::operator[] (inline) 7ms 0.044% 65.37% 263ms 1.66% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.038% 65.40% 260ms 1.64% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.013% 65.42% 256ms 1.61% std::set::set (inline) 30ms 0.19% 65.61% 253ms 1.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0063% 65.61% 253ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.11% 65.72% 251ms 1.58% std::num_put::_M_insert_float 0 0% 65.72% 249ms 1.57% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.082% 65.80% 233ms 1.47% std::_Rb_tree::_M_erase_aux (inline) 33ms 0.21% 66.01% 230ms 1.45% std::_Rb_tree::_M_copy (inline) 14ms 0.088% 66.10% 222ms 1.40% std::vector::push_back (inline) 13ms 0.082% 66.18% 216ms 1.36% Element::MarkAsDeleted 11ms 0.069% 66.25% 214ms 1.35% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.019% 66.27% 213ms 1.34% alternateaxes 164ms 1.03% 67.30% 210ms 1.32% AbstractElement::GetNodeGlobalIndex 28ms 0.18% 67.48% 210ms 1.32% AbstractTetrahedralElement::RefreshJacobian 204ms 1.29% 68.76% 210ms 1.32% vertexmedian 0 0% 68.76% 206ms 1.30% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0063% 68.77% 205ms 1.29% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.013% 68.78% 201ms 1.27% std::__cxx11::collate::do_transform 9ms 0.057% 68.84% 197ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.076% 68.92% 197ms 1.24% std::vector::_M_realloc_insert 1ms 0.0063% 68.92% 196ms 1.24% CellProliferativeTypesWriter::VisitCell 53ms 0.33% 69.26% 196ms 1.24% std::_Rb_tree::_M_clone_node (inline) 2ms 0.013% 69.27% 194ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 69.27% 194ms 1.22% ___vsnprintf 0 0% 69.27% 194ms 1.22% __vsnprintf_internal (inline) 14ms 0.088% 69.36% 193ms 1.22% __printf_buffer 7ms 0.044% 69.40% 189ms 1.19% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.1% 69.50% 189ms 1.19% TetrahedralMesh::Clear 178ms 1.12% 70.62% 178ms 1.12% std::_Rb_tree_insert_and_rebalance 128ms 0.81% 71.43% 170ms 1.07% malloc_consolidate 8ms 0.05% 71.48% 167ms 1.05% __printf_fp_l_buffer 0 0% 71.48% 167ms 1.05% __printf_fp_spec (inline) 76ms 0.48% 71.96% 165ms 1.04% AbstractElement::GetNodeLocation 11ms 0.069% 72.03% 163ms 1.03% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.025% 72.06% 157ms 0.99% boost::numeric::ublas::vector_assign (inline) 155ms 0.98% 73.03% 155ms 0.98% Node::GetIndex 102ms 0.64% 73.68% 155ms 0.98% std::_Rb_tree::equal_range (inline) 81ms 0.51% 74.19% 152ms 0.96% __printf_fp_buffer_1 2ms 0.013% 74.20% 150ms 0.95% OffLatticeSimulation::ApplyBoundaries 149ms 0.94% 75.14% 149ms 0.94% incircle 0 0% 75.14% 143ms 0.9% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.025% 75.17% 142ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 137ms 0.86% 76.03% 137ms 0.86% unlink_chunk 10ms 0.063% 76.09% 136ms 0.86% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.032% 76.12% 134ms 0.85% Cell::SetCellProliferativeType 6ms 0.038% 76.16% 128ms 0.81% CellPropertyCollection::HasProperty 24ms 0.15% 76.31% 127ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 17ms 0.11% 76.42% 125ms 0.79% boost::detail::shared_count::~shared_count (inline) 0 0% 76.42% 125ms 0.79% boost::shared_ptr::~shared_ptr (inline) 30ms 0.19% 76.61% 125ms 0.79% std::num_put::_M_insert_int 0 0% 76.61% 122ms 0.77% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 76.61% 122ms 0.77% Cell::HasCellProperty (inline) 1ms 0.0063% 76.62% 122ms 0.77% OutputFileHandler::OpenOutputFile 68ms 0.43% 77.04% 121ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 31ms 0.2% 77.24% 121ms 0.76% boost::numeric::ublas::indexing_vector_assign 121ms 0.76% 78.00% 121ms 0.76% std::_Rb_tree_increment 120ms 0.76% 78.76% 120ms 0.76% AbstractElement::IsDeleted 4ms 0.025% 78.79% 119ms 0.75% std::_Rb_tree_const_iterator::operator++ (inline) 10ms 0.063% 78.85% 118ms 0.74% Node::~Node 113ms 0.71% 79.56% 113ms 0.71% std::vector::size (inline) 0 0% 79.56% 111ms 0.7% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.025% 79.59% 110ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 103ms 0.65% 80.24% 107ms 0.67% boost::detail::sp_counted_base::release 39ms 0.25% 80.48% 106ms 0.67% std::__ostream_insert 97ms 0.61% 81.09% 105ms 0.66% vertexsort 0 0% 81.09% 104ms 0.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.032% 81.13% 103ms 0.65% Cylindrical2dMesh::CreateMirrorNodes 2ms 0.013% 81.14% 102ms 0.64% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 99ms 0.62% 81.76% 99ms 0.62% boost::shared_ptr::operator-> (inline) 96ms 0.61% 82.37% 96ms 0.61% counterclockwise 62ms 0.39% 82.76% 95ms 0.6% TetrahedralMesh::EdgeIterator::EdgeIterator 94ms 0.59% 83.35% 94ms 0.59% std::_Rb_tree_rebalance_for_erase 40ms 0.25% 83.60% 92ms 0.58% std::basic_filebuf::xsputn 8ms 0.05% 83.65% 91ms 0.57% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 0 0% 83.65% 91ms 0.57% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 37ms 0.23% 83.89% 91ms 0.57% boost::shared_ptr::shared_ptr (inline) 5ms 0.032% 83.92% 90ms 0.57% CellLocationIndexWriter::VisitCell 88ms 0.55% 84.47% 88ms 0.55% TetrahedralMesh::EdgeIterator::operator!= 88ms 0.55% 85.03% 88ms 0.55% [libchaste_mesh.so] 3ms 0.019% 85.05% 88ms 0.55% std::operator<< (inline) 1ms 0.0063% 85.05% 86ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 12ms 0.076% 85.13% 82ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.0063% 85.14% 81ms 0.51% std::vector::resize (inline) 51ms 0.32% 85.46% 80ms 0.5% boost::numeric::ublas::c_matrix::operator() 1ms 0.0063% 85.46% 80ms 0.5% std::vector::_M_default_append