File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16771ms, 84.14% of 19933ms total Dropped 759 nodes (cum <= 99.67ms) flat flat% sum% cum cum% 0 0% 0% 19887ms 99.77% __libc_start_call_main 0 0% 0% 19887ms 99.77% __libc_start_main_impl 0 0% 0% 19887ms 99.77% _start 0 0% 0% 19868ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19868ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19868ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19868ms 99.67% main 0 0% 0% 19831ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19831ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19831ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19803ms 99.35% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15372ms 77.12% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.02% 0.025% 10139ms 50.87% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.035% 10044ms 50.39% Cell::ReadyToDivide 7ms 0.035% 0.07% 9978ms 50.06% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.075% 9841ms 49.37% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.07% 0.15% 9833ms 49.33% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.16% 9816ms 49.24% CellCycleModelOdeHandler::SolveOdeToTime 83ms 0.42% 0.58% 9644ms 48.38% AbstractOneStepIvpOdeSolver::InternalSolve 879ms 4.41% 4.99% 8789ms 44.09% RungeKutta4IvpOdeSolver::CalculateNextYValue 3645ms 18.29% 23.27% 7716ms 38.71% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.28% 5117ms 25.67% MeshBasedCellPopulation::Update 182ms 0.91% 24.20% 4109ms 20.61% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.22% 3942ms 19.78% Cylindrical2dMesh::ReMesh 520ms 2.61% 26.83% 2845ms 14.27% AbstractCellProperty::IsSame 0 0% 26.83% 2470ms 12.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 441ms 2.21% 29.04% 2325ms 11.66% std::type_info::operator== (inline) 0 0% 29.04% 2169ms 10.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.04% 2153ms 10.80% MutableMesh::ReMesh 10ms 0.05% 29.09% 2123ms 10.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.09% 1959ms 9.83% AbstractCellPopulation::WriteResultsToFiles 838ms 4.20% 33.30% 1904ms 9.55% std::_Rb_tree::_M_lower_bound (inline) 1873ms 9.40% 42.69% 1873ms 9.40% __strcmp_avx2 168ms 0.84% 43.54% 1640ms 8.23% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.33% 43.87% 1396ms 7.00% std::_Rb_tree::find (inline) 0 0% 43.87% 1144ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.90% 1120ms 5.62% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.045% 43.94% 1062ms 5.33% TetrahedralMesh::ImportFromMesher 42ms 0.21% 44.15% 1024ms 5.14% operator new 14ms 0.07% 44.22% 1002ms 5.03% MeshBasedCellPopulation::SpringIterator::operator++ 232ms 1.16% 45.39% 976ms 4.90% __GI___libc_malloc 13ms 0.065% 45.45% 951ms 4.77% std::set::insert (inline) 17ms 0.085% 45.54% 938ms 4.71% std::_Rb_tree::_M_insert_unique 34ms 0.17% 45.71% 888ms 4.45% std::__new_allocator::allocate (inline) 0 0% 45.71% 878ms 4.40% std::allocator_traits::allocate (inline) 0 0% 45.71% 839ms 4.21% std::set::count (inline) 1ms 0.005% 45.71% 823ms 4.13% triangulate 1ms 0.005% 45.72% 749ms 3.76% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.72% 734ms 3.68% delaunay 4ms 0.02% 45.74% 734ms 3.68% divconqdelaunay 44ms 0.22% 45.96% 722ms 3.62% std::map::operator[] (partial-inline) 2ms 0.01% 45.97% 716ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 712ms 3.57% 49.54% 712ms 3.57% std::_Rb_tree::_S_right (inline) 373ms 1.87% 51.41% 666ms 3.34% _int_malloc 10ms 0.05% 51.46% 663ms 3.33% CellPopulationElementWriter::Visit 640ms 3.21% 54.67% 652ms 3.27% WntCellCycleOdeSystem::CalculateStoppingEvent 14ms 0.07% 54.74% 617ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 146ms 0.73% 55.48% 611ms 3.07% __dynamic_cast 21ms 0.11% 55.58% 602ms 3.02% std::less::operator() (inline) 28ms 0.14% 55.72% 598ms 3.00% std::_Rb_tree::_M_insert_ (inline) 4ms 0.02% 55.74% 597ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.74% 588ms 2.95% std::_Rb_tree::lower_bound (inline) 0 0% 55.74% 588ms 2.95% std::map::lower_bound (inline) 0 0% 55.74% 587ms 2.94% std::_Rb_tree::_M_create_node (inline) 581ms 2.91% 58.66% 581ms 2.91% std::operator< (inline) 25ms 0.13% 58.78% 579ms 2.90% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.015% 58.80% 552ms 2.77% Element::Element 0 0% 58.80% 551ms 2.76% std::_Rb_tree::_M_get_node (inline) 0 0% 58.80% 551ms 2.76% std::map::find (inline) 2ms 0.01% 58.81% 541ms 2.71% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.81% 533ms 2.67% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.05% 58.86% 502ms 2.52% Cylindrical2dMesh::ReconstructCylindricalMesh 7ms 0.035% 58.89% 502ms 2.52% MutableMesh::ReIndex 2ms 0.01% 58.90% 495ms 2.48% std::ostream::operator<< (inline) 59ms 0.3% 59.20% 493ms 2.47% std::ostream::_M_insert 338ms 1.70% 60.89% 490ms 2.46% AbstractCellMutationState::AbstractCellMutationState 6ms 0.03% 60.92% 489ms 2.45% Element::RegisterWithNodes (inline) 12ms 0.06% 60.98% 474ms 2.38% Node::AddElement 14ms 0.07% 61.05% 469ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.02% 61.07% 438ms 2.20% AbstractCellProperty::IsSubType (inline) 160ms 0.8% 61.88% 427ms 2.14% __GI___libc_free 20ms 0.1% 61.98% 380ms 1.91% divconqrecurse 12ms 0.06% 62.04% 360ms 1.81% std::__new_allocator::deallocate (inline) 110ms 0.55% 62.59% 358ms 1.80% std::_Rb_tree::_M_erase 99ms 0.5% 63.09% 354ms 1.78% mergehulls 0 0% 63.09% 351ms 1.76% std::allocator_traits::deallocate (inline) 1ms 0.005% 63.09% 349ms 1.75% std::set::erase (inline) 12ms 0.06% 63.15% 348ms 1.75% Node::RemoveElement 3ms 0.015% 63.17% 348ms 1.75% std::_Rb_tree::erase 29ms 0.15% 63.31% 336ms 1.69% Element::ResetIndex 172ms 0.86% 64.17% 336ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 64.20% 331ms 1.66% std::_Vector_base::_M_allocate (inline) 4ms 0.02% 64.22% 325ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 13ms 0.065% 64.28% 325ms 1.63% std::_Rb_tree::~_Rb_tree (inline) 131ms 0.66% 64.94% 323ms 1.62% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.055% 64.99% 312ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.99% 311ms 1.56% std::_Rb_tree::_M_drop_node (inline) 5ms 0.025% 65.02% 307ms 1.54% Cell::GetMutationState 3ms 0.015% 65.03% 302ms 1.52% NodeLocationWriter::Visit 0 0% 65.03% 298ms 1.50% std::set::~set (inline) 5ms 0.025% 65.06% 287ms 1.44% Cell::GetCellProliferativeType 3ms 0.015% 65.07% 286ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 37ms 0.19% 65.26% 286ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.26% 286ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 285ms 1.43% 66.69% 285ms 1.43% std::type_info::name (inline) 0 0% 66.69% 277ms 1.39% std::_Rb_tree::_M_put_node (inline) 17ms 0.085% 66.77% 269ms 1.35% std::_Rb_tree::_Rb_tree (partial-inline) 221ms 1.11% 67.88% 267ms 1.34% _int_free 13ms 0.065% 67.95% 266ms 1.33% std::num_put::_M_insert_float 22ms 0.11% 68.06% 263ms 1.32% AbstractTetrahedralElement::CalculateJacobian 260ms 1.30% 69.36% 260ms 1.30% [libchaste_cell_based.so] 9ms 0.045% 69.41% 257ms 1.29% std::vector::push_back (inline) 8ms 0.04% 69.45% 252ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 46ms 0.23% 69.68% 243ms 1.22% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.68% 243ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.025% 69.70% 239ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 11ms 0.055% 69.76% 238ms 1.19% std::vector::_M_realloc_insert 3ms 0.015% 69.77% 237ms 1.19% std::set::set (inline) 235ms 1.18% 70.95% 235ms 1.18% std::vector::operator[] (inline) 56ms 0.28% 71.23% 228ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.025% 71.26% 224ms 1.12% std::__cxx11::collate::do_transform 20ms 0.1% 71.36% 222ms 1.11% std::_Rb_tree::_M_copy (inline) 1ms 0.005% 71.36% 221ms 1.11% alternateaxes 1ms 0.005% 71.37% 220ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 204ms 1.02% 72.39% 220ms 1.10% vertexmedian 1ms 0.005% 72.40% 213ms 1.07% ___vsnprintf 0 0% 72.40% 212ms 1.06% __vsnprintf_internal (inline) 20ms 0.1% 72.50% 207ms 1.04% __printf_buffer 9ms 0.045% 72.54% 205ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.035% 72.58% 203ms 1.02% std::_Rb_tree::_M_erase_aux (inline) 64ms 0.32% 72.90% 200ms 1.00% std::_Rb_tree::_M_clone_node (inline) 33ms 0.17% 73.06% 198ms 0.99% AbstractTetrahedralElement::RefreshJacobian 192ms 0.96% 74.03% 192ms 0.96% std::_Rb_tree_insert_and_rebalance 136ms 0.68% 74.71% 188ms 0.94% malloc_consolidate 63ms 0.32% 75.03% 187ms 0.94% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.01% 75.04% 185ms 0.93% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.04% 185ms 0.93% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.04% 178ms 0.89% OffLatticeSimulation::ApplyBoundaries 10ms 0.05% 75.09% 177ms 0.89% Element::MarkAsDeleted 4ms 0.02% 75.11% 176ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.005% 75.11% 176ms 0.88% __printf_fp_spec (inline) 6ms 0.03% 75.14% 175ms 0.88% __printf_fp_l_buffer 130ms 0.65% 75.79% 174ms 0.87% AbstractElement::GetNodeGlobalIndex 20ms 0.1% 75.89% 174ms 0.87% TetrahedralMesh::Clear 172ms 0.86% 76.76% 172ms 0.86% incircle 3ms 0.015% 76.77% 168ms 0.84% boost::numeric::ublas::vector_assign (inline) 7ms 0.035% 76.81% 159ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 77ms 0.39% 77.19% 159ms 0.8% __printf_fp_buffer_1 2ms 0.01% 77.20% 156ms 0.78% CellProliferativeTypesWriter::VisitCell 37ms 0.19% 77.39% 153ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 90ms 0.45% 77.84% 153ms 0.77% std::_Rb_tree::equal_range (inline) 16ms 0.08% 77.92% 149ms 0.75% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 75ms 0.38% 78.30% 148ms 0.74% AbstractElement::GetNodeLocation 142ms 0.71% 79.01% 142ms 0.71% Node::GetIndex 141ms 0.71% 79.72% 141ms 0.71% unlink_chunk 83ms 0.42% 80.13% 138ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.04% 80.17% 137ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.01% 80.18% 134ms 0.67% CellPropertyCollection::HasProperty 131ms 0.66% 80.84% 131ms 0.66% std::vector::size (inline) 0 0% 80.84% 129ms 0.65% Cell::HasCellProperty (inline) 9ms 0.045% 80.89% 126ms 0.63% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 33ms 0.17% 81.05% 124ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 46ms 0.23% 81.28% 124ms 0.62% boost::numeric::ublas::indexing_vector_assign 34ms 0.17% 81.45% 123ms 0.62% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.01% 81.46% 123ms 0.62% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.02% 81.48% 122ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 118ms 0.59% 82.07% 120ms 0.6% vertexsort 27ms 0.14% 82.21% 118ms 0.59% std::num_put::_M_insert_int 0 0% 82.21% 115ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 115ms 0.58% 82.79% 115ms 0.58% AbstractElement::IsDeleted 0 0% 82.79% 113ms 0.57% OutputFileHandler::OpenOutputFile 1ms 0.005% 82.79% 112ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 112ms 0.56% 83.35% 112ms 0.56% AbstractCellMutationState::~AbstractCellMutationState 2ms 0.01% 83.36% 109ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 9ms 0.045% 83.41% 109ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.41% 109ms 0.55% boost::shared_ptr::~shared_ptr (inline) 0 0% 83.41% 105ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 83.41% 103ms 0.52% Cell::SetCellProliferativeType 43ms 0.22% 83.63% 103ms 0.52% std::__ostream_insert 102ms 0.51% 84.14% 102ms 0.51% AbstractCellProperty::~AbstractCellProperty