File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17421ms, 84.94% of 20509ms total Dropped 797 nodes (cum <= 102.55ms) flat flat% sum% cum cum% 0 0% 0% 20465ms 99.79% __libc_start_call_main 0 0% 0% 20465ms 99.79% __libc_start_main_impl 0 0% 0% 20465ms 99.79% _start 0 0% 0% 20446ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20446ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20446ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20446ms 99.69% main 0 0% 0% 20408ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20408ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20408ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20380ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 15794ms 77.01% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.0049% 10282ms 50.13% AbstractCellBasedSimulation::DoCellBirth 9ms 0.044% 0.049% 10197ms 49.72% Cell::ReadyToDivide 6ms 0.029% 0.078% 10114ms 49.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0098% 0.088% 9976ms 48.64% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.098% 0.19% 9967ms 48.60% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0098% 0.2% 9943ms 48.48% CellCycleModelOdeHandler::SolveOdeToTime 81ms 0.39% 0.59% 9719ms 47.39% AbstractOneStepIvpOdeSolver::InternalSolve 864ms 4.21% 4.80% 8920ms 43.49% RungeKutta4IvpOdeSolver::CalculateNextYValue 3710ms 18.09% 22.89% 7840ms 38.23% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.89% 5388ms 26.27% MeshBasedCellPopulation::Update 9ms 0.044% 22.94% 4200ms 20.48% Cylindrical2dMesh::ReMesh 185ms 0.9% 23.84% 4163ms 20.30% AbstractCellProperty::IsType (inline) 597ms 2.91% 26.75% 2888ms 14.08% AbstractCellProperty::IsSame 1ms 0.0049% 26.75% 2540ms 12.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 26.75% 2312ms 11.27% MutableMesh::ReMesh 451ms 2.20% 28.95% 2291ms 11.17% std::type_info::operator== (inline) 2ms 0.0098% 28.96% 2231ms 10.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.039% 29.00% 2185ms 10.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0049% 29.01% 2035ms 9.92% AbstractCellPopulation::WriteResultsToFiles 839ms 4.09% 33.10% 1900ms 9.26% std::_Rb_tree::_M_lower_bound (inline) 1780ms 8.68% 41.78% 1780ms 8.68% __strcmp_avx2 172ms 0.84% 42.62% 1719ms 8.38% TetrahedralMesh::EdgeIterator::operator++ 59ms 0.29% 42.90% 1415ms 6.90% std::_Rb_tree::find (inline) 16ms 0.078% 42.98% 1195ms 5.83% TetrahedralMesh::ImportFromMesher 2ms 0.0098% 42.99% 1148ms 5.60% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.049% 43.04% 1125ms 5.49% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 59ms 0.29% 43.33% 1078ms 5.26% operator new 15ms 0.073% 43.40% 1018ms 4.96% MeshBasedCellPopulation::SpringIterator::operator++ 237ms 1.16% 44.56% 1012ms 4.93% __GI___libc_malloc 11ms 0.054% 44.61% 943ms 4.60% std::set::insert (inline) 15ms 0.073% 44.68% 932ms 4.54% std::_Rb_tree::_M_insert_unique 40ms 0.2% 44.88% 925ms 4.51% std::__new_allocator::allocate (inline) 0 0% 44.88% 918ms 4.48% std::allocator_traits::allocate (inline) 0 0% 44.88% 862ms 4.20% std::set::count (inline) 1ms 0.0049% 44.88% 802ms 3.91% triangulate 64ms 0.31% 45.19% 761ms 3.71% std::map::operator[] (partial-inline) 2ms 0.0098% 45.20% 734ms 3.58% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.0049% 45.21% 723ms 3.53% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0049% 45.21% 720ms 3.51% delaunay 1ms 0.0049% 45.22% 718ms 3.50% divconqdelaunay 712ms 3.47% 48.69% 712ms 3.47% std::_Rb_tree::_S_right (inline) 395ms 1.93% 50.62% 705ms 3.44% _int_malloc 4ms 0.02% 50.64% 688ms 3.35% CellPopulationElementWriter::Visit 199ms 0.97% 51.61% 651ms 3.17% __dynamic_cast 29ms 0.14% 51.75% 647ms 3.15% std::less::operator() (inline) 10ms 0.049% 51.80% 628ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.13% 51.93% 620ms 3.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 618ms 3.01% 54.94% 618ms 3.01% std::operator< (inline) 603ms 2.94% 57.88% 610ms 2.97% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.015% 57.90% 599ms 2.92% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.90% 593ms 2.89% std::_Rb_tree::_M_create_node (inline) 14ms 0.068% 57.96% 592ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.96% 586ms 2.86% std::_Rb_tree::lower_bound (inline) 0 0% 57.96% 586ms 2.86% std::map::lower_bound (inline) 25ms 0.12% 58.09% 572ms 2.79% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.09% 571ms 2.78% std::_Rb_tree::_M_get_node (inline) 12ms 0.059% 58.15% 551ms 2.69% MutableMesh::ReIndex 0 0% 58.15% 547ms 2.67% std::map::find (inline) 0 0% 58.15% 521ms 2.54% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.039% 58.18% 509ms 2.48% Element::Element 4ms 0.02% 58.20% 485ms 2.36% AbstractCellProperty::IsSubType (inline) 1ms 0.0049% 58.21% 485ms 2.36% std::ostream::operator<< (inline) 11ms 0.054% 58.26% 483ms 2.36% Cylindrical2dMesh::ReconstructCylindricalMesh 63ms 0.31% 58.57% 482ms 2.35% std::ostream::_M_insert 341ms 1.66% 60.23% 479ms 2.34% AbstractCellMutationState::AbstractCellMutationState 8ms 0.039% 60.27% 473ms 2.31% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.034% 60.31% 471ms 2.30% Element::RegisterWithNodes (inline) 7ms 0.034% 60.34% 467ms 2.28% Node::AddElement 188ms 0.92% 61.26% 465ms 2.27% __GI___libc_free 164ms 0.8% 62.06% 437ms 2.13% std::_Rb_tree::_M_erase 27ms 0.13% 62.19% 407ms 1.98% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 62.21% 398ms 1.94% Cell::GetMutationState 13ms 0.063% 62.27% 383ms 1.87% std::_Rb_tree::erase 14ms 0.068% 62.34% 380ms 1.85% Node::RemoveElement 0 0% 62.34% 380ms 1.85% std::set::erase (inline) 0 0% 62.34% 373ms 1.82% std::set::~set (inline) 14ms 0.068% 62.41% 365ms 1.78% divconqrecurse 14ms 0.068% 62.48% 363ms 1.77% std::__new_allocator::deallocate (inline) 0 0% 62.48% 354ms 1.73% std::allocator_traits::deallocate (inline) 19ms 0.093% 62.57% 352ms 1.72% Element::ResetIndex 3ms 0.015% 62.58% 350ms 1.71% std::_Vector_base::_M_allocate (inline) 107ms 0.52% 63.10% 346ms 1.69% mergehulls 136ms 0.66% 63.77% 346ms 1.69% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.054% 63.82% 344ms 1.68% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 190ms 0.93% 64.75% 339ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.75% 331ms 1.61% std::_Rb_tree::_M_drop_node (inline) 4ms 0.02% 64.77% 318ms 1.55% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.02% 64.79% 317ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 44ms 0.21% 65.00% 316ms 1.54% TetrahedralMesh::Clear 310ms 1.51% 66.51% 310ms 1.51% std::type_info::name (inline) 4ms 0.02% 66.53% 309ms 1.51% NodeLocationWriter::Visit 0 0% 66.53% 294ms 1.43% std::_Rb_tree::_M_put_node (inline) 0 0% 66.53% 287ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.088% 66.62% 286ms 1.39% AbstractTetrahedralElement::CalculateJacobian 4ms 0.02% 66.64% 282ms 1.38% Cell::GetCellProliferativeType 0 0% 66.64% 279ms 1.36% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.18% 66.81% 277ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 220ms 1.07% 67.89% 275ms 1.34% _int_free 21ms 0.1% 67.99% 267ms 1.30% std::num_put::_M_insert_float 10ms 0.049% 68.04% 265ms 1.29% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.044% 68.08% 258ms 1.26% std::vector::push_back (inline) 257ms 1.25% 69.34% 257ms 1.25% std::vector::operator[] (inline) 0 0% 69.34% 253ms 1.23% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.34% 253ms 1.23% MeshBasedCellPopulation::GetDampingConstant 247ms 1.20% 70.54% 247ms 1.20% [libchaste_cell_based.so] 8ms 0.039% 70.58% 243ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.029% 70.61% 243ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.063% 70.67% 237ms 1.16% std::vector::_M_realloc_insert 1ms 0.0049% 70.68% 234ms 1.14% alternateaxes 1ms 0.0049% 70.68% 234ms 1.14% std::set::set (inline) 221ms 1.08% 71.76% 233ms 1.14% vertexmedian 6ms 0.029% 71.79% 232ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 23ms 0.11% 71.90% 229ms 1.12% AbstractTetrahedralElement::RefreshJacobian 25ms 0.12% 72.02% 228ms 1.11% std::_Rb_tree::_M_copy (inline) 12ms 0.059% 72.08% 224ms 1.09% std::_Rb_tree::_M_erase_aux (inline) 78ms 0.38% 72.46% 219ms 1.07% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 42ms 0.2% 72.67% 216ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 50ms 0.24% 72.91% 213ms 1.04% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 72.91% 207ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 72.93% 206ms 1.00% std::__cxx11::collate::do_transform 66ms 0.32% 73.25% 201ms 0.98% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0049% 73.26% 197ms 0.96% ___vsnprintf 1ms 0.0049% 73.26% 196ms 0.96% __vsnprintf_internal (inline) 12ms 0.059% 73.32% 195ms 0.95% Element::MarkAsDeleted 143ms 0.7% 74.02% 193ms 0.94% malloc_consolidate 17ms 0.083% 74.10% 192ms 0.94% __printf_buffer 14ms 0.068% 74.17% 188ms 0.92% Node::~Node 0 0% 74.17% 187ms 0.91% OffLatticeSimulation::ApplyBoundaries 79ms 0.39% 74.55% 184ms 0.9% AbstractElement::GetNodeLocation 9ms 0.044% 74.60% 181ms 0.88% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 181ms 0.88% 75.48% 181ms 0.88% std::_Rb_tree_insert_and_rebalance 137ms 0.67% 76.15% 178ms 0.87% AbstractElement::GetNodeGlobalIndex 166ms 0.81% 76.96% 166ms 0.81% unlink_chunk 164ms 0.8% 77.76% 164ms 0.8% Node::GetIndex 5ms 0.024% 77.78% 160ms 0.78% __printf_fp_l_buffer 0 0% 77.78% 160ms 0.78% __printf_fp_spec (inline) 7ms 0.034% 77.81% 158ms 0.77% CellPropertyCollection::HasProperty 5ms 0.024% 77.84% 156ms 0.76% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 77.84% 156ms 0.76% Cell::HasCellProperty (inline) 4ms 0.02% 77.86% 156ms 0.76% boost::numeric::ublas::vector_assign (inline) 5ms 0.024% 77.88% 155ms 0.76% CellProliferativeTypesWriter::VisitCell 103ms 0.5% 78.39% 151ms 0.74% std::_Rb_tree::equal_range (inline) 13ms 0.063% 78.45% 149ms 0.73% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 64ms 0.31% 78.76% 144ms 0.7% __printf_fp_buffer_1 1ms 0.0049% 78.77% 139ms 0.68% AbstractCellBasedWriter::OpenOutputFileForAppend 136ms 0.66% 79.43% 136ms 0.66% incircle 4ms 0.02% 79.45% 134ms 0.65% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 2ms 0.0098% 79.46% 134ms 0.65% OutputFileHandler::OpenOutputFile 9ms 0.044% 79.50% 133ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 129ms 0.63% 80.13% 129ms 0.63% std::vector::size (inline) 41ms 0.2% 80.33% 128ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 9ms 0.044% 80.37% 126ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 80.37% 124ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0098% 80.38% 122ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.38% 121ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 80.38% 121ms 0.59% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 43ms 0.21% 80.59% 120ms 0.59% std::__ostream_insert 37ms 0.18% 80.77% 119ms 0.58% boost::numeric::ublas::indexing_vector_assign 119ms 0.58% 81.35% 119ms 0.58% std::_Rb_tree_increment 26ms 0.13% 81.48% 117ms 0.57% TetrahedralMesh::EdgesEnd 73ms 0.36% 81.84% 116ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 7ms 0.034% 81.87% 115ms 0.56% Cylindrical2dMesh::CreateMirrorNodes 1ms 0.0049% 81.88% 114ms 0.56% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.88% 114ms 0.56% std::vector::resize (inline) 113ms 0.55% 82.43% 113ms 0.55% boost::shared_ptr::operator-> (inline) 19ms 0.093% 82.52% 113ms 0.55% std::num_put::_M_insert_int 0 0% 82.52% 113ms 0.55% std::vector::_M_default_append 107ms 0.52% 83.04% 113ms 0.55% vertexsort 18ms 0.088% 83.13% 111ms 0.54% boost::detail::shared_count::~shared_count (inline) 0 0% 83.13% 111ms 0.54% boost::shared_ptr::~shared_ptr (inline) 4ms 0.02% 83.15% 111ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 110ms 0.54% 83.69% 110ms 0.54% AbstractCellProperty::~AbstractCellProperty 36ms 0.18% 83.86% 108ms 0.53% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 107ms 0.52% 84.38% 107ms 0.52% AbstractElement::IsDeleted 0 0% 84.38% 105ms 0.51% NodeMap::NodeMap 6ms 0.029% 84.41% 104ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 104ms 0.51% 84.92% 104ms 0.51% [libchaste_mesh.so] 5ms 0.024% 84.94% 103ms 0.5% std::operator<< (inline)