File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17809ms, 84.59% of 21053ms total Dropped 836 nodes (cum <= 105.27ms) flat flat% sum% cum cum% 0 0% 0% 21006ms 99.78% __libc_start_call_main 0 0% 0% 21006ms 99.78% __libc_start_main_impl 0 0% 0% 21006ms 99.78% _start 0 0% 0% 20987ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20987ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20987ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20987ms 99.69% main 0 0% 0% 20945ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20945ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20945ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20916ms 99.35% AbstractCellBasedSimulation::Solve 1ms 0.0047% 0.0047% 16110ms 76.52% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0047% 0.0095% 10341ms 49.12% AbstractCellBasedSimulation::DoCellBirth 8ms 0.038% 0.047% 10233ms 48.61% Cell::ReadyToDivide 6ms 0.028% 0.076% 10104ms 47.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0047% 0.081% 9952ms 47.27% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 22ms 0.1% 0.19% 9945ms 47.24% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.024% 0.21% 9921ms 47.12% CellCycleModelOdeHandler::SolveOdeToTime 81ms 0.38% 0.59% 9705ms 46.10% AbstractOneStepIvpOdeSolver::InternalSolve 895ms 4.25% 4.84% 8906ms 42.30% RungeKutta4IvpOdeSolver::CalculateNextYValue 3649ms 17.33% 22.18% 7790ms 37.00% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.18% 5657ms 26.87% MeshBasedCellPopulation::Update 3ms 0.014% 22.19% 4477ms 21.27% Cylindrical2dMesh::ReMesh 207ms 0.98% 23.17% 4207ms 19.98% AbstractCellProperty::IsType (inline) 624ms 2.96% 26.14% 2913ms 13.84% AbstractCellProperty::IsSame 0 0% 26.14% 2676ms 12.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 26.14% 2571ms 12.21% MutableMesh::ReMesh 0 0% 26.14% 2370ms 11.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.052% 26.19% 2311ms 10.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 424ms 2.01% 28.21% 2289ms 10.87% std::type_info::operator== (inline) 0 0% 28.21% 2117ms 10.06% AbstractCellPopulation::WriteResultsToFiles 1837ms 8.73% 36.93% 1837ms 8.73% __strcmp_avx2 775ms 3.68% 40.61% 1806ms 8.58% std::_Rb_tree::_M_lower_bound (inline) 143ms 0.68% 41.29% 1675ms 7.96% TetrahedralMesh::EdgeIterator::operator++ 74ms 0.35% 41.64% 1359ms 6.46% std::_Rb_tree::find (inline) 16ms 0.076% 41.72% 1349ms 6.41% TetrahedralMesh::ImportFromMesher 45ms 0.21% 41.93% 1206ms 5.73% operator new 234ms 1.11% 43.04% 1152ms 5.47% __GI___libc_malloc 0 0% 43.04% 1138ms 5.41% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.033% 43.08% 1104ms 5.24% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.019% 43.10% 1022ms 4.85% MeshBasedCellPopulation::SpringIterator::operator++ 38ms 0.18% 43.28% 1022ms 4.85% std::__new_allocator::allocate (inline) 0 0% 43.28% 1017ms 4.83% std::allocator_traits::allocate (inline) 6ms 0.028% 43.30% 1001ms 4.75% std::set::insert (inline) 11ms 0.052% 43.36% 995ms 4.73% std::_Rb_tree::_M_insert_unique 522ms 2.48% 45.84% 844ms 4.01% _int_malloc 2ms 0.0095% 45.85% 829ms 3.94% triangulate 0 0% 45.85% 819ms 3.89% std::set::count (inline) 2ms 0.0095% 45.86% 805ms 3.82% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.028% 45.88% 766ms 3.64% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.88% 742ms 3.52% delaunay 277ms 1.32% 47.20% 740ms 3.51% __dynamic_cast 3ms 0.014% 47.21% 740ms 3.51% divconqdelaunay 17ms 0.081% 47.29% 737ms 3.50% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.1% 47.40% 691ms 3.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 61ms 0.29% 47.69% 690ms 3.28% std::map::operator[] (partial-inline) 681ms 3.23% 50.92% 681ms 3.23% std::_Rb_tree::_S_right (inline) 6ms 0.028% 50.95% 675ms 3.21% CellPopulationElementWriter::Visit 0 0% 50.95% 674ms 3.20% std::_Rb_tree::_M_create_node (inline) 19ms 0.09% 51.04% 651ms 3.09% std::less::operator() (inline) 0 0% 51.04% 643ms 3.05% std::_Rb_tree::_M_get_node (inline) 632ms 3.00% 54.04% 632ms 3.00% std::operator< (inline) 5ms 0.024% 54.07% 616ms 2.93% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.1% 54.17% 615ms 2.92% std::_Rb_tree::_M_insert_ (inline) 594ms 2.82% 56.99% 610ms 2.90% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 56.99% 607ms 2.88% std::_Rb_tree::_Alloc_node::operator() (inline) 18ms 0.085% 57.08% 599ms 2.85% AbstractCellPopulation::GetCellUsingLocationIndex 20ms 0.095% 57.17% 571ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.014% 57.19% 562ms 2.67% AbstractCellProperty::IsSubType (inline) 232ms 1.10% 58.29% 548ms 2.60% __GI___libc_free 9ms 0.043% 58.33% 538ms 2.56% Element::Element 0 0% 58.33% 536ms 2.55% std::map::find (inline) 0 0% 58.33% 521ms 2.47% std::_Rb_tree::lower_bound (inline) 0 0% 58.33% 521ms 2.47% std::map::lower_bound (inline) 2ms 0.0095% 58.34% 514ms 2.44% std::ostream::operator<< (inline) 55ms 0.26% 58.60% 512ms 2.43% std::ostream::_M_insert 336ms 1.60% 60.20% 511ms 2.43% AbstractCellMutationState::AbstractCellMutationState 10ms 0.047% 60.25% 488ms 2.32% MutableMesh::ReIndex 164ms 0.78% 61.03% 464ms 2.20% std::_Rb_tree::_M_erase 11ms 0.052% 61.08% 460ms 2.18% Element::RegisterWithNodes (inline) 7ms 0.033% 61.11% 451ms 2.14% Node::AddElement 10ms 0.047% 61.16% 433ms 2.06% Cylindrical2dMesh::CorrectNonPeriodicMesh 23ms 0.11% 61.27% 433ms 2.06% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0047% 61.27% 420ms 1.99% Cell::GetMutationState 56ms 0.27% 61.54% 417ms 1.98% TetrahedralMesh::Clear 0 0% 61.54% 410ms 1.95% std::set::~set (inline) 5ms 0.024% 61.56% 389ms 1.85% std::_Rb_tree::erase 1ms 0.0047% 61.57% 388ms 1.84% std::set::erase (inline) 17ms 0.081% 61.65% 384ms 1.82% divconqrecurse 14ms 0.066% 61.72% 383ms 1.82% Node::RemoveElement 9ms 0.043% 61.76% 378ms 1.80% std::__new_allocator::deallocate (inline) 2ms 0.0095% 61.77% 376ms 1.79% std::_Vector_base::_M_allocate (inline) 0 0% 61.77% 372ms 1.77% std::allocator_traits::deallocate (inline) 129ms 0.61% 62.38% 370ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.019% 62.40% 358ms 1.70% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.028% 62.43% 357ms 1.70% Cell::GetCellProliferativeType 102ms 0.48% 62.91% 356ms 1.69% mergehulls 2ms 0.0095% 62.92% 353ms 1.68% NodeLocationWriter::Visit 0 0% 62.92% 343ms 1.63% std::_Rb_tree::_M_drop_node (inline) 147ms 0.7% 63.62% 340ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 317ms 1.51% 65.13% 317ms 1.51% std::type_info::name (inline) 238ms 1.13% 66.26% 316ms 1.50% _int_free 0 0% 66.26% 315ms 1.50% MeshBasedCellPopulation::GetDampingConstant 3ms 0.014% 66.27% 313ms 1.49% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.028% 66.30% 303ms 1.44% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 18ms 0.085% 66.38% 301ms 1.43% std::num_put::_M_insert_float 21ms 0.1% 66.48% 298ms 1.42% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.48% 296ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.48% 293ms 1.39% std::_Rb_tree::_M_put_node (inline) 47ms 0.22% 66.71% 292ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.024% 66.73% 292ms 1.39% LegacyCellProliferativeTypesWriter::VisitCell 21ms 0.1% 66.83% 286ms 1.36% Element::ResetIndex 3ms 0.014% 66.85% 281ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.057% 66.90% 278ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.066% 66.97% 270ms 1.28% std::_Rb_tree::_Rb_tree (partial-inline) 267ms 1.27% 68.24% 268ms 1.27% std::vector::operator[] (inline) 11ms 0.052% 68.29% 258ms 1.23% std::vector::push_back (inline) 257ms 1.22% 69.51% 257ms 1.22% [libchaste_cell_based.so] 8ms 0.038% 69.55% 256ms 1.22% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.028% 69.58% 246ms 1.17% std::__cxx11::collate::do_transform 1ms 0.0047% 69.58% 244ms 1.16% std::set::set (inline) 6ms 0.028% 69.61% 242ms 1.15% std::vector::_M_realloc_insert 25ms 0.12% 69.73% 234ms 1.11% std::_Rb_tree::_M_copy (inline) 8ms 0.038% 69.77% 233ms 1.11% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.014% 69.78% 233ms 1.11% ___vsnprintf 6ms 0.028% 69.81% 230ms 1.09% Node::~Node 0 0% 69.81% 230ms 1.09% __vsnprintf_internal (inline) 61ms 0.29% 70.10% 228ms 1.08% ApcOneHitCellMutationState::ApcOneHitCellMutationState 29ms 0.14% 70.24% 227ms 1.08% AbstractTetrahedralElement::RefreshJacobian 13ms 0.062% 70.30% 227ms 1.08% Element::MarkAsDeleted 31ms 0.15% 70.45% 227ms 1.08% __printf_buffer 37ms 0.18% 70.62% 225ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 70ms 0.33% 70.95% 225ms 1.07% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.0095% 70.96% 225ms 1.07% alternateaxes 210ms 1% 71.96% 223ms 1.06% vertexmedian 8ms 0.038% 72.00% 218ms 1.04% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 154ms 0.73% 72.73% 218ms 1.04% AbstractElement::GetNodeGlobalIndex 1ms 0.0047% 72.74% 208ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 76ms 0.36% 73.10% 206ms 0.98% std::_Rb_tree::_M_clone_node (inline) 4ms 0.019% 73.12% 202ms 0.96% CellPropertyCollection::HasProperty 0 0% 73.12% 202ms 0.96% OffLatticeSimulation::ApplyBoundaries 0 0% 73.12% 197ms 0.94% Cell::HasCellProperty (inline) 151ms 0.72% 73.83% 197ms 0.94% malloc_consolidate 5ms 0.024% 73.86% 195ms 0.93% CellProliferativeTypesWriter::VisitCell 184ms 0.87% 74.73% 184ms 0.87% unlink_chunk 10ms 0.047% 74.78% 177ms 0.84% __printf_fp_l_buffer 0 0% 74.78% 177ms 0.84% __printf_fp_spec (inline) 83ms 0.39% 75.17% 176ms 0.84% AbstractElement::GetNodeLocation 14ms 0.066% 75.24% 174ms 0.83% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 166ms 0.79% 76.03% 166ms 0.79% Node::GetIndex 5ms 0.024% 76.05% 164ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 70ms 0.33% 76.38% 161ms 0.76% __printf_fp_buffer_1 3ms 0.014% 76.40% 157ms 0.75% boost::numeric::ublas::vector_assign (inline) 10ms 0.047% 76.45% 156ms 0.74% std::_Rb_tree_const_iterator::operator++ (inline) 156ms 0.74% 77.19% 156ms 0.74% std::_Rb_tree_increment 156ms 0.74% 77.93% 156ms 0.74% std::vector::size (inline) 155ms 0.74% 78.66% 155ms 0.74% AbstractElement::IsDeleted 149ms 0.71% 79.37% 149ms 0.71% incircle 16ms 0.076% 79.45% 144ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 141ms 0.67% 80.12% 141ms 0.67% std::_Rb_tree_insert_and_rebalance 2ms 0.0095% 80.13% 140ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.024% 80.15% 138ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 9ms 0.043% 80.19% 136ms 0.65% Cylindrical2dMesh::CreateMirrorNodes 37ms 0.18% 80.37% 135ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 87ms 0.41% 80.78% 135ms 0.64% std::_Rb_tree::equal_range (inline) 58ms 0.28% 81.06% 130ms 0.62% std::__ostream_insert 39ms 0.19% 81.24% 128ms 0.61% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 70ms 0.33% 81.58% 127ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.0095% 81.58% 125ms 0.59% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 3ms 0.014% 81.60% 125ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 40ms 0.19% 81.79% 125ms 0.59% boost::numeric::ublas::indexing_vector_assign 7ms 0.033% 81.82% 124ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.82% 124ms 0.59% boost::shared_ptr::~shared_ptr (inline) 13ms 0.062% 81.88% 123ms 0.58% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.0095% 81.89% 123ms 0.58% Cell::SetCellProliferativeType 9ms 0.043% 81.94% 122ms 0.58% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 120ms 0.57% 82.51% 120ms 0.57% boost::shared_ptr::operator-> (inline) 103ms 0.49% 83.00% 118ms 0.56% vertexsort 40ms 0.19% 83.19% 117ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 38ms 0.18% 83.37% 117ms 0.56% std::_Vector_base::_M_deallocate (inline) 110ms 0.52% 83.89% 114ms 0.54% boost::detail::sp_counted_base::release 0 0% 83.89% 113ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0047% 83.89% 113ms 0.54% std::vector::_M_default_append 0 0% 83.89% 113ms 0.54% std::vector::resize (inline) 111ms 0.53% 84.42% 111ms 0.53% std::_Rb_tree_rebalance_for_erase 0 0% 84.42% 110ms 0.52% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.033% 84.45% 109ms 0.52% Element::~Element 18ms 0.085% 84.54% 109ms 0.52% std::num_put::_M_insert_int 2ms 0.0095% 84.55% 108ms 0.51% OutputFileHandler::OpenOutputFile 2ms 0.0095% 84.56% 108ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0095% 84.57% 108ms 0.51% std::operator<< (inline) 5ms 0.024% 84.59% 107ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 84.59% 106ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 84.59% 106ms 0.5% std::basic_ofstream::basic_ofstream (inline)