File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13047ms, 77.66% of 16800ms total Dropped 894 nodes (cum <= 84ms) flat flat% sum% cum cum% 0 0% 0% 16753ms 99.72% __libc_start_call_main 0 0% 0% 16753ms 99.72% __libc_start_main_impl 0 0% 0% 16753ms 99.72% _start 0 0% 0% 16730ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16730ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16730ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16730ms 99.58% main 0 0% 0% 16687ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16687ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16687ms 99.33% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16662ms 99.18% AbstractCellBasedSimulation::Solve 0 0% 0% 12044ms 71.69% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.024% 0.024% 6510ms 38.75% AbstractCellBasedSimulation::DoCellBirth 21ms 0.12% 0.15% 6376ms 37.95% Cell::ReadyToDivide 6ms 0.036% 0.18% 6259ms 37.26% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.18% 6055ms 36.04% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 29ms 0.17% 0.36% 6043ms 35.97% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.048% 0.4% 6011ms 35.78% CellCycleModelOdeHandler::SolveOdeToTime 8ms 0.048% 0.45% 5831ms 34.71% CvodeAdaptor::Solve 0 0% 0.45% 5382ms 32.04% MeshBasedCellPopulation::Update 67ms 0.4% 0.85% 5279ms 31.42% CVode 70ms 0.42% 1.27% 4778ms 28.44% CVodeFree 2ms 0.012% 1.28% 4170ms 24.82% Cylindrical2dMesh::ReMesh 175ms 1.04% 2.32% 3712ms 22.10% cvRescale 9ms 0.054% 2.38% 3347ms 19.92% SUNNonlinSolSolve 40ms 0.24% 2.61% 3338ms 19.87% SUNNonlinSolSolve_Newton 85ms 0.51% 3.12% 3213ms 19.12% cvNlsInit 2ms 0.012% 3.13% 2600ms 15.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 3.13% 2292ms 13.64% MutableMesh::ReMesh 0 0% 3.13% 2243ms 13.35% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.036% 3.17% 2179ms 12.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 3.17% 2011ms 11.97% AbstractCellPopulation::WriteResultsToFiles 14ms 0.083% 3.25% 1910ms 11.37% cvLsSetup 821ms 4.89% 8.14% 1906ms 11.35% std::_Rb_tree::_M_lower_bound (inline) 162ms 0.96% 9.10% 1670ms 9.94% TetrahedralMesh::EdgeIterator::operator++ 78ms 0.46% 9.57% 1419ms 8.45% std::_Rb_tree::find (inline) 11ms 0.065% 9.63% 1365ms 8.12% cvLsDQJtimes 1ms 0.006% 9.64% 1171ms 6.97% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.06% 9.70% 1138ms 6.77% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.083% 9.78% 1130ms 6.73% TetrahedralMesh::ImportFromMesher 298ms 1.77% 11.55% 1120ms 6.67% __GI___libc_malloc 43ms 0.26% 11.81% 1105ms 6.58% operator new 12ms 0.071% 11.88% 1037ms 6.17% MeshBasedCellPopulation::SpringIterator::operator++ 37ms 0.22% 12.10% 984ms 5.86% std::__new_allocator::allocate (inline) 0 0% 12.10% 979ms 5.83% std::allocator_traits::allocate (inline) 12ms 0.071% 12.17% 976ms 5.81% std::set::insert (inline) 9ms 0.054% 12.23% 964ms 5.74% std::_Rb_tree::_M_insert_unique 1ms 0.006% 12.23% 920ms 5.48% triangulate 1ms 0.006% 12.24% 837ms 4.98% delaunay 6ms 0.036% 12.27% 836ms 4.98% divconqdelaunay 0 0% 12.27% 835ms 4.97% std::set::count (inline) 740ms 4.40% 16.68% 740ms 4.40% std::_Rb_tree::_S_right (inline) 5ms 0.03% 16.71% 732ms 4.36% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 53ms 0.32% 17.02% 731ms 4.35% std::map::operator[] (partial-inline) 33ms 0.2% 17.22% 711ms 4.23% cvLsSolve 377ms 2.24% 19.46% 710ms 4.23% _int_malloc 206ms 1.23% 20.69% 697ms 4.15% __dynamic_cast 12ms 0.071% 20.76% 690ms 4.11% CellPopulationElementWriter::Visit 5ms 0.03% 20.79% 677ms 4.03% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.012% 20.80% 670ms 3.99% AbstractTwoBodyInteractionForce::AddForceContribution 623ms 3.71% 24.51% 623ms 3.71% N_VBufUnpack_Serial 0 0% 24.51% 620ms 3.69% std::_Rb_tree::_M_create_node (inline) 19ms 0.11% 24.62% 611ms 3.64% std::less::operator() (inline) 13ms 0.077% 24.70% 604ms 3.60% MeshBasedCellPopulation::AcceptCellWriter 0 0% 24.70% 601ms 3.58% std::_Rb_tree::_M_get_node (inline) 39ms 0.23% 24.93% 598ms 3.56% std::_Rb_tree::_M_insert_ (inline) 592ms 3.52% 28.46% 592ms 3.52% std::operator< (inline) 5ms 0.03% 28.49% 585ms 3.48% Element::Element 0 0% 28.49% 580ms 3.45% std::map::find (inline) 25ms 0.15% 28.64% 576ms 3.43% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 23ms 0.14% 28.77% 573ms 3.41% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 28.77% 573ms 3.41% std::_Rb_tree::lower_bound (inline) 0 0% 28.77% 573ms 3.41% std::map::lower_bound (inline) 8ms 0.048% 28.82% 571ms 3.40% SUNLinSolSolve 182ms 1.08% 29.90% 571ms 3.40% __GI___libc_free 151ms 0.9% 30.80% 570ms 3.39% cvRestore 16ms 0.095% 30.90% 563ms 3.35% SUNLinSolSolve_Dense 12ms 0.071% 30.97% 560ms 3.33% MutableMesh::ReIndex 8ms 0.048% 31.02% 559ms 3.33% cvLsDQJac 0 0% 31.02% 556ms 3.31% AbstractCellProperty::IsSubType (inline) 0 0% 31.02% 556ms 3.31% std::_Rb_tree::_Alloc_node::operator() (inline) 46ms 0.27% 31.29% 553ms 3.29% N_VWrmsNorm 58ms 0.35% 31.64% 548ms 3.26% cvLsDenseDQJac 102ms 0.61% 32.24% 536ms 3.19% N_VLinearSum_Serial 16ms 0.095% 32.34% 529ms 3.15% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.012% 32.35% 521ms 3.10% SUNLinSolSetup 9ms 0.054% 32.40% 519ms 3.09% SUNLinSolSetup_Dense 10ms 0.06% 32.46% 508ms 3.02% Element::RegisterWithNodes (inline) 125ms 0.74% 33.21% 507ms 3.02% N_VWrmsNorm_Serial 0 0% 33.21% 495ms 2.95% std::ostream::operator<< (inline) 61ms 0.36% 33.57% 494ms 2.94% std::ostream::_M_insert 12ms 0.071% 33.64% 492ms 2.93% Node::AddElement 488ms 2.90% 36.55% 488ms 2.90% SUNDlsMat_denseGETRF 488ms 2.90% 39.45% 488ms 2.90% SUNDlsMat_denseGETRS 9ms 0.054% 39.51% 484ms 2.88% CvodeRhsAdaptor 58ms 0.35% 39.85% 479ms 2.85% N_VLinearSum 477ms 2.84% 42.69% 477ms 2.84% __strcmp_avx2 10ms 0.06% 42.75% 473ms 2.82% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.012% 42.76% 466ms 2.77% CvodeAdaptor::SetupCvode 6ms 0.036% 42.80% 427ms 2.54% SUNMatScaleAddI 6ms 0.036% 42.83% 425ms 2.53% AbstractCellProperty::IsType (inline) 421ms 2.51% 45.34% 421ms 2.51% SUNMatScaleAddI_Dense 151ms 0.9% 46.24% 419ms 2.49% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.012% 46.25% 398ms 2.37% std::set::erase (inline) 15ms 0.089% 46.34% 397ms 2.36% Node::RemoveElement 10ms 0.06% 46.40% 396ms 2.36% std::_Rb_tree::erase 311ms 1.85% 48.25% 384ms 2.29% _int_free 14ms 0.083% 48.33% 384ms 2.29% divconqrecurse 0 0% 48.33% 378ms 2.25% std::_Vector_base::_M_allocate (inline) 182ms 1.08% 49.42% 377ms 2.24% __cxxabiv1::__si_class_type_info::__do_dyncast 103ms 0.61% 50.03% 377ms 2.24% std::_Rb_tree::_M_erase 9ms 0.054% 50.08% 373ms 2.22% std::__new_allocator::deallocate (inline) 35ms 0.21% 50.29% 372ms 2.21% Element::ResetIndex 0 0% 50.29% 366ms 2.18% std::allocator_traits::deallocate (inline) 101ms 0.6% 50.89% 363ms 2.16% mergehulls 1ms 0.006% 50.90% 359ms 2.14% Cell::GetCellProliferativeType 147ms 0.88% 51.77% 357ms 2.12% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.048% 51.82% 353ms 2.10% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 51.82% 353ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.82% 347ms 2.07% std::_Rb_tree::_M_drop_node (inline) 24ms 0.14% 51.96% 346ms 2.06% std::_Rb_tree::~_Rb_tree (inline) 42ms 0.25% 52.21% 345ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 7ms 0.042% 52.26% 342ms 2.04% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.018% 52.27% 337ms 2.01% Cell::GetMutationState 334ms 1.99% 54.26% 334ms 1.99% N_VWSqrSumLocal_Serial 10ms 0.06% 54.32% 320ms 1.90% SUNMatCopy 0 0% 54.32% 319ms 1.90% NodeLocationWriter::Visit 0 0% 54.32% 318ms 1.89% std::set::~set (inline) 305ms 1.82% 56.14% 310ms 1.85% SUNMatCopy_Dense 0 0% 56.14% 304ms 1.81% std::_Rb_tree::_M_put_node (inline) 1ms 0.006% 56.14% 303ms 1.80% alternateaxes 73ms 0.43% 56.58% 301ms 1.79% AbstractCellProperty::IsSame 289ms 1.72% 58.30% 301ms 1.79% vertexmedian 6ms 0.036% 58.33% 299ms 1.78% LegacyCellProliferativeTypesWriter::VisitCell 19ms 0.11% 58.45% 283ms 1.68% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.065% 58.51% 277ms 1.65% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 13ms 0.077% 58.59% 275ms 1.64% std::vector::push_back (inline) 23ms 0.14% 58.73% 273ms 1.62% std::num_put::_M_insert_float 23ms 0.14% 58.86% 268ms 1.60% AbstractTetrahedralElement::CalculateJacobian 1ms 0.006% 58.87% 259ms 1.54% std::set::set (inline) 5ms 0.03% 58.90% 255ms 1.52% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.048% 58.95% 253ms 1.51% std::vector::_M_realloc_insert 5ms 0.03% 58.98% 250ms 1.49% AbstractCellPopulation::IsCellAttachedToLocationIndex 44ms 0.26% 59.24% 249ms 1.48% N_VScale 1ms 0.006% 59.24% 247ms 1.47% MeshBasedCellPopulation::GetDampingConstant 5ms 0.03% 59.27% 246ms 1.46% AbstractCentreBasedCellPopulation::GetDampingConstant 27ms 0.16% 59.43% 241ms 1.43% std::_Rb_tree::_M_copy (inline) 21ms 0.12% 59.56% 236ms 1.40% CVodeSetLinearSolver 0 0% 59.56% 230ms 1.37% OffLatticeSimulation::ApplyBoundaries 34ms 0.2% 59.76% 228ms 1.36% std::type_info::operator== (inline) 38ms 0.23% 59.99% 227ms 1.35% N_VScale_Serial 0 0% 59.99% 226ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.036% 60.02% 217ms 1.29% std::__cxx11::collate::do_transform 144ms 0.86% 60.88% 216ms 1.29% malloc_consolidate 161ms 0.96% 61.84% 213ms 1.27% AbstractElement::GetNodeGlobalIndex 83ms 0.49% 62.33% 210ms 1.25% std::_Rb_tree::_M_clone_node (inline) 4ms 0.024% 62.36% 209ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 35ms 0.21% 62.57% 202ms 1.20% AbstractTetrahedralElement::RefreshJacobian 12ms 0.071% 62.64% 199ms 1.18% Element::MarkAsDeleted 0 0% 62.64% 199ms 1.18% ___vsnprintf 0 0% 62.64% 199ms 1.18% __vsnprintf_internal (inline) 18ms 0.11% 62.74% 198ms 1.18% TetrahedralMesh::Clear 6ms 0.036% 62.78% 197ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 21ms 0.12% 62.90% 197ms 1.17% __printf_buffer 7ms 0.042% 62.95% 193ms 1.15% AbstractTetrahedralElement::AbstractTetrahedralElement 17ms 0.1% 63.05% 190ms 1.13% cvEwtSet 4ms 0.024% 63.07% 188ms 1.12% CellPropertyCollection::HasProperty 1ms 0.006% 63.08% 187ms 1.11% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 63.08% 185ms 1.10% Cell::HasCellProperty (inline) 112ms 0.67% 63.74% 185ms 1.10% std::_Rb_tree::equal_range (inline) 177ms 1.05% 64.80% 177ms 1.05% Node::GetIndex 3ms 0.018% 64.82% 173ms 1.03% CellProliferativeTypesWriter::VisitCell 4ms 0.024% 64.84% 171ms 1.02% __printf_fp_l_buffer 0 0% 64.84% 171ms 1.02% __printf_fp_spec (inline) 168ms 1.00% 65.84% 168ms 1.00% unlink_chunk 8ms 0.048% 65.89% 166ms 0.99% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 73ms 0.43% 66.32% 165ms 0.98% __printf_fp_buffer_1 2ms 0.012% 66.33% 159ms 0.95% Cell::SetCellProliferativeType 158ms 0.94% 67.27% 158ms 0.94% incircle 4ms 0.024% 67.30% 157ms 0.93% boost::numeric::ublas::vector_assign (inline) 12ms 0.071% 67.37% 152ms 0.9% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 67.37% 150ms 0.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 61ms 0.36% 67.73% 150ms 0.89% AbstractElement::GetNodeLocation 149ms 0.89% 68.62% 149ms 0.89% std::_Rb_tree_insert_and_rebalance 2ms 0.012% 68.63% 146ms 0.87% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 11ms 0.065% 68.70% 141ms 0.84% N_VCloneEmpty_Serial 91ms 0.54% 69.24% 139ms 0.83% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.03% 69.27% 139ms 0.83% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.06% 69.33% 132ms 0.79% SUNRpowerR 121ms 0.72% 70.05% 132ms 0.79% vertexsort 30ms 0.18% 70.23% 130ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 8ms 0.048% 70.27% 129ms 0.77% boost::numeric::ublas::c_vector::c_vector (inline) 126ms 0.75% 71.02% 126ms 0.75% std::vector::size (inline) 1ms 0.006% 71.03% 124ms 0.74% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 23ms 0.14% 71.17% 123ms 0.73% N_VScaleAddMulti 15ms 0.089% 71.26% 123ms 0.73% boost::detail::shared_count::~shared_count (inline) 0 0% 71.26% 123ms 0.73% boost::shared_ptr::~shared_ptr (inline) 8ms 0.048% 71.30% 122ms 0.73% __pow 0 0% 71.30% 120ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 71.30% 117ms 0.7% OutputFileHandler::OpenOutputFile 11ms 0.065% 71.37% 114ms 0.68% __ieee754_pow_fma 0 0% 71.37% 110ms 0.65% tcache_get (inline) 110ms 0.65% 72.02% 110ms 0.65% tcache_get_n (inline) 5ms 0.03% 72.05% 109ms 0.65% N_VClone 37ms 0.22% 72.27% 109ms 0.65% boost::numeric::ublas::indexing_vector_assign 13ms 0.077% 72.35% 109ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.042% 72.39% 108ms 0.64% Node::~Node 108ms 0.64% 73.04% 108ms 0.64% std::_Rb_tree_increment 17ms 0.1% 73.14% 108ms 0.64% std::num_put::_M_insert_int 0 0% 73.14% 107ms 0.64% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.006% 73.14% 106ms 0.63% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 8ms 0.048% 73.19% 105ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 104ms 0.62% 73.81% 104ms 0.62% AbstractElement::IsDeleted 14ms 0.083% 73.89% 104ms 0.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.03% 73.92% 104ms 0.62% N_VClone_Serial 25ms 0.15% 74.07% 103ms 0.61% std::__ostream_insert 102ms 0.61% 74.68% 102ms 0.61% TetrahedralMesh::EdgeIterator::operator!= 101ms 0.6% 75.28% 101ms 0.6% [libchaste_cell_based.so] 100ms 0.6% 75.88% 100ms 0.6% counterclockwise 23ms 0.14% 76.01% 97ms 0.58% N_VDestroy_Serial 2ms 0.012% 76.02% 97ms 0.58% cvLsFree 94ms 0.56% 76.58% 96ms 0.57% boost::detail::sp_counted_base::release 7ms 0.042% 76.62% 92ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 64ms 0.38% 77.01% 92ms 0.55% TetrahedralMesh::EdgeIterator::EdgeIterator 35ms 0.21% 77.21% 90ms 0.54% std::basic_filebuf::xsputn 42ms 0.25% 77.46% 88ms 0.52% AbstractTetrahedralMesh::GetElement 3ms 0.018% 77.48% 86ms 0.51% CellLocationIndexWriter::VisitCell 2ms 0.012% 77.49% 86ms 0.51% std::vector::resize (inline) 28ms 0.17% 77.66% 84ms 0.5% SUNDenseMatrix 0 0% 77.66% 84ms 0.5% std::vector::_M_default_append