File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12654ms, 77.32% of 16365ms total Dropped 906 nodes (cum <= 81.83ms) flat flat% sum% cum cum% 0 0% 0% 16315ms 99.69% __libc_start_call_main 0 0% 0% 16315ms 99.69% __libc_start_main_impl 0 0% 0% 16315ms 99.69% _start 0 0% 0% 16295ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16295ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16295ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16295ms 99.57% main 0 0% 0% 16258ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16258ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16258ms 99.35% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16232ms 99.19% AbstractCellBasedSimulation::Solve 0 0% 0% 11735ms 71.71% AbstractCellBasedSimulation::UpdateCellPopulation 10ms 0.061% 0.061% 6373ms 38.94% AbstractCellBasedSimulation::DoCellBirth 14ms 0.086% 0.15% 6248ms 38.18% Cell::ReadyToDivide 6ms 0.037% 0.18% 6151ms 37.59% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.18% 5972ms 36.49% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 32ms 0.2% 0.38% 5956ms 36.39% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.018% 0.4% 5923ms 36.19% CellCycleModelOdeHandler::SolveOdeToTime 3ms 0.018% 0.42% 5734ms 35.04% CvodeAdaptor::Solve 83ms 0.51% 0.92% 5248ms 32.07% CVode 1ms 0.0061% 0.93% 5235ms 31.99% MeshBasedCellPopulation::Update 64ms 0.39% 1.32% 4722ms 28.85% CVodeFree 9ms 0.055% 1.37% 4039ms 24.68% Cylindrical2dMesh::ReMesh 154ms 0.94% 2.32% 3802ms 23.23% cvRescale 4ms 0.024% 2.34% 3457ms 21.12% SUNNonlinSolSolve 45ms 0.27% 2.62% 3453ms 21.10% SUNNonlinSolSolve_Newton 83ms 0.51% 3.12% 3341ms 20.42% cvNlsInit 0 0% 3.12% 2489ms 15.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 3.12% 2216ms 13.54% MutableMesh::ReMesh 2ms 0.012% 3.13% 2187ms 13.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.049% 3.18% 2136ms 13.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.1% 3.29% 2045ms 12.50% cvLsSetup 0 0% 3.29% 2000ms 12.22% AbstractCellPopulation::WriteResultsToFiles 766ms 4.68% 7.97% 1834ms 11.21% std::_Rb_tree::_M_lower_bound (inline) 159ms 0.97% 8.94% 1712ms 10.46% TetrahedralMesh::EdgeIterator::operator++ 7ms 0.043% 8.98% 1456ms 8.90% cvLsDQJtimes 79ms 0.48% 9.47% 1382ms 8.44% std::_Rb_tree::find (inline) 0 0% 9.47% 1159ms 7.08% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.067% 9.53% 1117ms 6.83% TetrahedralMesh::ImportFromMesher 5ms 0.031% 9.56% 1108ms 6.77% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 258ms 1.58% 11.14% 1084ms 6.62% __GI___libc_malloc 35ms 0.21% 11.35% 1080ms 6.60% operator new 10ms 0.061% 11.41% 1037ms 6.34% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.061% 11.48% 1036ms 6.33% std::set::insert (inline) 24ms 0.15% 11.62% 1025ms 6.26% std::_Rb_tree::_M_insert_unique 54ms 0.33% 11.95% 961ms 5.87% std::__new_allocator::allocate (inline) 0 0% 11.95% 957ms 5.85% std::allocator_traits::allocate (inline) 0 0% 11.95% 833ms 5.09% std::set::count (inline) 3ms 0.018% 11.97% 808ms 4.94% triangulate 411ms 2.51% 14.48% 736ms 4.50% _int_malloc 0 0% 14.48% 732ms 4.47% delaunay 3ms 0.018% 14.50% 730ms 4.46% divconqdelaunay 6ms 0.037% 14.54% 712ms 4.35% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 682ms 4.17% 18.70% 682ms 4.17% std::_Rb_tree::_S_right (inline) 8ms 0.049% 18.75% 680ms 4.16% CellPopulationElementWriter::Visit 53ms 0.32% 19.08% 678ms 4.14% std::map::operator[] (partial-inline) 1ms 0.0061% 19.08% 673ms 4.11% AbstractTwoBodyInteractionForce::AddForceContribution 56ms 0.34% 19.43% 656ms 4.01% cvLsSolve 15ms 0.092% 19.52% 655ms 4.00% std::less::operator() (inline) 640ms 3.91% 23.43% 640ms 3.91% std::operator< (inline) 632ms 3.86% 27.29% 632ms 3.86% N_VBufUnpack_Serial 0 0% 27.29% 628ms 3.84% std::_Rb_tree::_M_create_node (inline) 32ms 0.2% 27.49% 628ms 3.84% std::_Rb_tree::_M_insert_ (inline) 221ms 1.35% 28.84% 616ms 3.76% __dynamic_cast 5ms 0.031% 28.87% 609ms 3.72% CellPropertyCollection::GetPropertiesType (inline) 0 0% 28.87% 603ms 3.68% std::_Rb_tree::_M_get_node (inline) 21ms 0.13% 28.99% 586ms 3.58% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 28.99% 579ms 3.54% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.17% 29.17% 576ms 3.52% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.049% 29.21% 559ms 3.42% SUNLinSolSetup 36ms 0.22% 29.43% 557ms 3.40% N_VWrmsNorm 199ms 1.22% 30.65% 556ms 3.40% __GI___libc_free 16ms 0.098% 30.75% 554ms 3.39% MutableMesh::ReIndex 0 0% 30.75% 553ms 3.38% std::_Rb_tree::lower_bound (inline) 0 0% 30.75% 553ms 3.38% std::map::lower_bound (inline) 5ms 0.031% 30.78% 551ms 3.37% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.037% 30.82% 551ms 3.37% SUNLinSolSetup_Dense 0 0% 30.82% 543ms 3.32% std::map::find (inline) 127ms 0.78% 31.59% 541ms 3.31% N_VLinearSum_Serial 164ms 1.00% 32.59% 538ms 3.29% cvRestore 4ms 0.024% 32.62% 535ms 3.27% cvLsDQJac 51ms 0.31% 32.93% 530ms 3.24% cvLsDenseDQJac 9ms 0.055% 32.99% 527ms 3.22% Element::Element 98ms 0.6% 33.58% 521ms 3.18% N_VWrmsNorm_Serial 11ms 0.067% 33.65% 520ms 3.18% SUNLinSolSolve 1ms 0.0061% 33.66% 515ms 3.15% std::ostream::operator<< (inline) 74ms 0.45% 34.11% 513ms 3.13% std::ostream::_M_insert 509ms 3.11% 37.22% 509ms 3.11% SUNDlsMat_denseGETRF 14ms 0.086% 37.31% 509ms 3.11% SUNLinSolSolve_Dense 12ms 0.073% 37.38% 492ms 3.01% Element::RegisterWithNodes (inline) 7ms 0.043% 37.42% 489ms 2.99% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.018% 37.44% 486ms 2.97% AbstractCellProperty::IsSubType (inline) 4ms 0.024% 37.46% 483ms 2.95% CvodeRhsAdaptor 8ms 0.049% 37.51% 476ms 2.91% Node::AddElement 40ms 0.24% 37.76% 472ms 2.88% N_VLinearSum 13ms 0.079% 37.84% 470ms 2.87% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.055% 37.89% 464ms 2.84% SUNMatCopy 444ms 2.71% 40.60% 455ms 2.78% SUNMatCopy_Dense 183ms 1.12% 41.72% 422ms 2.58% WntCellCycleOdeSystem::EvaluateYDerivatives 421ms 2.57% 44.30% 421ms 2.57% SUNDlsMat_denseGETRS 2ms 0.012% 44.31% 405ms 2.47% SUNMatScaleAddI 403ms 2.46% 46.77% 403ms 2.46% SUNMatScaleAddI_Dense 7ms 0.043% 46.81% 401ms 2.45% AbstractCellProperty::IsType (inline) 4ms 0.024% 46.84% 398ms 2.43% CvodeAdaptor::SetupCvode 389ms 2.38% 49.21% 389ms 2.38% __strcmp_avx2 385ms 2.35% 51.57% 385ms 2.35% N_VWSqrSumLocal_Serial 19ms 0.12% 51.68% 375ms 2.29% divconqrecurse 150ms 0.92% 52.60% 373ms 2.28% std::_Rb_tree::_M_get_insert_unique_pos 15ms 0.092% 52.69% 366ms 2.24% std::__new_allocator::deallocate (inline) 3ms 0.018% 52.71% 356ms 2.18% std::set::erase (inline) 287ms 1.75% 54.46% 355ms 2.17% _int_free 1ms 0.0061% 54.47% 355ms 2.17% std::_Vector_base::_M_allocate (inline) 2ms 0.012% 54.48% 353ms 2.16% std::_Rb_tree::erase 0 0% 54.48% 353ms 2.16% std::allocator_traits::deallocate (inline) 120ms 0.73% 55.22% 351ms 2.14% mergehulls 12ms 0.073% 55.29% 349ms 2.13% Node::RemoveElement 104ms 0.64% 55.92% 349ms 2.13% std::_Rb_tree::_M_erase 30ms 0.18% 56.11% 342ms 2.09% Element::ResetIndex 2ms 0.012% 56.12% 334ms 2.04% Cell::GetMutationState 1ms 0.0061% 56.13% 331ms 2.02% NodeLocationWriter::Visit 5ms 0.031% 56.16% 320ms 1.96% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 14ms 0.086% 56.24% 311ms 1.90% std::_Rb_tree::~_Rb_tree (inline) 0 0% 56.24% 310ms 1.89% std::_Rb_tree::_M_drop_node (inline) 7ms 0.043% 56.28% 304ms 1.86% Cell::GetCellProliferativeType 22ms 0.13% 56.42% 303ms 1.85% std::_Rb_tree::_Rb_tree (partial-inline) 39ms 0.24% 56.66% 298ms 1.82% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 56.66% 296ms 1.81% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.043% 56.70% 295ms 1.80% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.024% 56.72% 289ms 1.77% LegacyCellProliferativeTypesWriter::VisitCell 24ms 0.15% 56.87% 287ms 1.75% std::num_put::_M_insert_float 0 0% 56.87% 283ms 1.73% std::_Rb_tree::_M_put_node (inline) 145ms 0.89% 57.76% 282ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 57.76% 282ms 1.72% std::set::~set (inline) 66ms 0.4% 58.16% 276ms 1.69% AbstractCellProperty::IsSame 1ms 0.0061% 58.17% 273ms 1.67% std::set::set (inline) 8ms 0.049% 58.22% 264ms 1.61% std::vector::push_back (inline) 8ms 0.049% 58.26% 263ms 1.61% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 58.26% 258ms 1.58% TetrahedralMesh::RefreshJacobianCachedData 26ms 0.16% 58.42% 252ms 1.54% std::_Rb_tree::_M_copy (inline) 9ms 0.055% 58.48% 250ms 1.53% AbstractTetrahedralElement::CalculateJacobian 10ms 0.061% 58.54% 247ms 1.51% std::vector::_M_realloc_insert 2ms 0.012% 58.55% 242ms 1.48% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 58.55% 242ms 1.48% MeshBasedCellPopulation::GetDampingConstant 5ms 0.031% 58.58% 239ms 1.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 26ms 0.16% 58.74% 238ms 1.45% N_VScale 20ms 0.12% 58.86% 238ms 1.45% N_VScale_Serial 4ms 0.024% 58.89% 234ms 1.43% alternateaxes 4ms 0.024% 58.91% 232ms 1.42% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 216ms 1.32% 60.23% 230ms 1.41% vertexmedian 33ms 0.2% 60.43% 227ms 1.39% TetrahedralMesh::Clear 9ms 0.055% 60.49% 224ms 1.37% std::_Rb_tree::_M_erase_aux (inline) 67ms 0.41% 60.90% 221ms 1.35% std::_Rb_tree::_M_clone_node (inline) 3ms 0.018% 60.92% 218ms 1.33% std::__cxx11::collate::do_transform 9ms 0.055% 60.97% 213ms 1.30% AbstractTetrahedralElement::CalculateInverseJacobian 171ms 1.04% 62.02% 211ms 1.29% AbstractElement::GetNodeGlobalIndex 51ms 0.31% 62.33% 210ms 1.28% std::type_info::operator== (inline) 26ms 0.16% 62.49% 208ms 1.27% AbstractTetrahedralElement::RefreshJacobian 3ms 0.018% 62.51% 202ms 1.23% ___vsnprintf 1ms 0.0061% 62.51% 199ms 1.22% __vsnprintf_internal (inline) 16ms 0.098% 62.61% 191ms 1.17% __printf_buffer 0 0% 62.61% 190ms 1.16% OffLatticeSimulation::ApplyBoundaries 144ms 0.88% 63.49% 188ms 1.15% malloc_consolidate 22ms 0.13% 63.62% 185ms 1.13% CVodeSetLinearSolver 21ms 0.13% 63.75% 185ms 1.13% cvEwtSet 3ms 0.018% 63.77% 179ms 1.09% CellPropertyCollection::HasProperty 0 0% 63.77% 177ms 1.08% Cell::HasCellProperty (inline) 13ms 0.079% 63.85% 177ms 1.08% Element::MarkAsDeleted 175ms 1.07% 64.92% 175ms 1.07% std::_Rb_tree_insert_and_rebalance 167ms 1.02% 65.94% 167ms 1.02% Node::GetIndex 2ms 0.012% 65.95% 165ms 1.01% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.012% 65.96% 164ms 1.00% CellProliferativeTypesWriter::VisitCell 8ms 0.049% 66.01% 164ms 1.00% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 75ms 0.46% 66.47% 162ms 0.99% AbstractElement::GetNodeLocation 6ms 0.037% 66.51% 162ms 0.99% __printf_fp_l_buffer 0 0% 66.51% 162ms 0.99% __printf_fp_spec (inline) 158ms 0.97% 67.47% 158ms 0.97% unlink_chunk 5ms 0.031% 67.50% 156ms 0.95% AbstractTetrahedralElement::AbstractTetrahedralElement 151ms 0.92% 68.43% 151ms 0.92% incircle 71ms 0.43% 68.86% 147ms 0.9% __printf_fp_buffer_1 4ms 0.024% 68.88% 143ms 0.87% Cell::SetCellProliferativeType 3ms 0.018% 68.90% 136ms 0.83% boost::numeric::ublas::vector_assign (inline) 92ms 0.56% 69.47% 136ms 0.83% std::_Rb_tree::equal_range (inline) 10ms 0.061% 69.53% 133ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 13ms 0.079% 69.61% 125ms 0.76% Node::~Node 0 0% 69.61% 123ms 0.75% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.037% 69.64% 121ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 26ms 0.16% 69.80% 121ms 0.74% N_VScaleAddMulti 48ms 0.29% 70.09% 119ms 0.73% std::__ostream_insert 8ms 0.049% 70.14% 118ms 0.72% N_VCloneEmpty_Serial 1ms 0.0061% 70.15% 116ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.024% 70.17% 116ms 0.71% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 11ms 0.067% 70.24% 114ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 24ms 0.15% 70.39% 114ms 0.7% std::num_put::_M_insert_int 20ms 0.12% 70.51% 113ms 0.69% std::_Rb_tree_const_iterator::operator++ (inline) 113ms 0.69% 71.20% 113ms 0.69% std::vector::size (inline) 1ms 0.0061% 71.21% 112ms 0.68% OutputFileHandler::OpenOutputFile 111ms 0.68% 71.89% 111ms 0.68% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 103ms 0.63% 72.51% 110ms 0.67% vertexsort 109ms 0.67% 73.18% 109ms 0.67% std::_Rb_tree_increment 25ms 0.15% 73.33% 108ms 0.66% TetrahedralMesh::EdgesEnd (partial-inline) 64ms 0.39% 73.72% 107ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 73.72% 106ms 0.65% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0061% 73.73% 103ms 0.63% std::operator<< (inline) 1ms 0.0061% 73.74% 99ms 0.6% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 98ms 0.6% 74.34% 98ms 0.6% AbstractElement::IsDeleted 5ms 0.031% 74.37% 97ms 0.59% Cylindrical2dMesh::CreateMirrorNodes 3ms 0.018% 74.38% 97ms 0.59% N_VClone 29ms 0.18% 74.56% 97ms 0.59% boost::numeric::ublas::indexing_vector_assign 95ms 0.58% 75.14% 95ms 0.58% std::_Rb_tree_rebalance_for_erase 7ms 0.043% 75.18% 94ms 0.57% N_VClone_Serial 94ms 0.57% 75.76% 94ms 0.57% [libchaste_mesh.so] 1ms 0.0061% 75.77% 93ms 0.57% std::vector::resize (inline) 0 0% 75.77% 91ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 13ms 0.079% 75.84% 91ms 0.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.0061% 75.85% 91ms 0.56% std::vector::_M_default_append 0 0% 75.85% 91ms 0.56% tcache_get (inline) 91ms 0.56% 76.41% 91ms 0.56% tcache_get_n (inline) 40ms 0.24% 76.65% 90ms 0.55% std::basic_filebuf::xsputn 39ms 0.24% 76.89% 89ms 0.54% boost::shared_ptr::shared_ptr (inline) 18ms 0.11% 77.00% 88ms 0.54% std::_Vector_base::_M_deallocate (inline) 10ms 0.061% 77.06% 87ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 77.06% 87ms 0.53% boost::shared_ptr::~shared_ptr (inline) 43ms 0.26% 77.32% 83ms 0.51% AbstractTetrahedralMesh::GetElement