File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12629ms, 78.55% of 16077ms total Dropped 857 nodes (cum <= 80.39ms) flat flat% sum% cum cum% 0 0% 0% 16030ms 99.71% __libc_start_call_main 0 0% 0% 16030ms 99.71% __libc_start_main_impl 0 0% 0% 16030ms 99.71% _start 0 0% 0% 16009ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16009ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16009ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16009ms 99.58% main 0 0% 0% 15976ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15976ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15975ms 99.37% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15950ms 99.21% AbstractCellBasedSimulation::Solve 0 0% 0% 11537ms 71.76% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.044% 0.044% 6256ms 38.91% AbstractCellBasedSimulation::DoCellBirth 15ms 0.093% 0.14% 6140ms 38.19% Cell::ReadyToDivide 6ms 0.037% 0.17% 6060ms 37.69% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0062% 0.18% 5873ms 36.53% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.075% 0.26% 5856ms 36.42% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.025% 0.28% 5840ms 36.33% CellCycleModelOdeHandler::SolveOdeToTime 5ms 0.031% 0.31% 5682ms 35.34% CvodeAdaptor::Solve 70ms 0.44% 0.75% 5223ms 32.49% CVode 0 0% 0.75% 5153ms 32.05% MeshBasedCellPopulation::Update 58ms 0.36% 1.11% 4689ms 29.17% CVodeFree 1ms 0.0062% 1.11% 3953ms 24.59% Cylindrical2dMesh::ReMesh 158ms 0.98% 2.10% 3753ms 23.34% cvRescale 3ms 0.019% 2.11% 3406ms 21.19% SUNNonlinSolSolve 33ms 0.21% 2.32% 3403ms 21.17% SUNNonlinSolSolve_Newton 65ms 0.4% 2.72% 3304ms 20.55% cvNlsInit 2ms 0.012% 2.74% 2440ms 15.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.74% 2158ms 13.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 2.74% 2150ms 13.37% MutableMesh::ReMesh 8ms 0.05% 2.79% 2105ms 13.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.12% 2.91% 2044ms 12.71% cvLsSetup 0 0% 2.91% 1969ms 12.25% AbstractCellPopulation::WriteResultsToFiles 853ms 5.31% 8.22% 1922ms 11.95% std::_Rb_tree::_M_lower_bound (inline) 144ms 0.9% 9.11% 1737ms 10.80% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.037% 9.15% 1470ms 9.14% cvLsDQJtimes 60ms 0.37% 9.52% 1462ms 9.09% std::_Rb_tree::find (inline) 0 0% 9.52% 1164ms 7.24% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.012% 9.54% 1119ms 6.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.068% 9.60% 1062ms 6.61% TetrahedralMesh::ImportFromMesher 11ms 0.068% 9.67% 1043ms 6.49% MeshBasedCellPopulation::SpringIterator::operator++ 54ms 0.34% 10.01% 1035ms 6.44% operator new 270ms 1.68% 11.69% 1010ms 6.28% __GI___libc_malloc 6ms 0.037% 11.72% 1007ms 6.26% std::set::insert (inline) 20ms 0.12% 11.85% 1001ms 6.23% std::_Rb_tree::_M_insert_unique 57ms 0.35% 12.20% 898ms 5.59% std::__new_allocator::allocate (inline) 0 0% 12.20% 896ms 5.57% std::allocator_traits::allocate (inline) 0 0% 12.20% 891ms 5.54% std::set::count (inline) 0 0% 12.20% 821ms 5.11% triangulate 0 0% 12.20% 737ms 4.58% delaunay 5ms 0.031% 12.23% 736ms 4.58% divconqdelaunay 6ms 0.037% 12.27% 709ms 4.41% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.019% 12.29% 684ms 4.25% AbstractTwoBodyInteractionForce::AddForceContribution 683ms 4.25% 16.54% 683ms 4.25% std::_Rb_tree::_S_right (inline) 12ms 0.075% 16.61% 680ms 4.23% CellPopulationElementWriter::Visit 28ms 0.17% 16.79% 680ms 4.23% std::less::operator() (inline) 407ms 2.53% 19.32% 669ms 4.16% _int_malloc 49ms 0.3% 19.62% 653ms 4.06% std::map::operator[] (partial-inline) 652ms 4.06% 23.68% 652ms 4.06% std::operator< (inline) 193ms 1.20% 24.88% 618ms 3.84% __dynamic_cast 42ms 0.26% 25.14% 616ms 3.83% cvLsSolve 0 0% 25.14% 608ms 3.78% std::_Rb_tree::_M_create_node (inline) 602ms 3.74% 28.89% 602ms 3.74% N_VBufUnpack_Serial 5ms 0.031% 28.92% 592ms 3.68% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.15% 29.07% 589ms 3.66% AbstractCellPopulation::GetCellUsingLocationIndex 34ms 0.21% 29.28% 586ms 3.64% std::_Rb_tree::_M_insert_ (inline) 33ms 0.21% 29.48% 580ms 3.61% N_VWrmsNorm 0 0% 29.48% 579ms 3.60% std::_Rb_tree::_M_get_node (inline) 16ms 0.1% 29.58% 576ms 3.58% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 29.58% 568ms 3.53% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.58% 564ms 3.51% std::map::find (inline) 3ms 0.019% 29.60% 558ms 3.47% MeshBasedCellPopulation::AcceptCellWriter 109ms 0.68% 30.28% 547ms 3.40% N_VWrmsNorm_Serial 8ms 0.05% 30.33% 544ms 3.38% Element::Element 6ms 0.037% 30.37% 544ms 3.38% SUNLinSolSetup 0 0% 30.37% 541ms 3.37% std::_Rb_tree::lower_bound (inline) 0 0% 30.37% 541ms 3.37% std::map::lower_bound (inline) 15ms 0.093% 30.46% 538ms 3.35% SUNLinSolSetup_Dense 8ms 0.05% 30.51% 537ms 3.34% cvLsDQJac 57ms 0.35% 30.86% 528ms 3.28% cvLsDenseDQJac 155ms 0.96% 31.83% 528ms 3.28% cvRestore 9ms 0.056% 31.88% 527ms 3.28% MutableMesh::ReIndex 6ms 0.037% 31.92% 520ms 3.23% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.012% 31.93% 518ms 3.22% std::ostream::operator<< (inline) 71ms 0.44% 32.38% 516ms 3.21% std::ostream::_M_insert 10ms 0.062% 32.44% 505ms 3.14% CvodeRhsAdaptor 503ms 3.13% 35.57% 503ms 3.13% SUNDlsMat_denseGETRF 11ms 0.068% 35.63% 501ms 3.12% Element::RegisterWithNodes (inline) 10ms 0.062% 35.70% 499ms 3.10% SUNLinSolSolve 94ms 0.58% 36.28% 498ms 3.10% N_VLinearSum_Serial 13ms 0.081% 36.36% 489ms 3.04% SUNLinSolSolve_Dense 11ms 0.068% 36.43% 486ms 3.02% Node::AddElement 2ms 0.012% 36.44% 481ms 2.99% AbstractCellProperty::IsSubType (inline) 184ms 1.14% 37.59% 459ms 2.86% __GI___libc_free 10ms 0.062% 37.65% 455ms 2.83% Cylindrical2dMesh::CorrectNonPeriodicMesh 39ms 0.24% 37.89% 454ms 2.82% N_VLinearSum 1ms 0.0062% 37.90% 452ms 2.81% SUNMatScaleAddI 451ms 2.81% 40.70% 451ms 2.81% SUNMatScaleAddI_Dense 184ms 1.14% 41.85% 445ms 2.77% WntCellCycleOdeSystem::EvaluateYDerivatives 428ms 2.66% 44.51% 428ms 2.66% __strcmp_avx2 9ms 0.056% 44.57% 419ms 2.61% SUNMatCopy 9ms 0.056% 44.62% 413ms 2.57% AbstractCellProperty::IsType (inline) 404ms 2.51% 47.14% 410ms 2.55% SUNMatCopy_Dense 5ms 0.031% 47.17% 408ms 2.54% std::_Rb_tree::erase 0 0% 47.17% 405ms 2.52% std::set::erase (inline) 404ms 2.51% 49.68% 404ms 2.51% SUNDlsMat_denseGETRS 14ms 0.087% 49.77% 402ms 2.50% Node::RemoveElement 162ms 1.01% 50.77% 395ms 2.46% std::_Rb_tree::_M_get_insert_unique_pos 389ms 2.42% 53.19% 389ms 2.42% N_VWSqrSumLocal_Serial 2ms 0.012% 53.21% 384ms 2.39% CvodeAdaptor::SetupCvode 14ms 0.087% 53.29% 380ms 2.36% divconqrecurse 99ms 0.62% 53.91% 356ms 2.21% mergehulls 0 0% 53.91% 353ms 2.20% NodeLocationWriter::Visit 27ms 0.17% 54.08% 344ms 2.14% Element::ResetIndex 112ms 0.7% 54.77% 329ms 2.05% std::_Rb_tree::_M_erase 11ms 0.068% 54.84% 323ms 2.01% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.031% 54.87% 322ms 2.00% Cell::GetCellProliferativeType 2ms 0.012% 54.89% 319ms 1.98% std::_Vector_base::_M_allocate (inline) 84ms 0.52% 55.41% 316ms 1.97% AbstractCellProperty::IsSame 23ms 0.14% 55.55% 311ms 1.93% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.019% 55.57% 310ms 1.93% AbstractCellPopulation::GetLocationIndexUsingCell 149ms 0.93% 56.50% 303ms 1.88% __cxxabiv1::__si_class_type_info::__do_dyncast 14ms 0.087% 56.58% 303ms 1.88% std::__new_allocator::deallocate (inline) 1ms 0.0062% 56.59% 301ms 1.87% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.22% 56.81% 299ms 1.86% AbstractCellPopulation::Iterator::IsRealCell (inline) 26ms 0.16% 56.97% 298ms 1.85% std::num_put::_M_insert_float 3ms 0.019% 56.99% 297ms 1.85% Cell::GetMutationState 15ms 0.093% 57.08% 297ms 1.85% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.025% 57.11% 295ms 1.83% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 57.11% 295ms 1.83% std::allocator_traits::deallocate (inline) 0 0% 57.11% 287ms 1.79% std::set::~set (inline) 0 0% 57.11% 276ms 1.72% std::_Rb_tree::_M_drop_node (inline) 7ms 0.044% 57.15% 275ms 1.71% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 211ms 1.31% 58.46% 274ms 1.70% _int_free 0 0% 58.46% 265ms 1.65% std::set::set (inline) 26ms 0.16% 58.62% 251ms 1.56% std::_Rb_tree::_M_copy (inline) 20ms 0.12% 58.75% 250ms 1.56% AbstractTetrahedralElement::CalculateJacobian 51ms 0.32% 59.07% 249ms 1.55% N_VScale_Serial 0 0% 59.07% 247ms 1.54% std::_Rb_tree::_M_put_node (inline) 0 0% 59.07% 246ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 37ms 0.23% 59.30% 242ms 1.51% N_VScale 5ms 0.031% 59.33% 240ms 1.49% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.044% 59.37% 239ms 1.49% std::__cxx11::collate::do_transform 2ms 0.012% 59.38% 238ms 1.48% alternateaxes 218ms 1.36% 60.74% 236ms 1.47% vertexmedian 58ms 0.36% 61.10% 232ms 1.44% std::type_info::operator== (inline) 1ms 0.0062% 61.11% 230ms 1.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 14ms 0.087% 61.19% 228ms 1.42% std::_Rb_tree::_M_erase_aux (inline) 67ms 0.42% 61.61% 220ms 1.37% std::_Rb_tree::_M_clone_node (inline) 5ms 0.031% 61.64% 216ms 1.34% ___vsnprintf 12ms 0.075% 61.72% 214ms 1.33% std::vector::push_back (inline) 0 0% 61.72% 211ms 1.31% AbstractCentreBasedCellPopulation::GetDampingConstant 11ms 0.068% 61.78% 211ms 1.31% Element::MarkAsDeleted 0 0% 61.78% 211ms 1.31% MeshBasedCellPopulation::GetDampingConstant 0 0% 61.78% 211ms 1.31% __vsnprintf_internal (inline) 21ms 0.13% 61.91% 209ms 1.30% cvEwtSet 19ms 0.12% 62.03% 206ms 1.28% __printf_buffer 6ms 0.037% 62.07% 202ms 1.26% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.081% 62.15% 195ms 1.21% std::vector::_M_realloc_insert 20ms 0.12% 62.28% 189ms 1.18% AbstractTetrahedralElement::RefreshJacobian 0 0% 62.28% 185ms 1.15% OffLatticeSimulation::ApplyBoundaries 151ms 0.94% 63.21% 183ms 1.14% AbstractElement::GetNodeGlobalIndex 10ms 0.062% 63.28% 183ms 1.14% CVodeSetLinearSolver 117ms 0.73% 64.00% 180ms 1.12% std::_Rb_tree::equal_range (inline) 177ms 1.10% 65.11% 177ms 1.10% Node::GetIndex 1ms 0.0062% 65.11% 174ms 1.08% __printf_fp_spec (inline) 3ms 0.019% 65.13% 173ms 1.08% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 10ms 0.062% 65.19% 173ms 1.08% __printf_fp_l_buffer 19ms 0.12% 65.31% 170ms 1.06% TetrahedralMesh::Clear 163ms 1.01% 66.32% 163ms 1.01% incircle 66ms 0.41% 66.74% 160ms 1% __printf_fp_buffer_1 101ms 0.63% 67.36% 160ms 1% malloc_consolidate 64ms 0.4% 67.76% 157ms 0.98% AbstractElement::GetNodeLocation 0 0% 67.76% 156ms 0.97% CellProliferativeTypesWriter::VisitCell 5ms 0.031% 67.79% 156ms 0.97% CellPropertyCollection::HasProperty 5ms 0.031% 67.82% 153ms 0.95% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.037% 67.86% 152ms 0.95% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 67.86% 151ms 0.94% Cell::HasCellProperty (inline) 148ms 0.92% 68.78% 148ms 0.92% std::_Rb_tree_insert_and_rebalance 144ms 0.9% 69.68% 144ms 0.9% unlink_chunk 7ms 0.044% 69.72% 141ms 0.88% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0062% 69.73% 140ms 0.87% Cell::SetCellProliferativeType 1ms 0.0062% 69.73% 135ms 0.84% boost::numeric::ublas::vector_assign (inline) 80ms 0.5% 70.23% 134ms 0.83% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 70.23% 128ms 0.8% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.087% 70.32% 127ms 0.79% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 70.32% 124ms 0.77% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0062% 70.32% 124ms 0.77% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 70.32% 122ms 0.76% OutputFileHandler::OpenOutputFile 121ms 0.75% 71.08% 121ms 0.75% AbstractElement::IsDeleted 37ms 0.23% 71.31% 120ms 0.75% TetrahedralMesh::EdgesEnd (partial-inline) 120ms 0.75% 72.05% 120ms 0.75% std::vector::size (inline) 10ms 0.062% 72.12% 116ms 0.72% N_VCloneEmpty_Serial 5ms 0.031% 72.15% 112ms 0.7% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 40ms 0.25% 72.40% 111ms 0.69% N_VScaleAddMulti 47ms 0.29% 72.69% 108ms 0.67% std::__ostream_insert 24ms 0.15% 72.84% 108ms 0.67% std::num_put::_M_insert_int 100ms 0.62% 73.46% 107ms 0.67% vertexsort 7ms 0.044% 73.50% 106ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 73.50% 106ms 0.66% boost::shared_ptr::~shared_ptr (inline) 105ms 0.65% 74.16% 105ms 0.65% std::_Rb_tree_rebalance_for_erase 5ms 0.031% 74.19% 104ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 74.19% 102ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 7ms 0.044% 74.23% 102ms 0.63% Node::~Node 31ms 0.19% 74.42% 102ms 0.63% boost::numeric::ublas::indexing_vector_assign 10ms 0.062% 74.49% 99ms 0.62% N_VClone 98ms 0.61% 75.09% 98ms 0.61% boost::detail::sp_counted_base::release 93ms 0.58% 75.67% 93ms 0.58% counterclockwise 4ms 0.025% 75.70% 92ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 40ms 0.25% 75.95% 92ms 0.57% boost::shared_ptr::shared_ptr (inline) 4ms 0.025% 75.97% 92ms 0.57% std::operator<< (inline) 1ms 0.0062% 75.98% 89ms 0.55% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 6ms 0.037% 76.02% 89ms 0.55% N_VClone_Serial 11ms 0.068% 76.08% 88ms 0.55% SUNRpowerR 5ms 0.031% 76.11% 86ms 0.53% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 44ms 0.27% 76.39% 83ms 0.52% AbstractTetrahedralMesh::GetElement 43ms 0.27% 76.66% 83ms 0.52% SUNDenseMatrix 83ms 0.52% 77.17% 83ms 0.52% [libchaste_mesh.so] 0 0% 77.17% 83ms 0.52% tcache_get (inline) 83ms 0.52% 77.69% 83ms 0.52% tcache_get_n (inline) 58ms 0.36% 78.05% 82ms 0.51% boost::numeric::ublas::c_matrix::operator() 81ms 0.5% 78.55% 81ms 0.5% std::_Rb_tree_increment 0 0% 78.55% 81ms 0.5% std::vector::resize (inline)