File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 14102ms, 80.71% of 17472ms total Dropped 885 nodes (cum <= 87.36ms) flat flat% sum% cum cum% 0 0% 0% 17426ms 99.74% __libc_start_call_main 0 0% 0% 17426ms 99.74% __libc_start_main_impl 0 0% 0% 17426ms 99.74% _start 0 0% 0% 17403ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 17403ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 17403ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 17403ms 99.61% main 0 0% 0% 17368ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 17368ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 17368ms 99.40% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 17344ms 99.27% AbstractCellBasedSimulation::Solve 0 0% 0% 12950ms 74.12% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.011% 0.011% 7415ms 42.44% AbstractCellBasedSimulation::DoCellBirth 15ms 0.086% 0.097% 7283ms 41.68% Cell::ReadyToDivide 1ms 0.0057% 0.1% 7217ms 41.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.017% 0.12% 7022ms 40.19% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.074% 0.19% 7013ms 40.14% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.017% 0.21% 6995ms 40.04% CellCycleModelOdeHandler::SolveOdeToTime 3ms 0.017% 0.23% 6830ms 39.09% CvodeAdaptor::Solve 39ms 0.22% 0.45% 5939ms 33.99% CVode 1ms 0.0057% 0.46% 5393ms 30.87% MeshBasedCellPopulation::Update 69ms 0.39% 0.85% 5376ms 30.77% CVodeFree 127ms 0.73% 1.58% 4232ms 24.22% cvRescale 3ms 0.017% 1.60% 4123ms 23.60% Cylindrical2dMesh::ReMesh 4ms 0.023% 1.62% 3829ms 21.92% SUNNonlinSolSolve 55ms 0.31% 1.93% 3825ms 21.89% SUNNonlinSolSolve_Newton 92ms 0.53% 2.46% 3649ms 20.88% cvNlsInit 0 0% 2.46% 2519ms 14.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.46% 2278ms 13.04% MutableMesh::ReMesh 11ms 0.063% 2.52% 2229ms 12.76% cvLsSetup 0 0% 2.52% 2180ms 12.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.017% 2.54% 2130ms 12.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 851ms 4.87% 7.41% 1870ms 10.70% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.41% 1867ms 10.69% AbstractCellPopulation::WriteResultsToFiles 174ms 1% 8.41% 1805ms 10.33% TetrahedralMesh::EdgeIterator::operator++ 7ms 0.04% 8.45% 1544ms 8.84% cvLsDQJtimes 57ms 0.33% 8.77% 1497ms 8.57% std::_Rb_tree::find (inline) 59ms 0.34% 9.11% 1231ms 7.05% operator new 1ms 0.0057% 9.12% 1228ms 7.03% MeshBasedCellPopulation::UpdateNodePairs 435ms 2.49% 11.61% 1207ms 6.91% __GI___libc_malloc 5ms 0.029% 11.64% 1166ms 6.67% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.063% 11.70% 1147ms 6.56% TetrahedralMesh::ImportFromMesher 11ms 0.063% 11.76% 1098ms 6.28% std::set::insert (inline) 22ms 0.13% 11.89% 1094ms 6.26% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.034% 11.92% 1087ms 6.22% std::_Rb_tree::_M_insert_unique 26ms 0.15% 12.07% 1063ms 6.08% std::__new_allocator::allocate (inline) 0 0% 12.07% 1061ms 6.07% std::allocator_traits::allocate (inline) 1015ms 5.81% 17.88% 1015ms 5.81% N_VBufUnpack_Serial 0 0% 17.88% 917ms 5.25% std::set::count (inline) 1ms 0.0057% 17.89% 872ms 4.99% triangulate 41ms 0.23% 18.12% 821ms 4.70% cvLsSolve 0 0% 18.12% 783ms 4.48% delaunay 1ms 0.0057% 18.13% 782ms 4.48% divconqdelaunay 104ms 0.6% 18.72% 768ms 4.40% N_VLinearSum_Serial 15ms 0.086% 18.81% 751ms 4.30% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 6ms 0.034% 18.84% 748ms 4.28% CvodeAdaptor::SetupCvode 47ms 0.27% 19.11% 709ms 4.06% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.11% 706ms 4.04% std::_Rb_tree::_M_create_node (inline) 700ms 4.01% 23.12% 700ms 4.01% std::_Rb_tree::_S_right (inline) 0 0% 23.12% 694ms 3.97% std::_Rb_tree::_M_get_node (inline) 58ms 0.33% 23.45% 680ms 3.89% N_VLinearSum 1ms 0.0057% 23.45% 664ms 3.80% SUNLinSolSetup 17ms 0.097% 23.55% 663ms 3.79% SUNLinSolSetup_Dense 169ms 0.97% 24.52% 657ms 3.76% __GI___libc_free 10ms 0.057% 24.58% 648ms 3.71% SUNLinSolSolve 1ms 0.0057% 24.58% 640ms 3.66% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.11% 24.70% 638ms 3.65% SUNLinSolSolve_Dense 0 0% 24.70% 632ms 3.62% std::_Rb_tree::_Alloc_node::operator() (inline) 44ms 0.25% 24.95% 632ms 3.62% std::map::operator[] (partial-inline) 370ms 2.12% 27.07% 629ms 3.60% _int_malloc 7ms 0.04% 27.11% 621ms 3.55% CellPopulationElementWriter::Visit 7ms 0.04% 27.15% 610ms 3.49% CellPropertyCollection::GetPropertiesType (inline) 174ms 1% 28.14% 605ms 3.46% __dynamic_cast 602ms 3.45% 31.59% 602ms 3.45% SUNDlsMat_denseGETRF 159ms 0.91% 32.50% 602ms 3.45% cvRestore 20ms 0.11% 32.61% 598ms 3.42% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.023% 32.64% 582ms 3.33% cvLsDQJac 59ms 0.34% 32.97% 578ms 3.31% cvLsDenseDQJac 0 0% 32.97% 574ms 3.29% std::map::find (inline) 4ms 0.023% 33.00% 567ms 3.25% Element::Element 20ms 0.11% 33.11% 553ms 3.17% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 14ms 0.08% 33.19% 551ms 3.15% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.057% 33.25% 550ms 3.15% Element::RegisterWithNodes (inline) 26ms 0.15% 33.40% 539ms 3.08% Node::AddElement 522ms 2.99% 36.38% 522ms 2.99% SUNDlsMat_denseGETRS 25ms 0.14% 36.53% 519ms 2.97% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.029% 36.56% 518ms 2.96% MutableMesh::ReIndex 8ms 0.046% 36.60% 483ms 2.76% Cylindrical2dMesh::CorrectNonPeriodicMesh 391ms 2.24% 38.84% 479ms 2.74% _int_free 15ms 0.086% 38.93% 479ms 2.74% std::less::operator() (inline) 2ms 0.011% 38.94% 476ms 2.72% AbstractCellProperty::IsSubType (inline) 0 0% 38.94% 476ms 2.72% std::_Rb_tree::lower_bound (inline) 0 0% 38.94% 476ms 2.72% std::map::lower_bound (inline) 2ms 0.011% 38.95% 470ms 2.69% SUNMatScaleAddI 468ms 2.68% 41.63% 468ms 2.68% SUNMatScaleAddI_Dense 0 0% 41.63% 467ms 2.67% std::_Rb_tree::_M_drop_node (inline) 464ms 2.66% 44.28% 464ms 2.66% std::operator< (inline) 72ms 0.41% 44.69% 445ms 2.55% std::_Rb_tree::_M_erase 38ms 0.22% 44.91% 445ms 2.55% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.086% 45.00% 432ms 2.47% std::__new_allocator::deallocate (inline) 33ms 0.19% 45.19% 429ms 2.46% CVodeSetLinearSolver 16ms 0.092% 45.28% 429ms 2.46% CvodeRhsAdaptor 0 0% 45.28% 427ms 2.44% std::ostream::operator<< (inline) 0 0% 45.28% 425ms 2.43% std::allocator_traits::deallocate (inline) 44ms 0.25% 45.53% 424ms 2.43% N_VWrmsNorm 43ms 0.25% 45.78% 422ms 2.42% std::ostream::_M_insert 418ms 2.39% 48.17% 418ms 2.39% __strcmp_evex 0 0% 48.17% 418ms 2.39% std::set::~set (inline) 59ms 0.34% 48.51% 410ms 2.35% N_VScale_Serial 59ms 0.34% 48.84% 408ms 2.34% N_VScale 12ms 0.069% 48.91% 400ms 2.29% std::_Rb_tree::erase 0 0% 48.91% 398ms 2.28% std::set::erase (inline) 10ms 0.057% 48.97% 392ms 2.24% Node::RemoveElement 4ms 0.023% 48.99% 392ms 2.24% SUNMatCopy 380ms 2.17% 51.17% 388ms 2.22% SUNMatCopy_Dense 79ms 0.45% 51.62% 380ms 2.17% N_VWrmsNorm_Serial 14ms 0.08% 51.70% 378ms 2.16% divconqrecurse 4ms 0.023% 51.72% 374ms 2.14% Cell::GetMutationState 160ms 0.92% 52.64% 372ms 2.13% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 52.64% 368ms 2.11% std::_Rb_tree::_M_put_node (inline) 0 0% 52.64% 367ms 2.10% std::_Vector_base::_M_allocate (inline) 182ms 1.04% 53.68% 366ms 2.09% WntCellCycleOdeSystem::EvaluateYDerivatives 13ms 0.074% 53.75% 359ms 2.05% N_VCloneEmpty_Serial 110ms 0.63% 54.38% 351ms 2.01% mergehulls 19ms 0.11% 54.49% 344ms 1.97% Element::ResetIndex 20ms 0.11% 54.61% 337ms 1.93% AbstractCellProperty::IsType (inline) 1ms 0.0057% 54.61% 337ms 1.93% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.011% 54.62% 335ms 1.92% AbstractCellPopulation::Iterator::operator++ (inline) 19ms 0.11% 54.73% 332ms 1.90% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 40ms 0.23% 54.96% 327ms 1.87% AbstractCellPopulation::Iterator::IsRealCell (inline) 29ms 0.17% 55.13% 321ms 1.84% cvEwtSet 4ms 0.023% 55.15% 306ms 1.75% Cell::GetCellProliferativeType 7ms 0.04% 55.19% 301ms 1.72% boost::detail::shared_count::~shared_count (inline) 0 0% 55.19% 301ms 1.72% boost::shared_ptr::~shared_ptr (inline) 124ms 0.71% 55.90% 295ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 284ms 1.63% 57.53% 290ms 1.66% boost::detail::sp_counted_base::release 10ms 0.057% 57.58% 275ms 1.57% std::vector::push_back (inline) 1ms 0.0057% 57.59% 274ms 1.57% NodeLocationWriter::Visit 9ms 0.052% 57.64% 273ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.046% 57.69% 267ms 1.53% N_VClone 262ms 1.50% 59.19% 262ms 1.50% N_VWSqrSumLocal_Serial 8ms 0.046% 59.23% 261ms 1.49% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.074% 59.31% 260ms 1.49% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.023% 59.33% 259ms 1.48% N_VClone_Serial 11ms 0.063% 59.39% 258ms 1.48% std::vector::_M_realloc_insert 19ms 0.11% 59.50% 249ms 1.43% std::num_put::_M_insert_float 6ms 0.034% 59.54% 247ms 1.41% AbstractCellPopulation::IsCellAttachedToLocationIndex 34ms 0.19% 59.73% 247ms 1.41% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.011% 59.74% 247ms 1.41% alternateaxes 0 0% 59.74% 247ms 1.41% std::set::set (inline) 245ms 1.40% 61.14% 245ms 1.40% [libchaste_mesh.so] 224ms 1.28% 62.43% 245ms 1.40% vertexmedian 23ms 0.13% 62.56% 239ms 1.37% std::_Rb_tree::_M_copy (inline) 0 0% 62.56% 238ms 1.36% MeshBasedCellPopulation::GetDampingConstant 2ms 0.011% 62.57% 236ms 1.35% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0057% 62.57% 230ms 1.32% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 229ms 1.31% 63.89% 229ms 1.31% N_VCopyOps 0 0% 63.89% 227ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 0 0% 63.89% 220ms 1.26% OffLatticeSimulation::ApplyBoundaries 47ms 0.27% 64.15% 218ms 1.25% AbstractCellProperty::IsSame 14ms 0.08% 64.23% 218ms 1.25% AbstractTetrahedralElement::CalculateJacobian 5ms 0.029% 64.26% 214ms 1.22% Element::MarkAsDeleted 5ms 0.029% 64.29% 207ms 1.18% std::__cxx11::collate::do_transform 92ms 0.53% 64.82% 205ms 1.17% std::_Rb_tree::_M_clone_node (inline) 5ms 0.029% 64.85% 196ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 196ms 1.12% 65.97% 196ms 1.12% [libchaste_cell_based.so] 2ms 0.011% 65.98% 196ms 1.12% ___vsnprintf 1ms 0.0057% 65.99% 194ms 1.11% __vsnprintf_internal (inline) 22ms 0.13% 66.11% 193ms 1.10% __printf_buffer 1ms 0.0057% 66.12% 192ms 1.10% TetrahedralMesh::Clear 1ms 0.0057% 66.12% 191ms 1.09% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 137ms 0.78% 66.91% 171ms 0.98% malloc_consolidate 16ms 0.092% 67.00% 171ms 0.98% std::type_info::operator== (inline) 85ms 0.49% 67.49% 167ms 0.96% AbstractElement::GetNodeGlobalIndex 9ms 0.052% 67.54% 161ms 0.92% Cell::SetCellProliferativeType 34ms 0.19% 67.73% 160ms 0.92% N_VScaleAddMulti 18ms 0.1% 67.83% 159ms 0.91% AbstractTetrahedralElement::RefreshJacobian 2ms 0.011% 67.85% 158ms 0.9% CellPropertyCollection::HasProperty 158ms 0.9% 68.75% 158ms 0.9% std::_Rb_tree_insert_and_rebalance 0 0% 68.75% 156ms 0.89% Cell::HasCellProperty (inline) 8ms 0.046% 68.80% 155ms 0.89% __printf_fp_l_buffer 0 0% 68.80% 155ms 0.89% __printf_fp_spec (inline) 8ms 0.046% 68.84% 152ms 0.87% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 150ms 0.86% 69.70% 150ms 0.86% incircle 6ms 0.034% 69.73% 147ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0057% 69.74% 147ms 0.84% boost::numeric::ublas::vector_assign (inline) 12ms 0.069% 69.81% 144ms 0.82% N_VMake_Serial 87ms 0.5% 70.31% 143ms 0.82% SUNDenseMatrix 121ms 0.69% 71.00% 142ms 0.81% vertexsort 141ms 0.81% 71.81% 141ms 0.81% std::vector::size (inline) 53ms 0.3% 72.11% 140ms 0.8% __printf_fp_buffer_1 125ms 0.72% 72.83% 139ms 0.8% N_VNewEmpty 0 0% 72.83% 138ms 0.79% AbstractCellBasedSimulation::DoCellRemoval (inline) 73ms 0.42% 73.24% 135ms 0.77% std::_Rb_tree::equal_range (inline) 9ms 0.052% 73.29% 133ms 0.76% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 95ms 0.54% 73.84% 132ms 0.76% N_VNewEmpty_Serial 131ms 0.75% 74.59% 131ms 0.75% std::_Rb_tree::_S_left (inline) 54ms 0.31% 74.90% 129ms 0.74% AbstractElement::GetNodeLocation 0 0% 74.90% 129ms 0.74% CellProliferativeTypesWriter::VisitCell 5ms 0.029% 74.93% 127ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.034% 74.96% 121ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 24ms 0.14% 75.10% 119ms 0.68% TetrahedralMesh::EdgesEnd (partial-inline) 17ms 0.097% 75.19% 116ms 0.66% cvLsFree 4ms 0.023% 75.22% 114ms 0.65% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 15ms 0.086% 75.30% 113ms 0.65% N_VAbs 4ms 0.023% 75.33% 112ms 0.64% N_VCloneEmpty 3ms 0.017% 75.34% 112ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.34% 110ms 0.63% tcache_get (inline) 110ms 0.63% 75.97% 110ms 0.63% tcache_get_n (inline) 3ms 0.017% 75.99% 107ms 0.61% Cylindrical2dMesh::CreateMirrorNodes 2ms 0.011% 76.00% 107ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.017% 76.02% 106ms 0.61% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 3ms 0.017% 76.04% 106ms 0.61% Node::~Node 105ms 0.6% 76.64% 105ms 0.6% unlink_chunk 33ms 0.19% 76.83% 103ms 0.59% boost::numeric::ublas::indexing_vector_assign 63ms 0.36% 77.19% 102ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 30ms 0.17% 77.36% 102ms 0.58% std::num_put::_M_insert_int 0 0% 77.36% 100ms 0.57% std::__new_allocator::destroy (inline) 0 0% 77.36% 100ms 0.57% std::allocator_traits::destroy (inline) 0 0% 77.36% 99ms 0.57% std::_Rb_tree::_M_destroy_node (inline) 98ms 0.56% 77.92% 98ms 0.56% N_VAbs_Serial 98ms 0.56% 78.48% 98ms 0.56% std::_Rb_tree_rebalance_for_erase 15ms 0.086% 78.57% 97ms 0.56% cvLsInitialize 1ms 0.0057% 78.57% 96ms 0.55% AbstractCellBasedWriter::OpenOutputFileForAppend 11ms 0.063% 78.63% 96ms 0.55% N_VInv 95ms 0.54% 79.18% 95ms 0.54% std::_Rb_tree_increment 2ms 0.011% 79.19% 93ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0057% 79.20% 92ms 0.53% OutputFileHandler::OpenOutputFile 91ms 0.52% 79.72% 91ms 0.52% Node::GetIndex 30ms 0.17% 79.89% 91ms 0.52% std::__ostream_insert 0 0% 79.89% 90ms 0.52% std::vector::vector (inline) 89ms 0.51% 80.40% 89ms 0.51% [libstdc++.so.6.0.33] 52ms 0.3% 80.69% 88ms 0.5% AbstractTetrahedralMesh::GetElement 3ms 0.017% 80.71% 88ms 0.5% SUNMatZero