File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13868ms, 81.27% of 17065ms total Dropped 853 nodes (cum <= 85.33ms) flat flat% sum% cum cum% 0 0% 0% 17024ms 99.76% __libc_start_call_main 0 0% 0% 17024ms 99.76% __libc_start_main_impl 0 0% 0% 17024ms 99.76% _start 0 0% 0% 17001ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 17001ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 17001ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 17001ms 99.62% main 0 0% 0% 16966ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16966ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16966ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0059% 0.0059% 16943ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0.0059% 12618ms 73.94% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.012% 0.018% 7320ms 42.89% AbstractCellBasedSimulation::DoCellBirth 5ms 0.029% 0.047% 7218ms 42.30% Cell::ReadyToDivide 1ms 0.0059% 0.053% 7150ms 41.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0059% 0.059% 6989ms 40.96% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.064% 0.12% 6981ms 40.91% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.012% 0.13% 6964ms 40.81% CellCycleModelOdeHandler::SolveOdeToTime 3ms 0.018% 0.15% 6816ms 39.94% CvodeAdaptor::Solve 53ms 0.31% 0.46% 5933ms 34.77% CVode 60ms 0.35% 0.81% 5357ms 31.39% CVodeFree 0 0% 0.81% 5178ms 30.34% MeshBasedCellPopulation::Update 146ms 0.86% 1.67% 4227ms 24.77% cvRescale 1ms 0.0059% 1.68% 3918ms 22.96% Cylindrical2dMesh::ReMesh 13ms 0.076% 1.75% 3821ms 22.39% SUNNonlinSolSolve 60ms 0.35% 2.10% 3808ms 22.31% SUNNonlinSolSolve_Newton 79ms 0.46% 2.57% 3635ms 21.30% cvNlsInit 0 0% 2.57% 2479ms 14.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.082% 2.65% 2289ms 13.41% cvLsSetup 0 0% 2.65% 2147ms 12.58% MutableMesh::ReMesh 0 0% 2.65% 2107ms 12.35% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 2.65% 2071ms 12.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 864ms 5.06% 7.71% 1865ms 10.93% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.71% 1842ms 10.79% AbstractCellPopulation::WriteResultsToFiles 157ms 0.92% 8.63% 1821ms 10.67% TetrahedralMesh::EdgeIterator::operator++ 12ms 0.07% 8.70% 1556ms 9.12% cvLsDQJtimes 50ms 0.29% 9.00% 1480ms 8.67% std::_Rb_tree::find (inline) 0 0% 9.00% 1213ms 7.11% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.035% 9.03% 1177ms 6.90% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 54ms 0.32% 9.35% 1130ms 6.62% operator new 402ms 2.36% 11.70% 1126ms 6.60% __GI___libc_malloc 21ms 0.12% 11.83% 1091ms 6.39% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.064% 11.89% 1077ms 6.31% std::set::insert (inline) 11ms 0.064% 11.95% 1065ms 6.24% TetrahedralMesh::ImportFromMesher 21ms 0.12% 12.08% 1065ms 6.24% std::_Rb_tree::_M_insert_unique 28ms 0.16% 12.24% 962ms 5.64% std::__new_allocator::allocate (inline) 0 0% 12.24% 961ms 5.63% std::allocator_traits::allocate (inline) 945ms 5.54% 17.78% 945ms 5.54% N_VBufUnpack_Serial 0 0% 17.78% 917ms 5.37% std::set::count (inline) 4ms 0.023% 17.80% 850ms 4.98% triangulate 19ms 0.11% 17.91% 786ms 4.61% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 49ms 0.29% 18.20% 764ms 4.48% cvLsSolve 0 0% 18.20% 763ms 4.47% delaunay 5ms 0.029% 18.23% 763ms 4.47% divconqdelaunay 3ms 0.018% 18.25% 761ms 4.46% CvodeAdaptor::SetupCvode 117ms 0.69% 18.93% 731ms 4.28% N_VLinearSum_Serial 4ms 0.023% 18.96% 713ms 4.18% SUNLinSolSetup 19ms 0.11% 19.07% 709ms 4.15% SUNLinSolSetup_Dense 38ms 0.22% 19.29% 664ms 3.89% std::_Rb_tree::_M_insert_ (inline) 661ms 3.87% 23.16% 661ms 3.87% std::_Rb_tree::_S_right (inline) 0 0% 23.16% 659ms 3.86% std::_Rb_tree::_M_create_node (inline) 64ms 0.38% 23.54% 646ms 3.79% std::map::operator[] (partial-inline) 73ms 0.43% 23.97% 643ms 3.77% N_VLinearSum 0 0% 23.97% 643ms 3.77% std::_Rb_tree::_M_get_node (inline) 639ms 3.74% 27.71% 639ms 3.74% SUNDlsMat_denseGETRF 181ms 1.06% 28.77% 637ms 3.73% cvRestore 2ms 0.012% 28.78% 633ms 3.71% CellPopulationElementWriter::Visit 5ms 0.029% 28.81% 628ms 3.68% AbstractTwoBodyInteractionForce::AddForceContribution 388ms 2.27% 31.09% 605ms 3.55% _int_malloc 6ms 0.035% 31.12% 598ms 3.50% cvLsDQJac 12ms 0.07% 31.19% 597ms 3.50% MeshBasedCellPopulation::AcceptCellWriter 167ms 0.98% 32.17% 594ms 3.48% __dynamic_cast 51ms 0.3% 32.47% 591ms 3.46% cvLsDenseDQJac 161ms 0.94% 33.41% 587ms 3.44% __GI___libc_free 0 0% 33.41% 583ms 3.42% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.023% 33.44% 579ms 3.39% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.053% 33.49% 578ms 3.39% AbstractCellPopulation::GetCellUsingLocationIndex 23ms 0.13% 33.62% 571ms 3.35% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.047% 33.67% 571ms 3.35% SUNLinSolSolve 21ms 0.12% 33.79% 563ms 3.30% SUNLinSolSolve_Dense 0 0% 33.79% 561ms 3.29% std::map::find (inline) 20ms 0.12% 33.91% 545ms 3.19% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 6ms 0.035% 33.95% 545ms 3.19% Element::Element 5ms 0.029% 33.98% 522ms 3.06% Element::RegisterWithNodes (inline) 22ms 0.13% 34.10% 513ms 3.01% Node::AddElement 16ms 0.094% 34.20% 512ms 3.00% std::less::operator() (inline) 496ms 2.91% 37.11% 496ms 2.91% std::operator< (inline) 0 0% 37.11% 475ms 2.78% std::_Rb_tree::lower_bound (inline) 0 0% 37.11% 475ms 2.78% std::map::lower_bound (inline) 1ms 0.0059% 37.11% 466ms 2.73% AbstractCellProperty::IsSubType (inline) 6ms 0.035% 37.15% 458ms 2.68% MutableMesh::ReIndex 1ms 0.0059% 37.15% 457ms 2.68% SUNMatScaleAddI 456ms 2.67% 39.82% 456ms 2.67% SUNMatScaleAddI_Dense 9ms 0.053% 39.88% 449ms 2.63% Cylindrical2dMesh::CorrectNonPeriodicMesh 33ms 0.19% 40.07% 444ms 2.60% N_VWrmsNorm 442ms 2.59% 42.66% 442ms 2.59% SUNDlsMat_denseGETRS 21ms 0.12% 42.78% 428ms 2.51% CvodeRhsAdaptor 0 0% 42.78% 427ms 2.50% std::_Rb_tree::_M_drop_node (inline) 345ms 2.02% 44.81% 418ms 2.45% _int_free 28ms 0.16% 44.97% 417ms 2.44% CVodeSetLinearSolver 83ms 0.49% 45.46% 411ms 2.41% N_VWrmsNorm_Serial 409ms 2.40% 47.85% 409ms 2.40% __strcmp_evex 4ms 0.023% 47.88% 407ms 2.38% SUNMatCopy 11ms 0.064% 47.94% 406ms 2.38% std::_Rb_tree::erase 1ms 0.0059% 47.95% 405ms 2.37% std::set::erase (inline) 64ms 0.38% 48.32% 404ms 2.37% N_VScale 392ms 2.30% 50.62% 403ms 2.36% SUNMatCopy_Dense 8ms 0.047% 50.67% 403ms 2.36% std::__new_allocator::deallocate (inline) 9ms 0.053% 50.72% 400ms 2.34% Node::RemoveElement 5ms 0.029% 50.75% 399ms 2.34% divconqrecurse 0 0% 50.75% 394ms 2.31% std::allocator_traits::deallocate (inline) 14ms 0.082% 50.83% 391ms 2.29% N_VCloneEmpty_Serial 60ms 0.35% 51.18% 391ms 2.29% std::_Rb_tree::~_Rb_tree (inline) 0 0% 51.18% 388ms 2.27% std::ostream::operator<< (inline) 54ms 0.32% 51.50% 385ms 2.26% N_VScale_Serial 125ms 0.73% 52.23% 384ms 2.25% mergehulls 59ms 0.35% 52.58% 382ms 2.24% std::_Rb_tree::_M_erase 48ms 0.28% 52.86% 382ms 2.24% std::ostream::_M_insert 147ms 0.86% 53.72% 380ms 2.23% std::_Rb_tree::_M_get_insert_unique_pos 163ms 0.96% 54.67% 369ms 2.16% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 54.67% 368ms 2.16% std::set::~set (inline) 21ms 0.12% 54.80% 352ms 2.06% AbstractCellProperty::IsType (inline) 0 0% 54.80% 336ms 1.97% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.12% 54.91% 335ms 1.96% Element::ResetIndex 35ms 0.21% 55.12% 334ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 55.12% 333ms 1.95% Cell::GetCellProliferativeType 3ms 0.018% 55.14% 332ms 1.95% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 55.14% 330ms 1.93% std::_Rb_tree::_M_put_node (inline) 31ms 0.18% 55.32% 327ms 1.92% cvEwtSet 1ms 0.0059% 55.32% 319ms 1.87% std::_Vector_base::_M_allocate (inline) 10ms 0.059% 55.38% 318ms 1.86% boost::detail::shared_count::~shared_count (inline) 0 0% 55.38% 318ms 1.86% boost::shared_ptr::~shared_ptr (inline) 139ms 0.81% 56.20% 317ms 1.86% __cxxabiv1::__si_class_type_info::__do_dyncast 298ms 1.75% 57.94% 301ms 1.76% boost::detail::sp_counted_base::release 22ms 0.13% 58.07% 299ms 1.75% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 58.07% 298ms 1.75% Cell::GetMutationState 12ms 0.07% 58.14% 287ms 1.68% N_VClone 283ms 1.66% 59.80% 283ms 1.66% N_VWSqrSumLocal_Serial 10ms 0.059% 59.86% 283ms 1.66% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.018% 59.88% 275ms 1.61% N_VClone_Serial 13ms 0.076% 59.95% 272ms 1.59% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0059% 59.96% 266ms 1.56% std::set::set (inline) 10ms 0.059% 60.02% 257ms 1.51% std::vector::push_back (inline) 4ms 0.023% 60.04% 256ms 1.50% alternateaxes 26ms 0.15% 60.19% 253ms 1.48% std::_Rb_tree::_M_copy (inline) 233ms 1.37% 61.56% 252ms 1.48% vertexmedian 1ms 0.0059% 61.56% 251ms 1.47% NodeLocationWriter::Visit 34ms 0.2% 61.76% 250ms 1.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 11ms 0.064% 61.83% 248ms 1.45% std::_Rb_tree::_M_erase_aux (inline) 0 0% 61.83% 246ms 1.44% OffLatticeSimulation::ApplyBoundaries 242ms 1.42% 63.25% 242ms 1.42% N_VCopyOps 12ms 0.07% 63.32% 236ms 1.38% std::vector::_M_realloc_insert 9ms 0.053% 63.37% 235ms 1.38% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.029% 63.40% 234ms 1.37% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.082% 63.48% 224ms 1.31% std::num_put::_M_insert_float 101ms 0.59% 64.07% 221ms 1.30% std::_Rb_tree::_M_clone_node (inline) 8ms 0.047% 64.12% 218ms 1.28% AbstractTetrahedralElement::CalculateJacobian 215ms 1.26% 65.38% 215ms 1.26% [libchaste_mesh.so] 7ms 0.041% 65.42% 214ms 1.25% Element::MarkAsDeleted 0 0% 65.42% 214ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 214ms 1.25% 66.67% 214ms 1.25% [libchaste_cell_based.so] 34ms 0.2% 66.87% 207ms 1.21% AbstractCellProperty::IsSame 1ms 0.0059% 66.88% 193ms 1.13% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0059% 66.89% 192ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.047% 66.93% 188ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.023% 66.96% 183ms 1.07% std::__cxx11::collate::do_transform 71ms 0.42% 67.37% 178ms 1.04% AbstractElement::GetNodeGlobalIndex 27ms 0.16% 67.53% 176ms 1.03% N_VScaleAddMulti 1ms 0.0059% 67.54% 174ms 1.02% ___vsnprintf 0 0% 67.54% 173ms 1.01% __vsnprintf_internal (inline) 17ms 0.1% 67.64% 173ms 1.01% std::type_info::operator== (inline) 17ms 0.1% 67.74% 171ms 1.00% __printf_buffer 170ms 1% 68.73% 170ms 1% std::_Rb_tree_insert_and_rebalance 33ms 0.19% 68.92% 167ms 0.98% AbstractTetrahedralElement::RefreshJacobian 167ms 0.98% 69.90% 167ms 0.98% std::vector::size (inline) 149ms 0.87% 70.78% 166ms 0.97% N_VNewEmpty 159ms 0.93% 71.71% 159ms 0.93% incircle 2ms 0.012% 71.72% 158ms 0.93% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.012% 71.73% 152ms 0.89% CellPropertyCollection::HasProperty 0 0% 71.73% 151ms 0.88% Cell::HasCellProperty (inline) 78ms 0.46% 72.19% 145ms 0.85% std::_Rb_tree::equal_range (inline) 1ms 0.0059% 72.19% 144ms 0.84% CellProliferativeTypesWriter::VisitCell 1ms 0.0059% 72.20% 142ms 0.83% __printf_fp_l_buffer 0 0% 72.20% 142ms 0.83% __printf_fp_spec (inline) 103ms 0.6% 72.80% 141ms 0.83% malloc_consolidate 12ms 0.07% 72.87% 140ms 0.82% N_VMake_Serial 1ms 0.0059% 72.88% 139ms 0.81% TetrahedralMesh::Clear 2ms 0.012% 72.89% 138ms 0.81% Cell::SetCellProliferativeType 1ms 0.0059% 72.90% 137ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.041% 72.94% 137ms 0.8% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 52ms 0.3% 73.24% 135ms 0.79% __printf_fp_buffer_1 1ms 0.0059% 73.25% 132ms 0.77% boost::numeric::ublas::vector_assign (inline) 3ms 0.018% 73.27% 131ms 0.77% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.023% 73.29% 129ms 0.76% N_VCloneEmpty 129ms 0.76% 74.05% 129ms 0.76% std::_Rb_tree::_S_left (inline) 85ms 0.5% 74.54% 128ms 0.75% N_VNewEmpty_Serial 2ms 0.012% 74.56% 123ms 0.72% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.029% 74.59% 123ms 0.72% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 63ms 0.37% 74.95% 121ms 0.71% SUNDenseMatrix 0 0% 74.95% 120ms 0.7% AbstractCellBasedSimulation::DoCellRemoval (inline) 47ms 0.28% 75.23% 120ms 0.7% AbstractElement::GetNodeLocation 16ms 0.094% 75.32% 116ms 0.68% TetrahedralMesh::EdgesEnd 4ms 0.023% 75.35% 115ms 0.67% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 8ms 0.047% 75.39% 115ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.018% 75.41% 113ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.035% 75.45% 113ms 0.66% N_VInv 0 0% 75.45% 108ms 0.63% tcache_get (inline) 108ms 0.63% 76.08% 108ms 0.63% tcache_get_n (inline) 107ms 0.63% 76.71% 107ms 0.63% N_VInv_Serial 2ms 0.012% 76.72% 107ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 58ms 0.34% 77.06% 106ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 23ms 0.13% 77.19% 103ms 0.6% MeshBasedCellPopulation::SpringIterator::SpringIterator 90ms 0.53% 77.72% 101ms 0.59% vertexsort 69ms 0.4% 78.12% 100ms 0.59% AbstractTetrahedralMesh::GetElement 1ms 0.0059% 78.13% 98ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 0 0% 78.13% 98ms 0.57% std::__new_allocator::destroy (inline) 0 0% 78.13% 98ms 0.57% std::allocator_traits::destroy (inline) 0 0% 78.13% 97ms 0.57% std::_Rb_tree::_M_destroy_node (inline) 96ms 0.56% 78.69% 96ms 0.56% std::_Rb_tree_increment 95ms 0.56% 79.25% 95ms 0.56% Node::GetIndex 95ms 0.56% 79.81% 95ms 0.56% counterclockwise 46ms 0.27% 80.08% 95ms 0.56% std::__ostream_insert 76ms 0.45% 80.52% 94ms 0.55% TetrahedralMesh::EdgeIterator::EdgeIterator 3ms 0.018% 80.54% 94ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 33ms 0.19% 80.73% 90ms 0.53% boost::numeric::ublas::indexing_vector_assign 6ms 0.035% 80.77% 89ms 0.52% N_VAbs 7ms 0.041% 80.81% 89ms 0.52% cvLsFree 10ms 0.059% 80.87% 88ms 0.52% N_VConst 68ms 0.4% 81.27% 87ms 0.51% SUNMatGetID