File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12653ms, 77.05% of 16421ms total Dropped 868 nodes (cum <= 82.11ms) flat flat% sum% cum cum% 0 0% 0% 16374ms 99.71% __libc_start_call_main 0 0% 0% 16374ms 99.71% __libc_start_main_impl 0 0% 0% 16374ms 99.71% _start 0 0% 0% 16353ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16353ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16353ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16353ms 99.59% main 0 0% 0% 16314ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16314ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16314ms 99.35% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16289ms 99.20% AbstractCellBasedSimulation::Solve 0 0% 0% 11804ms 71.88% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.03% 0.03% 6515ms 39.67% AbstractCellBasedSimulation::DoCellBirth 13ms 0.079% 0.11% 6412ms 39.05% Cell::ReadyToDivide 5ms 0.03% 0.14% 6333ms 38.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0061% 0.15% 6116ms 37.24% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.1% 0.25% 6102ms 37.16% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.024% 0.27% 6078ms 37.01% CellCycleModelOdeHandler::SolveOdeToTime 5ms 0.03% 0.3% 5897ms 35.91% CvodeAdaptor::Solve 74ms 0.45% 0.76% 5403ms 32.90% CVode 0 0% 0.76% 5175ms 31.51% MeshBasedCellPopulation::Update 57ms 0.35% 1.10% 4865ms 29.63% CVodeFree 4ms 0.024% 1.13% 3968ms 24.16% Cylindrical2dMesh::ReMesh 150ms 0.91% 2.04% 3734ms 22.74% cvRescale 2ms 0.012% 2.05% 3413ms 20.78% SUNNonlinSolSolve 36ms 0.22% 2.27% 3411ms 20.77% SUNNonlinSolSolve_Newton 69ms 0.42% 2.69% 3307ms 20.14% cvNlsInit 1ms 0.0061% 2.70% 2467ms 15.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.70% 2194ms 13.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0061% 2.70% 2183ms 13.29% MutableMesh::ReMesh 8ms 0.049% 2.75% 2135ms 13.00% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 2.75% 2015ms 12.27% AbstractCellPopulation::WriteResultsToFiles 22ms 0.13% 2.89% 2013ms 12.26% cvLsSetup 764ms 4.65% 7.54% 1821ms 11.09% std::_Rb_tree::_M_lower_bound (inline) 165ms 1.00% 8.54% 1681ms 10.24% TetrahedralMesh::EdgeIterator::operator++ 10ms 0.061% 8.60% 1463ms 8.91% cvLsDQJtimes 56ms 0.34% 8.95% 1344ms 8.18% std::_Rb_tree::find (inline) 0 0% 8.95% 1164ms 7.09% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.037% 8.98% 1134ms 6.91% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 58ms 0.35% 9.34% 1134ms 6.91% operator new 265ms 1.61% 10.95% 1121ms 6.83% __GI___libc_malloc 12ms 0.073% 11.02% 1093ms 6.66% TetrahedralMesh::ImportFromMesher 10ms 0.061% 11.08% 1053ms 6.41% std::set::insert (inline) 18ms 0.11% 11.19% 1043ms 6.35% std::_Rb_tree::_M_insert_unique 10ms 0.061% 11.25% 1023ms 6.23% MeshBasedCellPopulation::SpringIterator::operator++ 43ms 0.26% 11.52% 995ms 6.06% std::__new_allocator::allocate (inline) 0 0% 11.52% 992ms 6.04% std::allocator_traits::allocate (inline) 0 0% 11.52% 839ms 5.11% triangulate 0 0% 11.52% 816ms 4.97% std::set::count (inline) 0 0% 11.52% 768ms 4.68% delaunay 6ms 0.037% 11.55% 768ms 4.68% divconqdelaunay 3ms 0.018% 11.57% 742ms 4.52% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 56ms 0.34% 11.91% 733ms 4.46% N_VWrmsNorm 413ms 2.52% 14.43% 720ms 4.38% _int_malloc 717ms 4.37% 18.79% 717ms 4.37% std::_Rb_tree::_S_right (inline) 3ms 0.018% 18.81% 704ms 4.29% AbstractTwoBodyInteractionForce::AddForceContribution 51ms 0.31% 19.12% 688ms 4.19% std::map::operator[] (partial-inline) 102ms 0.62% 19.74% 677ms 4.12% N_VWrmsNorm_Serial 8ms 0.049% 19.79% 666ms 4.06% CellPopulationElementWriter::Visit 34ms 0.21% 20.00% 661ms 4.03% cvLsSolve 21ms 0.13% 20.13% 658ms 4.01% std::less::operator() (inline) 637ms 3.88% 24.01% 637ms 3.88% std::operator< (inline) 177ms 1.08% 25.08% 632ms 3.85% cvRestore 34ms 0.21% 25.29% 631ms 3.84% std::_Rb_tree::_M_insert_ (inline) 3ms 0.018% 25.31% 630ms 3.84% CellPropertyCollection::GetPropertiesType (inline) 0 0% 25.31% 619ms 3.77% std::_Rb_tree::_M_create_node (inline) 180ms 1.10% 26.41% 612ms 3.73% __dynamic_cast 603ms 3.67% 30.08% 603ms 3.67% N_VBufUnpack_Serial 0 0% 30.08% 595ms 3.62% std::_Rb_tree::_M_get_node (inline) 5ms 0.03% 30.11% 586ms 3.57% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.13% 30.24% 585ms 3.56% AbstractCellPopulation::GetCellUsingLocationIndex 29ms 0.18% 30.42% 576ms 3.51% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 30.42% 570ms 3.47% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 30.42% 561ms 3.42% std::_Rb_tree::lower_bound (inline) 0 0% 30.42% 561ms 3.42% std::map::lower_bound (inline) 129ms 0.79% 31.20% 558ms 3.40% N_VLinearSum_Serial 3ms 0.018% 31.22% 550ms 3.35% cvLsDQJac 53ms 0.32% 31.54% 547ms 3.33% cvLsDenseDQJac 11ms 0.067% 31.61% 540ms 3.29% SUNLinSolSolve 13ms 0.079% 31.69% 537ms 3.27% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.03% 31.72% 532ms 3.24% Element::Element 20ms 0.12% 31.84% 529ms 3.22% SUNLinSolSolve_Dense 0 0% 31.84% 524ms 3.19% std::map::find (inline) 523ms 3.18% 35.03% 523ms 3.18% N_VWSqrSumLocal_Serial 10ms 0.061% 35.09% 519ms 3.16% SUNLinSolSetup 10ms 0.061% 35.15% 516ms 3.14% MutableMesh::ReIndex 9ms 0.055% 35.20% 509ms 3.10% SUNLinSolSetup_Dense 193ms 1.18% 36.38% 507ms 3.09% __GI___libc_free 30ms 0.18% 36.56% 503ms 3.06% N_VLinearSum 5ms 0.03% 36.59% 502ms 3.06% CvodeRhsAdaptor 11ms 0.067% 36.66% 492ms 3.00% Element::RegisterWithNodes (inline) 4ms 0.024% 36.68% 487ms 2.97% AbstractCellProperty::IsSubType (inline) 3ms 0.018% 36.70% 487ms 2.97% std::ostream::operator<< (inline) 57ms 0.35% 37.05% 484ms 2.95% std::ostream::_M_insert 483ms 2.94% 39.99% 483ms 2.94% SUNDlsMat_denseGETRF 5ms 0.03% 40.02% 473ms 2.88% Node::AddElement 8ms 0.049% 40.07% 448ms 2.73% Cylindrical2dMesh::CorrectNonPeriodicMesh 182ms 1.11% 41.18% 444ms 2.70% WntCellCycleOdeSystem::EvaluateYDerivatives 438ms 2.67% 43.85% 438ms 2.67% SUNDlsMat_denseGETRS 427ms 2.60% 46.45% 427ms 2.60% __strcmp_avx2 6ms 0.037% 46.48% 425ms 2.59% SUNMatCopy 4ms 0.024% 46.51% 420ms 2.56% SUNMatScaleAddI 405ms 2.47% 48.97% 419ms 2.55% SUNMatCopy_Dense 14ms 0.085% 49.06% 417ms 2.54% divconqrecurse 416ms 2.53% 51.59% 416ms 2.53% SUNMatScaleAddI_Dense 9ms 0.055% 51.65% 408ms 2.48% AbstractCellProperty::IsType (inline) 17ms 0.1% 51.75% 401ms 2.44% Node::RemoveElement 1ms 0.0061% 51.76% 398ms 2.42% std::_Vector_base::_M_allocate (inline) 5ms 0.03% 51.79% 397ms 2.42% CvodeAdaptor::SetupCvode 5ms 0.03% 51.82% 396ms 2.41% std::_Rb_tree::erase 150ms 0.91% 52.73% 395ms 2.41% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.012% 52.74% 395ms 2.41% std::set::erase (inline) 118ms 0.72% 53.46% 393ms 2.39% mergehulls 120ms 0.73% 54.19% 380ms 2.31% std::_Rb_tree::_M_erase 3ms 0.018% 54.21% 366ms 2.23% Cell::GetCellProliferativeType 8ms 0.049% 54.26% 347ms 2.11% std::__new_allocator::deallocate (inline) 21ms 0.13% 54.39% 346ms 2.11% std::_Rb_tree::~_Rb_tree (inline) 165ms 1.00% 55.39% 339ms 2.06% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.16% 55.55% 338ms 2.06% Element::ResetIndex 0 0% 55.55% 338ms 2.06% std::allocator_traits::deallocate (inline) 0 0% 55.55% 325ms 1.98% NodeLocationWriter::Visit 0 0% 55.55% 315ms 1.92% std::set::~set (inline) 0 0% 55.55% 313ms 1.91% std::_Rb_tree::_M_drop_node (inline) 4ms 0.024% 55.58% 311ms 1.89% Cell::GetMutationState 247ms 1.50% 57.08% 310ms 1.89% _int_free 12ms 0.073% 57.15% 309ms 1.88% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.037% 57.19% 307ms 1.87% LegacyCellProliferativeTypesWriter::VisitCell 68ms 0.41% 57.60% 300ms 1.83% AbstractCellProperty::IsSame 3ms 0.018% 57.62% 294ms 1.79% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.055% 57.68% 282ms 1.72% std::vector::push_back (inline) 0 0% 57.68% 279ms 1.70% std::_Rb_tree::_M_put_node (inline) 0 0% 57.68% 276ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.21% 57.89% 274ms 1.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 13ms 0.079% 57.97% 269ms 1.64% std::num_put::_M_insert_float 12ms 0.073% 58.04% 267ms 1.63% std::_Rb_tree::_Rb_tree (partial-inline) 23ms 0.14% 58.18% 263ms 1.60% std::vector::_M_realloc_insert 11ms 0.067% 58.25% 253ms 1.54% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.085% 58.33% 243ms 1.48% AbstractTetrahedralElement::CalculateJacobian 2ms 0.012% 58.35% 241ms 1.47% std::set::set (inline) 6ms 0.037% 58.38% 240ms 1.46% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.097% 58.48% 236ms 1.44% Element::MarkAsDeleted 5ms 0.03% 58.51% 235ms 1.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 49ms 0.3% 58.81% 232ms 1.41% std::type_info::operator== (inline) 1ms 0.0061% 58.81% 230ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.024% 58.84% 227ms 1.38% alternateaxes 38ms 0.23% 59.07% 226ms 1.38% N_VScale 28ms 0.17% 59.24% 225ms 1.37% std::_Rb_tree::_M_copy (inline) 215ms 1.31% 60.55% 223ms 1.36% vertexmedian 5ms 0.03% 60.58% 220ms 1.34% std::__cxx11::collate::do_transform 43ms 0.26% 60.84% 217ms 1.32% N_VScale_Serial 2ms 0.012% 60.86% 211ms 1.28% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.037% 60.89% 211ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 60.89% 211ms 1.28% MeshBasedCellPopulation::GetDampingConstant 2ms 0.012% 60.90% 206ms 1.25% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 14ms 0.085% 60.99% 206ms 1.25% cvEwtSet 1ms 0.0061% 61.00% 205ms 1.25% ___vsnprintf 0 0% 61.00% 205ms 1.25% __vsnprintf_internal (inline) 20ms 0.12% 61.12% 202ms 1.23% __printf_buffer 8ms 0.049% 61.17% 193ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 136ms 0.83% 61.99% 193ms 1.18% malloc_consolidate 53ms 0.32% 62.32% 191ms 1.16% std::_Rb_tree::_M_clone_node (inline) 4ms 0.024% 62.34% 185ms 1.13% Cell::SetCellProliferativeType 16ms 0.097% 62.44% 179ms 1.09% TetrahedralMesh::Clear 20ms 0.12% 62.56% 177ms 1.08% AbstractTetrahedralElement::RefreshJacobian 173ms 1.05% 63.61% 173ms 1.05% std::_Rb_tree_insert_and_rebalance 11ms 0.067% 63.68% 171ms 1.04% CVodeSetLinearSolver 124ms 0.76% 64.44% 170ms 1.04% AbstractElement::GetNodeGlobalIndex 1ms 0.0061% 64.44% 170ms 1.04% OffLatticeSimulation::ApplyBoundaries 6ms 0.037% 64.48% 169ms 1.03% CellProliferativeTypesWriter::VisitCell 10ms 0.061% 64.54% 169ms 1.03% __printf_fp_l_buffer 0 0% 64.54% 169ms 1.03% __printf_fp_spec (inline) 167ms 1.02% 65.56% 167ms 1.02% incircle 9ms 0.055% 65.61% 163ms 0.99% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.03% 65.64% 158ms 0.96% CellPropertyCollection::HasProperty 158ms 0.96% 66.60% 158ms 0.96% Node::GetIndex 5ms 0.03% 66.63% 158ms 0.96% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 66.63% 157ms 0.96% Cell::HasCellProperty (inline) 157ms 0.96% 67.59% 157ms 0.96% unlink_chunk 2ms 0.012% 67.60% 154ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0061% 67.61% 153ms 0.93% boost::numeric::ublas::vector_assign (inline) 90ms 0.55% 68.16% 149ms 0.91% std::_Rb_tree::equal_range (inline) 80ms 0.49% 68.64% 148ms 0.9% __printf_fp_buffer_1 0 0% 68.64% 144ms 0.88% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 68.64% 143ms 0.87% OutputFileHandler::OpenOutputFile 143ms 0.87% 69.51% 143ms 0.87% std::vector::size (inline) 58ms 0.35% 69.87% 137ms 0.83% AbstractElement::GetNodeLocation 3ms 0.018% 69.89% 134ms 0.82% MeshBasedCellPopulation::SpringsEnd (inline) 31ms 0.19% 70.07% 131ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 70.07% 128ms 0.78% tcache_get (inline) 128ms 0.78% 70.85% 128ms 0.78% tcache_get_n (inline) 0 0% 70.85% 126ms 0.77% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 71ms 0.43% 71.29% 124ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 122ms 0.74% 72.03% 122ms 0.74% AbstractElement::IsDeleted 11ms 0.067% 72.10% 122ms 0.74% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.03% 72.13% 116ms 0.71% SUNRpowerR 32ms 0.19% 72.32% 115ms 0.7% boost::numeric::ublas::indexing_vector_assign 115ms 0.7% 73.02% 115ms 0.7% std::_Rb_tree_rebalance_for_erase 41ms 0.25% 73.27% 115ms 0.7% std::__ostream_insert 0 0% 73.27% 113ms 0.69% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.049% 73.32% 111ms 0.68% __pow 35ms 0.21% 73.53% 110ms 0.67% N_VScaleAddMulti 0 0% 73.53% 110ms 0.67% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 11ms 0.067% 73.60% 109ms 0.66% Node::~Node 0 0% 73.60% 109ms 0.66% std::vector::vector (inline) 104ms 0.63% 74.23% 109ms 0.66% vertexsort 9ms 0.055% 74.29% 107ms 0.65% N_VCloneEmpty_Serial 25ms 0.15% 74.44% 107ms 0.65% std::num_put::_M_insert_int 57ms 0.35% 74.79% 104ms 0.63% AbstractTetrahedralMesh::GetElement 104ms 0.63% 75.42% 104ms 0.63% std::_Rb_tree_increment 9ms 0.055% 75.48% 103ms 0.63% __ieee754_pow_fma 0 0% 75.48% 102ms 0.62% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 0 0% 75.48% 102ms 0.62% std::_Vector_base::_Vector_base (inline) 101ms 0.62% 76.09% 101ms 0.62% counterclockwise 5ms 0.03% 76.12% 100ms 0.61% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 7ms 0.043% 76.16% 100ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.012% 76.18% 99ms 0.6% std::_Vector_base::_M_create_storage (inline) 2ms 0.012% 76.19% 98ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 13ms 0.079% 76.27% 95ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 76.27% 95ms 0.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.27% 94ms 0.57% std::operator<< (inline) 12ms 0.073% 76.34% 93ms 0.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 76.34% 93ms 0.57% std::basic_ofstream::basic_ofstream (inline) 0 0% 76.34% 93ms 0.57% std::vector::resize (inline) 0 0% 76.34% 91ms 0.55% std::basic_filebuf::open 0 0% 76.34% 91ms 0.55% std::basic_ofstream::open (inline) 0 0% 76.34% 91ms 0.55% std::vector::_M_default_append 8ms 0.049% 76.39% 90ms 0.55% N_VClone 59ms 0.36% 76.75% 90ms 0.55% TetrahedralMesh::EdgeIterator::EdgeIterator 42ms 0.26% 77.01% 88ms 0.54% boost::shared_ptr::shared_ptr (inline) 8ms 0.049% 77.05% 86ms 0.52% CellPropertyCollection::AddProperty 0 0% 77.05% 86ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 77.05% 85ms 0.52% NodeMap::NodeMap