File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 9773ms, 78.26% of 12488ms total Dropped 832 nodes (cum <= 62.44ms) flat flat% sum% cum cum% 0 0% 0% 12446ms 99.66% __libc_start_call_main 0 0% 0% 12446ms 99.66% __libc_start_main_impl 0 0% 0% 12446ms 99.66% _start 0 0% 0% 12428ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12428ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12428ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12428ms 99.52% main 0 0% 0% 12387ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12387ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12387ms 99.19% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 12368ms 99.04% AbstractCellBasedSimulation::Solve 0 0% 0% 9023ms 72.25% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.016% 0.016% 4909ms 39.31% AbstractCellBasedSimulation::DoCellBirth 10ms 0.08% 0.096% 4832ms 38.69% Cell::ReadyToDivide 8ms 0.064% 0.16% 4762ms 38.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.008% 0.17% 4596ms 36.80% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.16% 0.33% 4583ms 36.70% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.008% 0.34% 4561ms 36.52% CellCycleModelOdeHandler::SolveOdeToTime 4ms 0.032% 0.37% 4440ms 35.55% CvodeAdaptor::Solve 67ms 0.54% 0.9% 4066ms 32.56% CVode 0 0% 0.9% 4002ms 32.05% MeshBasedCellPopulation::Update 36ms 0.29% 1.19% 3645ms 29.19% CVodeFree 3ms 0.024% 1.22% 3060ms 24.50% Cylindrical2dMesh::ReMesh 131ms 1.05% 2.27% 2880ms 23.06% cvRescale 0 0% 2.27% 2593ms 20.76% SUNNonlinSolSolve 36ms 0.29% 2.55% 2593ms 20.76% SUNNonlinSolSolve_Newton 59ms 0.47% 3.03% 2491ms 19.95% cvNlsInit 0 0% 3.03% 1806ms 14.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 3.03% 1696ms 13.58% MutableMesh::ReMesh 0 0% 3.03% 1574ms 12.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.048% 3.07% 1544ms 12.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 3.07% 1537ms 12.31% AbstractCellPopulation::WriteResultsToFiles 18ms 0.14% 3.22% 1499ms 12.00% cvLsSetup 672ms 5.38% 8.60% 1449ms 11.60% std::_Rb_tree::_M_lower_bound (inline) 110ms 0.88% 9.48% 1347ms 10.79% TetrahedralMesh::EdgeIterator::operator++ 52ms 0.42% 9.90% 1099ms 8.80% std::_Rb_tree::find (inline) 5ms 0.04% 9.94% 1054ms 8.44% cvLsDQJtimes 4ms 0.032% 9.97% 912ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3ms 0.024% 9.99% 909ms 7.28% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.056% 10.05% 892ms 7.14% TetrahedralMesh::ImportFromMesher 6ms 0.048% 10.10% 817ms 6.54% MeshBasedCellPopulation::SpringIterator::operator++ 36ms 0.29% 10.39% 817ms 6.54% operator new 219ms 1.75% 12.14% 805ms 6.45% __GI___libc_malloc 10ms 0.08% 12.22% 781ms 6.25% std::set::insert (inline) 8ms 0.064% 12.28% 771ms 6.17% std::_Rb_tree::_M_insert_unique 27ms 0.22% 12.50% 729ms 5.84% std::__new_allocator::allocate (inline) 0 0% 12.50% 723ms 5.79% std::allocator_traits::allocate (inline) 0 0% 12.50% 680ms 5.45% std::set::count (inline) 1ms 0.008% 12.51% 632ms 5.06% triangulate 8ms 0.064% 12.57% 609ms 4.88% CellPopulationElementWriter::Visit 1ms 0.008% 12.58% 557ms 4.46% delaunay 2ms 0.016% 12.60% 555ms 4.44% divconqdelaunay 2ms 0.016% 12.61% 542ms 4.34% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 49ms 0.39% 13.00% 540ms 4.32% std::map::operator[] (partial-inline) 20ms 0.16% 13.16% 528ms 4.23% cvLsSolve 505ms 4.04% 17.21% 505ms 4.04% N_VBufUnpack_Serial 269ms 2.15% 19.36% 505ms 4.04% _int_malloc 499ms 4.00% 23.36% 499ms 4.00% std::_Rb_tree::_S_right (inline) 0 0% 23.36% 484ms 3.88% std::_Rb_tree::_M_create_node (inline) 11ms 0.088% 23.45% 484ms 3.88% std::less::operator() (inline) 26ms 0.21% 23.65% 481ms 3.85% std::_Rb_tree::_M_insert_ (inline) 14ms 0.11% 23.77% 475ms 3.80% Cylindrical2dMesh::ReconstructCylindricalMesh 473ms 3.79% 27.55% 473ms 3.79% std::operator< (inline) 4ms 0.032% 27.59% 470ms 3.76% Element::Element 0 0% 27.59% 467ms 3.74% std::_Rb_tree::_M_get_node (inline) 93ms 0.74% 28.33% 452ms 3.62% N_VLinearSum_Serial 33ms 0.26% 28.60% 451ms 3.61% N_VWrmsNorm 3ms 0.024% 28.62% 448ms 3.59% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.056% 28.68% 448ms 3.59% SUNLinSolSolve 123ms 0.98% 29.66% 444ms 3.56% __dynamic_cast 13ms 0.1% 29.76% 443ms 3.55% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.008% 29.77% 443ms 3.55% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.008% 29.78% 441ms 3.53% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.08% 29.86% 441ms 3.53% SUNLinSolSolve_Dense 0 0% 29.86% 438ms 3.51% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.024% 29.88% 424ms 3.40% SUNLinSolSetup 3ms 0.024% 29.91% 421ms 3.37% SUNLinSolSetup_Dense 141ms 1.13% 31.04% 419ms 3.36% __GI___libc_free 0 0% 31.04% 419ms 3.36% std::_Rb_tree::lower_bound (inline) 0 0% 31.04% 419ms 3.36% std::map::lower_bound (inline) 111ms 0.89% 31.93% 418ms 3.35% N_VWrmsNorm_Serial 0 0% 31.93% 414ms 3.32% std::map::find (inline) 115ms 0.92% 32.85% 408ms 3.27% cvRestore 405ms 3.24% 36.09% 405ms 3.24% SUNDlsMat_denseGETRF 39ms 0.31% 36.40% 403ms 3.23% N_VLinearSum 3ms 0.024% 36.43% 398ms 3.19% cvLsDQJac 55ms 0.44% 36.87% 395ms 3.16% cvLsDenseDQJac 12ms 0.096% 36.96% 386ms 3.09% Element::RegisterWithNodes (inline) 17ms 0.14% 37.10% 380ms 3.04% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.072% 37.17% 371ms 2.97% Node::AddElement 370ms 2.96% 40.13% 370ms 2.96% SUNDlsMat_denseGETRS 0 0% 40.13% 350ms 2.80% AbstractCellProperty::IsSubType (inline) 2ms 0.016% 40.15% 340ms 2.72% std::ostream::operator<< (inline) 65ms 0.52% 40.67% 338ms 2.71% std::ostream::_M_insert 327ms 2.62% 43.29% 327ms 2.62% __strcmp_evex 5ms 0.04% 43.33% 323ms 2.59% SUNMatScaleAddI 6ms 0.048% 43.38% 322ms 2.58% MutableMesh::ReIndex 22ms 0.18% 43.55% 321ms 2.57% std::__new_allocator::deallocate (inline) 318ms 2.55% 46.10% 318ms 2.55% SUNMatScaleAddI_Dense 0 0% 46.10% 316ms 2.53% std::allocator_traits::deallocate (inline) 1ms 0.008% 46.11% 308ms 2.47% CvodeAdaptor::SetupCvode 7ms 0.056% 46.16% 300ms 2.40% CvodeRhsAdaptor 4ms 0.032% 46.20% 294ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.088% 46.28% 291ms 2.33% std::_Rb_tree::erase 0 0% 46.28% 289ms 2.31% std::set::erase (inline) 0 0% 46.28% 285ms 2.28% Cell::GetCellProliferativeType 285ms 2.28% 48.57% 285ms 2.28% N_VWSqrSumLocal_Serial 10ms 0.08% 48.65% 284ms 2.27% Node::RemoveElement 0 0% 48.65% 283ms 2.27% std::_Rb_tree::_M_drop_node (inline) 4ms 0.032% 48.68% 282ms 2.26% SUNMatCopy 110ms 0.88% 49.56% 282ms 2.26% std::_Rb_tree::_M_get_insert_unique_pos 62ms 0.5% 50.06% 281ms 2.25% std::_Rb_tree::_M_erase 267ms 2.14% 52.19% 278ms 2.23% SUNMatCopy_Dense 243ms 1.95% 54.14% 277ms 2.22% _int_free 6ms 0.048% 54.19% 272ms 2.18% AbstractCellProperty::IsType (inline) 112ms 0.9% 55.08% 259ms 2.07% WntCellCycleOdeSystem::EvaluateYDerivatives 14ms 0.11% 55.20% 258ms 2.07% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.008% 55.20% 257ms 2.06% std::_Vector_base::_M_allocate (inline) 7ms 0.056% 55.26% 256ms 2.05% divconqrecurse 0 0% 55.26% 253ms 2.03% std::_Rb_tree::_M_put_node (inline) 76ms 0.61% 55.87% 248ms 1.99% mergehulls 0 0% 55.87% 240ms 1.92% std::set::~set (inline) 4ms 0.032% 55.90% 237ms 1.90% LegacyCellProliferativeTypesWriter::VisitCell 6ms 0.048% 55.95% 234ms 1.87% AbstractCellPopulation::GetLocationIndexUsingCell 110ms 0.88% 56.83% 230ms 1.84% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.016% 56.85% 227ms 1.82% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.12% 56.97% 224ms 1.79% AbstractCellPopulation::Iterator::IsRealCell (inline) 10ms 0.08% 57.05% 217ms 1.74% std::vector::push_back (inline) 15ms 0.12% 57.17% 215ms 1.72% std::_Rb_tree::_Rb_tree 12ms 0.096% 57.26% 210ms 1.68% Element::ResetIndex 6ms 0.048% 57.31% 209ms 1.67% std::set::set (inline) 15ms 0.12% 57.43% 202ms 1.62% AbstractTetrahedralElement::CalculateJacobian 35ms 0.28% 57.71% 198ms 1.59% N_VScale 43ms 0.34% 58.06% 197ms 1.58% AbstractCellProperty::IsSame 8ms 0.064% 58.12% 196ms 1.57% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 15ms 0.12% 58.24% 196ms 1.57% std::vector::_M_realloc_insert 1ms 0.008% 58.25% 195ms 1.56% Cell::GetMutationState 5ms 0.04% 58.29% 193ms 1.55% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.08% 58.37% 192ms 1.54% Element::MarkAsDeleted 11ms 0.088% 58.46% 189ms 1.51% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.17% 58.62% 188ms 1.51% cvEwtSet 40ms 0.32% 58.94% 186ms 1.49% N_VScale_Serial 2ms 0.016% 58.96% 181ms 1.45% NodeLocationWriter::Visit 2ms 0.016% 58.98% 179ms 1.43% alternateaxes 169ms 1.35% 60.33% 177ms 1.42% vertexmedian 1ms 0.008% 60.34% 175ms 1.40% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.064% 60.40% 174ms 1.39% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.04% 60.44% 168ms 1.35% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 21ms 0.17% 60.61% 168ms 1.35% std::_Rb_tree::_M_copy (inline) 0 0% 60.61% 158ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.048% 60.66% 158ms 1.27% std::num_put::_M_insert_float 22ms 0.18% 60.83% 157ms 1.26% AbstractTetrahedralElement::RefreshJacobian 32ms 0.26% 61.09% 154ms 1.23% std::type_info::operator== (inline) 1ms 0.008% 61.10% 152ms 1.22% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 61.10% 150ms 1.20% OffLatticeSimulation::ApplyBoundaries 50ms 0.4% 61.50% 147ms 1.18% std::_Rb_tree::_M_clone_node (inline) 8ms 0.064% 61.56% 145ms 1.16% TetrahedralMesh::Clear 97ms 0.78% 62.34% 143ms 1.15% AbstractElement::GetNodeGlobalIndex 6ms 0.048% 62.39% 142ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.032% 62.42% 135ms 1.08% std::__cxx11::collate::do_transform 1ms 0.008% 62.43% 132ms 1.06% CellProliferativeTypesWriter::VisitCell 96ms 0.77% 63.20% 132ms 1.06% malloc_consolidate 3ms 0.024% 63.22% 130ms 1.04% Cell::SetCellProliferativeType 3ms 0.024% 63.24% 130ms 1.04% CellPropertyCollection::HasProperty 0 0% 63.24% 128ms 1.02% Cell::HasCellProperty (inline) 0 0% 63.24% 128ms 1.02% ___vsnprintf 16ms 0.13% 63.37% 128ms 1.02% __printf_buffer 0 0% 63.37% 128ms 1.02% __vsnprintf_internal (inline) 13ms 0.1% 63.48% 127ms 1.02% CVodeSetLinearSolver 5ms 0.04% 63.52% 127ms 1.02% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 125ms 1.00% 64.52% 125ms 1.00% std::_Rb_tree_insert_and_rebalance 45ms 0.36% 64.88% 120ms 0.96% AbstractElement::GetNodeLocation 1ms 0.008% 64.89% 120ms 0.96% MeshBasedCellPopulation::GetDampingConstant 2ms 0.016% 64.90% 119ms 0.95% AbstractCentreBasedCellPopulation::GetDampingConstant 119ms 0.95% 65.86% 119ms 0.95% unlink_chunk 0 0% 65.86% 112ms 0.9% AbstractCellBasedSimulation::DoCellRemoval (inline) 112ms 0.9% 66.75% 112ms 0.9% incircle 5ms 0.04% 66.79% 112ms 0.9% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 111ms 0.89% 67.68% 111ms 0.89% Node::GetIndex 103ms 0.82% 68.51% 111ms 0.89% vertexsort 1ms 0.008% 68.51% 108ms 0.86% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.024% 68.54% 108ms 0.86% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 108ms 0.86% 69.40% 108ms 0.86% std::vector::size (inline) 3ms 0.024% 69.43% 106ms 0.85% __printf_fp_l_buffer 0 0% 69.43% 106ms 0.85% __printf_fp_spec (inline) 2ms 0.016% 69.44% 106ms 0.85% boost::numeric::ublas::vector_assign (inline) 47ms 0.38% 69.82% 103ms 0.82% __printf_fp_buffer_1 65ms 0.52% 70.34% 100ms 0.8% std::_Rb_tree::equal_range (inline) 64ms 0.51% 70.85% 99ms 0.79% Cylindrical2dMesh::GetVectorFromAtoB 18ms 0.14% 71.00% 98ms 0.78% N_VScaleAddMulti 98ms 0.78% 71.78% 98ms 0.78% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 21ms 0.17% 71.95% 96ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.088% 72.04% 94ms 0.75% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 72.04% 93ms 0.74% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 72.04% 93ms 0.74% OutputFileHandler::OpenOutputFile 44ms 0.35% 72.39% 92ms 0.74% AbstractTetrahedralMesh::GetElement 5ms 0.04% 72.43% 91ms 0.73% N_VCloneEmpty_Serial 90ms 0.72% 73.15% 90ms 0.72% std::_Rb_tree_increment 9ms 0.072% 73.22% 88ms 0.7% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.048% 73.27% 87ms 0.7% Node::~Node 15ms 0.12% 73.39% 86ms 0.69% std::num_put::_M_insert_int 7ms 0.056% 73.45% 84ms 0.67% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.048% 73.49% 83ms 0.66% Cylindrical2dMesh::CreateMirrorNodes 13ms 0.1% 73.60% 83ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 73.60% 83ms 0.66% boost::shared_ptr::~shared_ptr (inline) 0 0% 73.60% 82ms 0.66% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.016% 73.61% 82ms 0.66% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 8ms 0.064% 73.68% 82ms 0.66% SUNRpowerR 26ms 0.21% 73.89% 79ms 0.63% std::__ostream_insert 14ms 0.11% 74.00% 77ms 0.62% std::_Vector_base::_M_deallocate (inline) 0 0% 74.00% 77ms 0.62% tcache_get (inline) 77ms 0.62% 74.62% 77ms 0.62% tcache_get_n (inline) 49ms 0.39% 75.01% 75ms 0.6% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 6ms 0.048% 75.06% 74ms 0.59% __pow 72ms 0.58% 75.63% 72ms 0.58% AbstractElement::IsDeleted 20ms 0.16% 75.79% 72ms 0.58% boost::numeric::ublas::indexing_vector_assign 2ms 0.016% 75.81% 72ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 31ms 0.25% 76.06% 72ms 0.58% std::basic_filebuf::xsputn 71ms 0.57% 76.63% 71ms 0.57% std::_Rb_tree_rebalance_for_erase 38ms 0.3% 76.93% 69ms 0.55% boost::shared_ptr::shared_ptr (inline) 0 0% 76.93% 69ms 0.55% std::operator<< (inline) 0 0% 76.93% 68ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 68ms 0.54% 77.47% 68ms 0.54% Node::rGetLocation 11ms 0.088% 77.56% 68ms 0.54% __ieee754_pow_fma 3ms 0.024% 77.59% 65ms 0.52% N_VClone 1ms 0.008% 77.59% 65ms 0.52% std::vector::resize (inline) 0 0% 77.59% 65ms 0.52% std::vector::vector (inline) 4ms 0.032% 77.63% 64ms 0.51% TetrahedralMesh::EdgeIterator::GetNodeB 62ms 0.5% 78.12% 64ms 0.51% boost::detail::sp_counted_base::release 17ms 0.14% 78.26% 63ms 0.5% SUNDenseMatrix