File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 7688ms, 78.79% of 9758ms total Dropped 753 nodes (cum <= 48.79ms) flat flat% sum% cum cum% 0 0% 0% 9726ms 99.67% __libc_start_call_main 0 0% 0% 9726ms 99.67% __libc_start_main_impl 0 0% 0% 9726ms 99.67% _start 0 0% 0% 9710ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 9710ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 9710ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 9710ms 99.51% main 0 0% 0% 9680ms 99.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 9680ms 99.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 9680ms 99.20% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 9665ms 99.05% AbstractCellBasedSimulation::Solve 0 0% 0% 6744ms 69.11% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 3380ms 34.64% MeshBasedCellPopulation::Update 1ms 0.01% 0.01% 3296ms 33.78% AbstractCellBasedSimulation::DoCellBirth 5ms 0.051% 0.061% 3217ms 32.97% Cell::ReadyToDivide 5ms 0.051% 0.11% 3170ms 32.49% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.01% 0.12% 3053ms 31.29% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.11% 0.24% 3039ms 31.14% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.01% 0.25% 3026ms 31.01% CellCycleModelOdeHandler::SolveOdeToTime 4ms 0.041% 0.29% 2927ms 30.00% CvodeAdaptor::Solve 37ms 0.38% 0.67% 2705ms 27.72% CVode 2ms 0.02% 0.69% 2559ms 26.22% Cylindrical2dMesh::ReMesh 34ms 0.35% 1.04% 2444ms 25.05% CVodeFree 79ms 0.81% 1.84% 1883ms 19.30% cvRescale 5ms 0.051% 1.90% 1730ms 17.73% SUNNonlinSolSolve 11ms 0.11% 2.01% 1725ms 17.68% SUNNonlinSolSolve_Newton 41ms 0.42% 2.43% 1681ms 17.23% cvNlsInit 1ms 0.01% 2.44% 1624ms 16.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.44% 1413ms 14.48% MutableMesh::ReMesh 1ms 0.01% 2.45% 1370ms 14.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.01% 2.46% 1343ms 13.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.01% 2.47% 1291ms 13.23% AbstractCellPopulation::WriteResultsToFiles 604ms 6.19% 8.66% 1187ms 12.16% std::_Rb_tree::_M_lower_bound (inline) 126ms 1.29% 9.95% 1138ms 11.66% TetrahedralMesh::EdgeIterator::operator++ 14ms 0.14% 10.09% 981ms 10.05% cvLsSetup 51ms 0.52% 10.62% 924ms 9.47% std::_Rb_tree::find (inline) 0 0% 10.62% 803ms 8.23% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.051% 10.67% 744ms 7.62% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.14% 10.81% 712ms 7.30% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.031% 10.84% 691ms 7.08% cvLsDQJtimes 43ms 0.44% 11.28% 680ms 6.97% operator new 252ms 2.58% 13.87% 674ms 6.91% __GI___libc_malloc 5ms 0.051% 13.92% 653ms 6.69% TetrahedralMesh::ImportFromMesher 11ms 0.11% 14.03% 624ms 6.39% std::set::insert (inline) 11ms 0.11% 14.14% 613ms 6.28% std::_Rb_tree::_M_insert_unique 0 0% 14.14% 590ms 6.05% triangulate 21ms 0.22% 14.36% 582ms 5.96% std::__new_allocator::allocate (inline) 0 0% 14.36% 580ms 5.94% std::allocator_traits::allocate (inline) 0 0% 14.36% 574ms 5.88% std::set::count (inline) 1ms 0.01% 14.37% 529ms 5.42% delaunay 2ms 0.02% 14.39% 528ms 5.41% divconqdelaunay 3ms 0.031% 14.42% 488ms 5.00% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.02% 14.44% 446ms 4.57% CellPopulationElementWriter::Visit 41ms 0.42% 14.86% 416ms 4.26% std::map::operator[] (partial-inline) 0 0% 14.86% 415ms 4.25% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.16% 15.02% 401ms 4.11% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 15.02% 386ms 3.96% std::_Rb_tree::_M_create_node (inline) 8ms 0.082% 15.11% 382ms 3.91% MeshBasedCellPopulation::AcceptCellWriter 87ms 0.89% 16.00% 375ms 3.84% __GI___libc_free 7ms 0.072% 16.07% 373ms 3.82% std::less::operator() (inline) 14ms 0.14% 16.21% 371ms 3.80% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 93ms 0.95% 17.17% 371ms 3.80% __dynamic_cast 1ms 0.01% 17.18% 369ms 3.78% CellPropertyCollection::GetPropertiesType (inline) 0 0% 17.18% 369ms 3.78% std::_Rb_tree::_M_get_node (inline) 21ms 0.22% 17.39% 367ms 3.76% std::_Rb_tree::_M_insert_ (inline) 366ms 3.75% 21.14% 366ms 3.75% std::operator< (inline) 202ms 2.07% 23.21% 356ms 3.65% _int_malloc 0 0% 23.21% 355ms 3.64% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.11% 23.32% 349ms 3.58% cvLsSolve 347ms 3.56% 26.88% 347ms 3.56% std::_Rb_tree::_S_right (inline) 0 0% 26.88% 347ms 3.56% std::map::find (inline) 15ms 0.15% 27.03% 338ms 3.46% Cylindrical2dMesh::ReconstructCylindricalMesh 23ms 0.24% 27.27% 331ms 3.39% N_VWrmsNorm 8ms 0.082% 27.35% 329ms 3.37% Element::Element 6ms 0.061% 27.41% 324ms 3.32% MutableMesh::ReIndex 0 0% 27.41% 318ms 3.26% std::_Rb_tree::lower_bound (inline) 0 0% 27.41% 318ms 3.26% std::map::lower_bound (inline) 96ms 0.98% 28.40% 316ms 3.24% cvRestore 4ms 0.041% 28.44% 313ms 3.21% cvLsDQJac 4ms 0.041% 28.48% 310ms 3.18% CvodeRhsAdaptor 52ms 0.53% 29.01% 309ms 3.17% cvLsDenseDQJac 82ms 0.84% 29.85% 308ms 3.16% N_VWrmsNorm_Serial 6ms 0.061% 29.91% 305ms 3.13% SUNLinSolSolve 0 0% 29.91% 304ms 3.12% AbstractCellProperty::IsSubType (inline) 5ms 0.051% 29.97% 302ms 3.09% Element::RegisterWithNodes (inline) 2ms 0.02% 29.99% 299ms 3.06% SUNLinSolSolve_Dense 14ms 0.14% 30.13% 296ms 3.03% Node::AddElement 263ms 2.70% 32.82% 287ms 2.94% _int_free 3ms 0.031% 32.86% 285ms 2.92% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 32.86% 279ms 2.86% std::_Rb_tree::_M_drop_node (inline) 113ms 1.16% 34.01% 273ms 2.80% WntCellCycleOdeSystem::EvaluateYDerivatives 270ms 2.77% 36.78% 270ms 2.77% __strcmp_evex 6ms 0.061% 36.84% 268ms 2.75% SUNLinSolSetup 45ms 0.46% 37.30% 266ms 2.73% std::_Rb_tree::~_Rb_tree (inline) 265ms 2.72% 40.02% 265ms 2.72% SUNDlsMat_denseGETRS 6ms 0.061% 40.08% 262ms 2.68% SUNLinSolSetup_Dense 260ms 2.66% 42.74% 260ms 2.66% N_VBufUnpack_Serial 2ms 0.02% 42.76% 258ms 2.64% AbstractCellProperty::IsType (inline) 6ms 0.061% 42.83% 257ms 2.63% std::__new_allocator::deallocate (inline) 15ms 0.15% 42.98% 256ms 2.62% Node::RemoveElement 4ms 0.041% 43.02% 252ms 2.58% std::_Rb_tree::erase 0 0% 43.02% 252ms 2.58% std::set::~set (inline) 0 0% 43.02% 251ms 2.57% std::allocator_traits::deallocate (inline) 0 0% 43.02% 251ms 2.57% std::set::erase (inline) 250ms 2.56% 45.58% 250ms 2.56% SUNDlsMat_denseGETRF 37ms 0.38% 45.96% 250ms 2.56% std::_Rb_tree::_M_erase 12ms 0.12% 46.09% 248ms 2.54% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.02% 46.11% 243ms 2.49% std::ostream::operator<< (inline) 32ms 0.33% 46.43% 241ms 2.47% std::ostream::_M_insert 70ms 0.72% 47.15% 240ms 2.46% N_VLinearSum_Serial 10ms 0.1% 47.25% 237ms 2.43% divconqrecurse 103ms 1.06% 48.31% 235ms 2.41% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.072% 48.38% 234ms 2.40% boost::detail::shared_count::~shared_count (inline) 0 0% 48.38% 234ms 2.40% boost::shared_ptr::~shared_ptr (inline) 0 0% 48.38% 234ms 2.40% std::set::set (inline) 224ms 2.30% 50.68% 226ms 2.32% boost::detail::sp_counted_base::release 1ms 0.01% 50.69% 224ms 2.30% LegacyCellProliferativeTypesWriter::VisitCell 73ms 0.75% 51.43% 224ms 2.30% mergehulls 0 0% 51.43% 215ms 2.20% std::_Rb_tree::_M_put_node (inline) 122ms 1.25% 52.68% 214ms 2.19% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.19% 52.88% 213ms 2.18% Element::ResetIndex 18ms 0.18% 53.06% 212ms 2.17% N_VLinearSum 31ms 0.32% 53.38% 212ms 2.17% std::_Rb_tree::_M_copy (inline) 2ms 0.02% 53.40% 211ms 2.16% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 53.40% 211ms 2.16% std::_Vector_base::_M_allocate (inline) 207ms 2.12% 55.52% 207ms 2.12% N_VWSqrSumLocal_Serial 21ms 0.22% 55.74% 206ms 2.11% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.031% 55.77% 204ms 2.09% alternateaxes 1ms 0.01% 55.78% 201ms 2.06% Cell::GetCellProliferativeType 3ms 0.031% 55.81% 200ms 2.05% Cell::GetMutationState 2ms 0.02% 55.83% 200ms 2.05% SUNMatScaleAddI 188ms 1.93% 57.76% 199ms 2.04% vertexmedian 198ms 2.03% 59.79% 198ms 2.03% SUNMatScaleAddI_Dense 3ms 0.031% 59.82% 193ms 1.98% AbstractCellPopulation::GetLocationIndexUsingCell 39ms 0.4% 60.22% 191ms 1.96% AbstractCellProperty::IsSame 4ms 0.041% 60.26% 183ms 1.88% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.02% 60.28% 183ms 1.88% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 79ms 0.81% 61.09% 181ms 1.85% std::_Rb_tree::_M_clone_node (inline) 1ms 0.01% 61.10% 176ms 1.80% CvodeAdaptor::SetupCvode 11ms 0.11% 61.21% 168ms 1.72% std::_Rb_tree::_M_erase_aux (inline) 0 0% 61.21% 167ms 1.71% NodeLocationWriter::Visit 13ms 0.13% 61.34% 166ms 1.70% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 61.34% 164ms 1.68% OffLatticeSimulation::ApplyBoundaries 7ms 0.072% 61.42% 164ms 1.68% std::vector::push_back (inline) 9ms 0.092% 61.51% 158ms 1.62% AbstractTetrahedralElement::CalculateJacobian 13ms 0.13% 61.64% 154ms 1.58% std::vector::_M_realloc_insert 25ms 0.26% 61.90% 152ms 1.56% std::type_info::operator== (inline) 1ms 0.01% 61.91% 151ms 1.55% TetrahedralMesh::RefreshJacobianCachedData 0 0% 61.91% 145ms 1.49% SUNMatCopy 134ms 1.37% 63.28% 145ms 1.49% SUNMatCopy_Dense 1ms 0.01% 63.29% 144ms 1.48% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.051% 63.34% 143ms 1.47% Element::MarkAsDeleted 12ms 0.12% 63.47% 138ms 1.41% std::num_put::_M_insert_float 4ms 0.041% 63.51% 133ms 1.36% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.01% 63.52% 130ms 1.33% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 63.52% 130ms 1.33% MeshBasedCellPopulation::GetDampingConstant 18ms 0.18% 63.70% 124ms 1.27% AbstractTetrahedralElement::RefreshJacobian 87ms 0.89% 64.59% 118ms 1.21% AbstractElement::GetNodeGlobalIndex 22ms 0.23% 64.82% 118ms 1.21% N_VScale 1ms 0.01% 64.83% 115ms 1.18% CellPropertyCollection::HasProperty 23ms 0.24% 65.06% 113ms 1.16% N_VScale_Serial 0 0% 65.06% 112ms 1.15% Cell::HasCellProperty (inline) 0 0% 65.06% 111ms 1.14% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 111ms 1.14% 66.20% 111ms 1.14% std::vector::size (inline) 6ms 0.061% 66.26% 110ms 1.13% cvEwtSet 110ms 1.13% 67.39% 110ms 1.13% std::_Rb_tree_insert_and_rebalance 2ms 0.02% 67.41% 110ms 1.13% std::__cxx11::collate::do_transform 2ms 0.02% 67.43% 108ms 1.11% ___vsnprintf 84ms 0.86% 68.29% 107ms 1.10% malloc_consolidate 0 0% 68.29% 106ms 1.09% __vsnprintf_internal (inline) 13ms 0.13% 68.43% 105ms 1.08% __printf_buffer 16ms 0.16% 68.59% 102ms 1.05% TetrahedralMesh::EdgesEnd (partial-inline) 98ms 1.00% 69.59% 98ms 1.00% incircle 61ms 0.63% 70.22% 97ms 0.99% AbstractElement::GetNodeLocation 3ms 0.031% 70.25% 96ms 0.98% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.041% 70.29% 96ms 0.98% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 1ms 0.01% 70.30% 95ms 0.97% Cell::SetCellProliferativeType 1ms 0.01% 70.31% 93ms 0.95% boost::numeric::ublas::vector_assign (inline) 2ms 0.02% 70.33% 90ms 0.92% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 7ms 0.072% 70.40% 89ms 0.91% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.041% 70.44% 88ms 0.9% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.051% 70.50% 87ms 0.89% boost::numeric::ublas::c_vector::c_vector (inline) 50ms 0.51% 71.01% 86ms 0.88% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 54ms 0.55% 71.56% 86ms 0.88% std::_Rb_tree::equal_range (inline) 2ms 0.02% 71.58% 84ms 0.86% __printf_fp_l_buffer 0 0% 71.58% 84ms 0.86% __printf_fp_spec (inline) 0 0% 71.58% 83ms 0.85% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 71.58% 83ms 0.85% OutputFileHandler::OpenOutputFile 27ms 0.28% 71.86% 82ms 0.84% __printf_fp_buffer_1 0 0% 71.86% 81ms 0.83% CellProliferativeTypesWriter::VisitCell 73ms 0.75% 72.61% 81ms 0.83% vertexsort 1ms 0.01% 72.62% 80ms 0.82% TetrahedralMesh::Clear 10ms 0.1% 72.72% 79ms 0.81% CVodeSetLinearSolver 1ms 0.01% 72.73% 77ms 0.79% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.041% 72.77% 75ms 0.77% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 38ms 0.39% 73.16% 75ms 0.77% Cylindrical2dMesh::GetVectorFromAtoB 9ms 0.092% 73.25% 75ms 0.77% SUNRpowerR 71ms 0.73% 73.98% 71ms 0.73% [libchaste_mesh.so] 5ms 0.051% 74.03% 69ms 0.71% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 74.03% 68ms 0.7% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.031% 74.06% 67ms 0.69% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.06% 66ms 0.68% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 9ms 0.092% 74.15% 66ms 0.68% __pow 15ms 0.15% 74.31% 66ms 0.68% boost::numeric::ublas::indexing_vector_assign 0 0% 74.31% 66ms 0.68% std::__new_allocator::destroy (inline) 0 0% 74.31% 66ms 0.68% std::allocator_traits::destroy (inline) 23ms 0.24% 74.54% 65ms 0.67% AbstractTetrahedralMesh::GetElement 0 0% 74.54% 65ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 63ms 0.65% 75.19% 63ms 0.65% std::_Rb_tree_rebalance_for_erase 19ms 0.19% 75.38% 61ms 0.63% N_VScaleAddMulti 61ms 0.63% 76.01% 61ms 0.63% unlink_chunk 60ms 0.61% 76.62% 60ms 0.61% std::_Rb_tree_increment 1ms 0.01% 76.63% 60ms 0.61% tcache_get (inline) 59ms 0.6% 77.24% 59ms 0.6% tcache_get_n (inline) 0 0% 77.24% 57ms 0.58% AbstractCellBasedWriter::CloseFile 6ms 0.061% 77.30% 57ms 0.58% Cylindrical2dMesh::CreateMirrorNodes 4ms 0.041% 77.34% 57ms 0.58% __ieee754_pow_fma 2ms 0.02% 77.36% 57ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.02% 77.38% 57ms 0.58% std::basic_filebuf::close 0 0% 77.38% 57ms 0.58% std::basic_ofstream::close (inline) 2ms 0.02% 77.40% 55ms 0.56% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 77.40% 54ms 0.55% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 77.40% 54ms 0.55% std::vector::resize (inline) 52ms 0.53% 77.94% 52ms 0.53% Node::GetIndex 8ms 0.082% 78.02% 52ms 0.53% std::__ostream_insert 51ms 0.52% 78.54% 51ms 0.52% [libchaste_cell_based.so] 10ms 0.1% 78.64% 51ms 0.52% std::num_put::_M_insert_int 0 0% 78.64% 50ms 0.51% NodeMap::NodeMap 0 0% 78.64% 50ms 0.51% std::vector::_M_default_append (inline) 1ms 0.01% 78.65% 49ms 0.5% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 4ms 0.041% 78.69% 49ms 0.5% CellLocationIndexWriter::VisitCell 9ms 0.092% 78.79% 49ms 0.5% TetrahedralMesh::EdgeIterator::GetNodeA