File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12974ms, 80.25% of 16167ms total Dropped 853 nodes (cum <= 80.83ms) flat flat% sum% cum cum% 0 0% 0% 16120ms 99.71% __libc_start_call_main 0 0% 0% 16120ms 99.71% __libc_start_main_impl 0 0% 0% 16120ms 99.71% _start 0 0% 0% 16099ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16099ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16099ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16099ms 99.58% main 0 0% 0% 16062ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16062ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16062ms 99.35% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16039ms 99.21% AbstractCellBasedSimulation::Solve 1ms 0.0062% 0.0062% 11546ms 71.42% AbstractCellBasedSimulation::UpdateCellPopulation 8ms 0.049% 0.056% 6274ms 38.81% AbstractCellBasedSimulation::DoCellBirth 9ms 0.056% 0.11% 6136ms 37.95% Cell::ReadyToDivide 11ms 0.068% 0.18% 6050ms 37.42% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.019% 0.2% 5822ms 36.01% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.056% 0.25% 5811ms 35.94% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.031% 0.28% 5797ms 35.86% CellCycleModelOdeHandler::SolveOdeToTime 4ms 0.025% 0.31% 5620ms 34.76% CvodeAdaptor::Solve 4ms 0.025% 0.33% 5145ms 31.82% MeshBasedCellPopulation::Update 78ms 0.48% 0.82% 5131ms 31.74% CVode 57ms 0.35% 1.17% 4609ms 28.51% CVodeFree 3ms 0.019% 1.19% 3958ms 24.48% Cylindrical2dMesh::ReMesh 161ms 1% 2.18% 3659ms 22.63% cvRescale 4ms 0.025% 2.21% 3335ms 20.63% SUNNonlinSolSolve 35ms 0.22% 2.42% 3331ms 20.60% SUNNonlinSolSolve_Newton 70ms 0.43% 2.86% 3216ms 19.89% cvNlsInit 0 0% 2.86% 2475ms 15.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.86% 2189ms 13.54% MutableMesh::ReMesh 0 0% 2.86% 2175ms 13.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.087% 2.94% 2116ms 13.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 2.94% 2012ms 12.45% AbstractCellPopulation::WriteResultsToFiles 15ms 0.093% 3.04% 1968ms 12.17% cvLsSetup 816ms 5.05% 8.08% 1821ms 11.26% std::_Rb_tree::_M_lower_bound (inline) 151ms 0.93% 9.02% 1723ms 10.66% TetrahedralMesh::EdgeIterator::operator++ 18ms 0.11% 9.13% 1431ms 8.85% cvLsDQJtimes 54ms 0.33% 9.46% 1373ms 8.49% std::_Rb_tree::find (inline) 0 0% 9.46% 1151ms 7.12% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.031% 9.49% 1123ms 6.95% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 55ms 0.34% 9.83% 1070ms 6.62% operator new 15ms 0.093% 9.93% 1064ms 6.58% TetrahedralMesh::ImportFromMesher 275ms 1.70% 11.63% 1050ms 6.49% __GI___libc_malloc 5ms 0.031% 11.66% 1043ms 6.45% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.043% 11.70% 987ms 6.11% std::set::insert (inline) 11ms 0.068% 11.77% 980ms 6.06% std::_Rb_tree::_M_insert_unique 44ms 0.27% 12.04% 950ms 5.88% std::__new_allocator::allocate (inline) 0 0% 12.04% 947ms 5.86% std::allocator_traits::allocate (inline) 0 0% 12.04% 874ms 5.41% std::set::count (inline) 1ms 0.0062% 12.05% 841ms 5.20% triangulate 0 0% 12.05% 763ms 4.72% delaunay 1ms 0.0062% 12.06% 763ms 4.72% divconqdelaunay 0 0% 12.06% 728ms 4.50% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.019% 12.07% 701ms 4.34% CellPopulationElementWriter::Visit 2ms 0.012% 12.09% 695ms 4.30% AbstractTwoBodyInteractionForce::AddForceContribution 415ms 2.57% 14.65% 683ms 4.22% _int_malloc 53ms 0.33% 14.98% 660ms 4.08% std::map::operator[] (partial-inline) 19ms 0.12% 15.10% 655ms 4.05% std::less::operator() (inline) 636ms 3.93% 19.03% 636ms 3.93% std::operator< (inline) 39ms 0.24% 19.27% 628ms 3.88% cvLsSolve 208ms 1.29% 20.56% 626ms 3.87% __dynamic_cast 0 0% 20.56% 621ms 3.84% std::_Rb_tree::_M_create_node (inline) 617ms 3.82% 24.38% 617ms 3.82% std::_Rb_tree::_S_right (inline) 31ms 0.19% 24.57% 616ms 3.81% std::_Rb_tree::_M_insert_ (inline) 5ms 0.031% 24.60% 599ms 3.71% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.099% 24.70% 594ms 3.67% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 24.70% 594ms 3.67% std::_Rb_tree::_M_get_node (inline) 4ms 0.025% 24.72% 586ms 3.62% MeshBasedCellPopulation::AcceptCellWriter 586ms 3.62% 28.35% 586ms 3.62% N_VBufUnpack_Serial 20ms 0.12% 28.47% 577ms 3.57% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 28.47% 573ms 3.54% std::_Rb_tree::_Alloc_node::operator() (inline) 32ms 0.2% 28.67% 571ms 3.53% N_VWrmsNorm 179ms 1.11% 29.78% 565ms 3.49% cvRestore 197ms 1.22% 31.00% 559ms 3.46% __GI___libc_free 9ms 0.056% 31.05% 556ms 3.44% Element::Element 6ms 0.037% 31.09% 552ms 3.41% cvLsDQJac 53ms 0.33% 31.42% 545ms 3.37% cvLsDenseDQJac 101ms 0.62% 32.04% 539ms 3.33% N_VWrmsNorm_Serial 0 0% 32.04% 539ms 3.33% std::_Rb_tree::lower_bound (inline) 0 0% 32.04% 539ms 3.33% std::map::lower_bound (inline) 80ms 0.49% 32.54% 533ms 3.30% std::ostream::_M_insert 0 0% 32.54% 533ms 3.30% std::ostream::operator<< (inline) 9ms 0.056% 32.59% 527ms 3.26% SUNLinSolSolve 11ms 0.068% 32.66% 522ms 3.23% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.087% 32.75% 518ms 3.20% SUNLinSolSolve_Dense 8ms 0.049% 32.80% 513ms 3.17% SUNLinSolSetup 10ms 0.062% 32.86% 511ms 3.16% MutableMesh::ReIndex 117ms 0.72% 33.58% 507ms 3.14% N_VLinearSum_Serial 5ms 0.031% 33.61% 505ms 3.12% SUNLinSolSetup_Dense 4ms 0.025% 33.64% 501ms 3.10% AbstractCellProperty::IsSubType (inline) 0 0% 33.64% 494ms 3.06% std::map::find (inline) 14ms 0.087% 33.72% 491ms 3.04% CvodeRhsAdaptor 488ms 3.02% 36.74% 488ms 3.02% SUNDlsMat_denseGETRF 56ms 0.35% 37.09% 480ms 2.97% N_VLinearSum 5ms 0.031% 37.12% 475ms 2.94% Element::RegisterWithNodes (inline) 6ms 0.037% 37.16% 469ms 2.90% Node::AddElement 11ms 0.068% 37.22% 448ms 2.77% Cylindrical2dMesh::CorrectNonPeriodicMesh 442ms 2.73% 39.96% 442ms 2.73% SUNDlsMat_denseGETRS 432ms 2.67% 42.63% 432ms 2.67% __strcmp_avx2 180ms 1.11% 43.74% 430ms 2.66% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.019% 43.76% 420ms 2.60% SUNMatCopy 404ms 2.50% 46.26% 417ms 2.58% SUNMatCopy_Dense 107ms 0.66% 46.92% 410ms 2.54% std::_Rb_tree::_M_erase 10ms 0.062% 46.98% 403ms 2.49% std::_Rb_tree::erase 1ms 0.0062% 46.99% 403ms 2.49% std::set::erase (inline) 11ms 0.068% 47.06% 393ms 2.43% AbstractCellProperty::IsType (inline) 10ms 0.062% 47.12% 393ms 2.43% std::__new_allocator::deallocate (inline) 3ms 0.019% 47.14% 391ms 2.42% SUNMatScaleAddI 0 0% 47.14% 390ms 2.41% std::allocator_traits::deallocate (inline) 389ms 2.41% 49.55% 389ms 2.41% N_VWSqrSumLocal_Serial 11ms 0.068% 49.61% 388ms 2.40% Node::RemoveElement 388ms 2.40% 52.01% 388ms 2.40% SUNMatScaleAddI_Dense 5ms 0.031% 52.04% 382ms 2.36% CvodeAdaptor::SetupCvode 0 0% 52.04% 381ms 2.36% std::_Rb_tree::_M_drop_node (inline) 13ms 0.08% 52.12% 373ms 2.31% divconqrecurse 17ms 0.11% 52.23% 364ms 2.25% std::_Rb_tree::~_Rb_tree (inline) 306ms 1.89% 54.12% 362ms 2.24% _int_free 113ms 0.7% 54.82% 355ms 2.20% mergehulls 2ms 0.012% 54.83% 355ms 2.20% std::_Vector_base::_M_allocate (inline) 146ms 0.9% 55.74% 353ms 2.18% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0062% 55.74% 341ms 2.11% Cell::GetCellProliferativeType 28ms 0.17% 55.92% 339ms 2.10% Element::ResetIndex 0 0% 55.92% 331ms 2.05% std::set::~set (inline) 0 0% 55.92% 327ms 2.02% std::_Rb_tree::_M_put_node (inline) 2ms 0.012% 55.93% 317ms 1.96% NodeLocationWriter::Visit 0 0% 55.93% 315ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.025% 55.95% 313ms 1.94% LegacyCellProliferativeTypesWriter::VisitCell 42ms 0.26% 56.21% 311ms 1.92% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.025% 56.24% 306ms 1.89% Cell::GetMutationState 12ms 0.074% 56.31% 306ms 1.89% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 145ms 0.9% 57.21% 299ms 1.85% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.12% 57.33% 297ms 1.84% AbstractTetrahedralElement::CalculateJacobian 72ms 0.45% 57.77% 296ms 1.83% AbstractCellProperty::IsSame 6ms 0.037% 57.81% 284ms 1.76% AbstractCellPopulation::GetLocationIndexUsingCell 14ms 0.087% 57.90% 284ms 1.76% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.08% 57.98% 278ms 1.72% std::_Rb_tree::_M_erase_aux (partial-inline) 22ms 0.14% 58.11% 278ms 1.72% std::num_put::_M_insert_float 0 0% 58.11% 263ms 1.63% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0062% 58.12% 262ms 1.62% std::set::set (inline) 8ms 0.049% 58.17% 255ms 1.58% alternateaxes 8ms 0.049% 58.22% 252ms 1.56% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 227ms 1.40% 59.62% 246ms 1.52% vertexmedian 25ms 0.15% 59.78% 245ms 1.52% std::_Rb_tree::_M_copy (inline) 7ms 0.043% 59.82% 237ms 1.47% AbstractCellPopulation::IsCellAttachedToLocationIndex 31ms 0.19% 60.01% 236ms 1.46% AbstractTetrahedralElement::RefreshJacobian 25ms 0.15% 60.17% 232ms 1.44% N_VScale 4ms 0.025% 60.19% 231ms 1.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 32ms 0.2% 60.39% 228ms 1.41% N_VScale_Serial 10ms 0.062% 60.45% 228ms 1.41% std::vector::push_back (inline) 43ms 0.27% 60.72% 224ms 1.39% std::type_info::operator== (inline) 13ms 0.08% 60.80% 222ms 1.37% Element::MarkAsDeleted 76ms 0.47% 61.27% 217ms 1.34% std::_Rb_tree::_M_clone_node (inline) 5ms 0.031% 61.30% 214ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.012% 61.31% 211ms 1.31% std::__cxx11::collate::do_transform 3ms 0.019% 61.33% 210ms 1.30% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.031% 61.36% 207ms 1.28% std::vector::_M_realloc_insert 155ms 0.96% 62.32% 203ms 1.26% AbstractElement::GetNodeGlobalIndex 2ms 0.012% 62.33% 203ms 1.26% ___vsnprintf 0 0% 62.33% 201ms 1.24% __vsnprintf_internal (inline) 25ms 0.15% 62.49% 200ms 1.24% __printf_buffer 10ms 0.062% 62.55% 196ms 1.21% CVodeSetLinearSolver 0 0% 62.55% 194ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.037% 62.58% 194ms 1.20% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 62.58% 194ms 1.20% MeshBasedCellPopulation::GetDampingConstant 87ms 0.54% 63.12% 183ms 1.13% AbstractElement::GetNodeLocation 179ms 1.11% 64.23% 179ms 1.11% Node::GetIndex 3ms 0.019% 64.25% 177ms 1.09% Cell::SetCellProliferativeType 22ms 0.14% 64.38% 176ms 1.09% TetrahedralMesh::Clear 134ms 0.83% 65.21% 176ms 1.09% malloc_consolidate 0 0% 65.21% 173ms 1.07% OffLatticeSimulation::ApplyBoundaries 18ms 0.11% 65.32% 172ms 1.06% cvEwtSet 4ms 0.025% 65.35% 171ms 1.06% CellPropertyCollection::HasProperty 0 0% 65.35% 168ms 1.04% Cell::HasCellProperty (inline) 6ms 0.037% 65.39% 165ms 1.02% __printf_fp_l_buffer 0 0% 65.39% 165ms 1.02% __printf_fp_spec (inline) 1ms 0.0062% 65.39% 164ms 1.01% CellProliferativeTypesWriter::VisitCell 161ms 1% 66.39% 161ms 1% std::_Rb_tree_insert_and_rebalance 10ms 0.062% 66.45% 159ms 0.98% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 73ms 0.45% 66.90% 155ms 0.96% __printf_fp_buffer_1 10ms 0.062% 66.96% 146ms 0.9% N_VCloneEmpty_Serial 9ms 0.056% 67.02% 145ms 0.9% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 145ms 0.9% 67.92% 145ms 0.9% incircle 92ms 0.57% 68.49% 137ms 0.85% std::_Rb_tree::equal_range (inline) 135ms 0.84% 69.32% 135ms 0.84% AbstractElement::IsDeleted 25ms 0.15% 69.47% 130ms 0.8% std::num_put::_M_insert_int 129ms 0.8% 70.27% 129ms 0.8% std::_Rb_tree_rebalance_for_erase 4ms 0.025% 70.30% 127ms 0.79% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 70.30% 124ms 0.77% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.087% 70.38% 124ms 0.77% boost::detail::shared_count::~shared_count (inline) 0 0% 70.38% 124ms 0.77% boost::shared_ptr::~shared_ptr (inline) 30ms 0.19% 70.57% 123ms 0.76% TetrahedralMesh::EdgesEnd (partial-inline) 113ms 0.7% 71.27% 120ms 0.74% vertexsort 77ms 0.48% 71.74% 119ms 0.74% Cylindrical2dMesh::GetVectorFromAtoB 119ms 0.74% 72.48% 119ms 0.74% unlink_chunk 118ms 0.73% 73.21% 118ms 0.73% std::vector::size (inline) 0 0% 73.21% 117ms 0.72% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.031% 73.24% 117ms 0.72% N_VClone 0 0% 73.24% 116ms 0.72% OutputFileHandler::OpenOutputFile 2ms 0.012% 73.25% 116ms 0.72% boost::numeric::ublas::vector_assign (inline) 1ms 0.0062% 73.26% 114ms 0.71% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 9ms 0.056% 73.32% 112ms 0.69% N_VClone_Serial 105ms 0.65% 73.97% 108ms 0.67% boost::detail::sp_counted_base::release 50ms 0.31% 74.27% 104ms 0.64% std::__ostream_insert 8ms 0.049% 74.32% 103ms 0.64% Node::~Node 12ms 0.074% 74.40% 100ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 74.40% 99ms 0.61% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 99ms 0.61% 75.01% 99ms 0.61% std::_Rb_tree_increment 6ms 0.037% 75.05% 98ms 0.61% AbstractTetrahedralMesh::ElementIterator::IsAllowedElement (inline) 29ms 0.18% 75.23% 97ms 0.6% N_VScaleAddMulti 0 0% 75.23% 96ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 96ms 0.59% 75.82% 96ms 0.59% Node::IsDeleted 0 0% 75.82% 95ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 63ms 0.39% 76.21% 95ms 0.59% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 76.21% 94ms 0.58% std::vector::vector (inline) 13ms 0.08% 76.29% 93ms 0.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.031% 76.32% 92ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 28ms 0.17% 76.50% 92ms 0.57% boost::numeric::ublas::indexing_vector_assign 1ms 0.0062% 76.50% 92ms 0.57% std::vector::resize (inline) 91ms 0.56% 77.06% 91ms 0.56% N_VCopyOps 0 0% 77.06% 91ms 0.56% tcache_get (inline) 91ms 0.56% 77.63% 91ms 0.56% tcache_get_n (inline) 90ms 0.56% 78.18% 90ms 0.56% counterclockwise 0 0% 78.18% 89ms 0.55% std::vector::_M_default_append 0 0% 78.18% 88ms 0.54% std::_Vector_base::_Vector_base (inline) 1ms 0.0062% 78.19% 87ms 0.54% std::_Vector_base::_M_create_storage (inline) 86ms 0.53% 78.72% 86ms 0.53% TetrahedralMesh::EdgeIterator::operator!= 86ms 0.53% 79.25% 86ms 0.53% [libchaste_mesh.so] 42ms 0.26% 79.51% 85ms 0.53% AbstractTetrahedralMesh::GetElement 25ms 0.15% 79.67% 85ms 0.53% N_VDestroy_Serial 40ms 0.25% 79.92% 85ms 0.53% boost::shared_ptr::shared_ptr (inline) 3ms 0.019% 79.93% 85ms 0.53% std::operator<< (inline) 51ms 0.32% 80.25% 84ms 0.52% boost::numeric::ublas::c_matrix::operator() 0 0% 80.25% 81ms 0.5% NodeMap::NodeMap