File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 7635ms, 78.71% of 9700ms total Dropped 756 nodes (cum <= 48.50ms) flat flat% sum% cum cum% 0 0% 0% 9666ms 99.65% __libc_start_call_main 0 0% 0% 9666ms 99.65% __libc_start_main_impl 0 0% 0% 9666ms 99.65% _start 0 0% 0% 9651ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 9651ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 9651ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 9651ms 99.49% main 0 0% 0% 9617ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 9617ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 9617ms 99.14% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.01% 0.01% 9602ms 98.99% AbstractCellBasedSimulation::Solve 0 0% 0.01% 6717ms 69.25% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.01% 3398ms 35.03% MeshBasedCellPopulation::Update 3ms 0.031% 0.041% 3239ms 33.39% AbstractCellBasedSimulation::DoCellBirth 15ms 0.15% 0.2% 3168ms 32.66% Cell::ReadyToDivide 0 0% 0.2% 3105ms 32.01% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.01% 0.21% 3012ms 31.05% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.072% 0.28% 3004ms 30.97% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.28% 2993ms 30.86% CellCycleModelOdeHandler::SolveOdeToTime 0 0% 0.28% 2888ms 29.77% CvodeAdaptor::Solve 44ms 0.45% 0.73% 2609ms 26.90% CVode 4ms 0.041% 0.77% 2577ms 26.57% Cylindrical2dMesh::ReMesh 43ms 0.44% 1.22% 2331ms 24.03% CVodeFree 52ms 0.54% 1.75% 1791ms 18.46% cvRescale 0 0% 1.75% 1665ms 17.16% SUNNonlinSolSolve 20ms 0.21% 1.96% 1665ms 17.16% SUNNonlinSolSolve_Newton 37ms 0.38% 2.34% 1623ms 16.73% cvNlsInit 0 0% 2.34% 1599ms 16.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.34% 1436ms 14.80% MutableMesh::ReMesh 0 0% 2.34% 1347ms 13.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.031% 2.37% 1317ms 13.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.021% 2.39% 1281ms 13.21% AbstractCellPopulation::WriteResultsToFiles 603ms 6.22% 8.61% 1176ms 12.12% std::_Rb_tree::_M_lower_bound (inline) 103ms 1.06% 9.67% 1117ms 11.52% TetrahedralMesh::EdgeIterator::operator++ 12ms 0.12% 9.79% 942ms 9.71% cvLsSetup 53ms 0.55% 10.34% 882ms 9.09% std::_Rb_tree::find (inline) 2ms 0.021% 10.36% 783ms 8.07% MeshBasedCellPopulation::UpdateNodePairs 0 0% 10.36% 715ms 7.37% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.093% 10.45% 697ms 7.19% std::set::insert (inline) 6ms 0.062% 10.52% 688ms 7.09% std::_Rb_tree::_M_insert_unique 7ms 0.072% 10.59% 682ms 7.03% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.041% 10.63% 679ms 7.00% cvLsDQJtimes 33ms 0.34% 10.97% 675ms 6.96% operator new 278ms 2.87% 13.84% 671ms 6.92% __GI___libc_malloc 4ms 0.041% 13.88% 637ms 6.57% TetrahedralMesh::ImportFromMesher 1ms 0.01% 13.89% 627ms 6.46% triangulate 9ms 0.093% 13.98% 576ms 5.94% std::__new_allocator::allocate (inline) 0 0% 13.98% 570ms 5.88% std::allocator_traits::allocate (inline) 1ms 0.01% 13.99% 567ms 5.85% delaunay 1ms 0.01% 14.00% 566ms 5.84% divconqdelaunay 0 0% 14.00% 538ms 5.55% std::set::count (inline) 11ms 0.11% 14.11% 492ms 5.07% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 38ms 0.39% 14.51% 451ms 4.65% std::map::operator[] (partial-inline) 5ms 0.052% 14.56% 448ms 4.62% CellPopulationElementWriter::Visit 2ms 0.021% 14.58% 416ms 4.29% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.18% 14.75% 412ms 4.25% std::less::operator() (inline) 30ms 0.31% 15.06% 409ms 4.22% std::_Rb_tree::_M_insert_ (inline) 12ms 0.12% 15.19% 395ms 4.07% AbstractCellPopulation::GetCellUsingLocationIndex 395ms 4.07% 19.26% 395ms 4.07% std::operator< (inline) 0 0% 19.26% 393ms 4.05% std::_Rb_tree::_M_create_node (inline) 0 0% 19.26% 380ms 3.92% std::_Rb_tree::_M_get_node (inline) 8ms 0.082% 19.34% 379ms 3.91% MeshBasedCellPopulation::AcceptCellWriter 82ms 0.85% 20.19% 379ms 3.91% __GI___libc_free 12ms 0.12% 20.31% 372ms 3.84% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 362ms 3.73% 24.04% 362ms 3.73% std::_Rb_tree::_S_right (inline) 8ms 0.082% 24.12% 360ms 3.71% cvLsSolve 0 0% 24.12% 356ms 3.67% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 24.12% 353ms 3.64% std::_Rb_tree::lower_bound (inline) 0 0% 24.12% 353ms 3.64% std::map::lower_bound (inline) 95ms 0.98% 25.10% 347ms 3.58% __dynamic_cast 0 0% 25.10% 342ms 3.53% std::map::find (inline) 20ms 0.21% 25.31% 339ms 3.49% N_VWrmsNorm 3ms 0.031% 25.34% 337ms 3.47% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.15% 25.49% 334ms 3.44% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.052% 25.55% 328ms 3.38% Element::Element 157ms 1.62% 27.16% 328ms 3.38% _int_malloc 0 0% 27.16% 328ms 3.38% std::_Rb_tree::_M_drop_node (inline) 48ms 0.49% 27.66% 327ms 3.37% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.01% 27.67% 320ms 3.30% Element::RegisterWithNodes (inline) 9ms 0.093% 27.76% 320ms 3.30% Node::AddElement 79ms 0.81% 28.58% 319ms 3.29% N_VWrmsNorm_Serial 3ms 0.031% 28.61% 316ms 3.26% MutableMesh::ReIndex 4ms 0.041% 28.65% 316ms 3.26% SUNLinSolSolve 2ms 0.021% 28.67% 314ms 3.24% cvLsDQJac 51ms 0.53% 29.20% 314ms 3.24% std::_Rb_tree::_M_erase 8ms 0.082% 29.28% 312ms 3.22% SUNLinSolSolve_Dense 51ms 0.53% 29.80% 311ms 3.21% cvLsDenseDQJac 0 0% 29.80% 306ms 3.15% std::set::~set (inline) 81ms 0.84% 30.64% 304ms 3.13% cvRestore 274ms 2.82% 33.46% 297ms 3.06% _int_free 7ms 0.072% 33.54% 287ms 2.96% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.15% 33.69% 276ms 2.85% std::__new_allocator::deallocate (inline) 83ms 0.86% 34.55% 273ms 2.81% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 34.55% 271ms 2.79% std::allocator_traits::deallocate (inline) 9ms 0.093% 34.64% 268ms 2.76% CvodeRhsAdaptor 261ms 2.69% 37.33% 261ms 2.69% SUNDlsMat_denseGETRS 2ms 0.021% 37.35% 259ms 2.67% AbstractCellProperty::IsSubType (inline) 8ms 0.082% 37.43% 255ms 2.63% std::_Rb_tree::erase 0 0% 37.43% 254ms 2.62% std::set::erase (inline) 252ms 2.60% 40.03% 252ms 2.60% N_VBufUnpack_Serial 8ms 0.082% 40.11% 250ms 2.58% divconqrecurse 4ms 0.041% 40.15% 247ms 2.55% SUNLinSolSetup 6ms 0.062% 40.22% 246ms 2.54% Node::RemoveElement 4ms 0.041% 40.26% 243ms 2.51% SUNLinSolSetup_Dense 0 0% 40.26% 242ms 2.49% std::_Rb_tree::_M_put_node (inline) 66ms 0.68% 40.94% 239ms 2.46% mergehulls 1ms 0.01% 40.95% 239ms 2.46% std::ostream::operator<< (inline) 22ms 0.23% 41.18% 237ms 2.44% std::ostream::_M_insert 8ms 0.082% 41.26% 233ms 2.40% AbstractCellProperty::IsType (inline) 56ms 0.58% 41.84% 233ms 2.40% N_VLinearSum_Serial 7ms 0.072% 41.91% 233ms 2.40% boost::detail::shared_count::~shared_count (inline) 0 0% 41.91% 233ms 2.40% boost::shared_ptr::~shared_ptr (inline) 232ms 2.39% 44.30% 232ms 2.39% SUNDlsMat_denseGETRF 1ms 0.01% 44.31% 224ms 2.31% CvodeAdaptor::SetupCvode 223ms 2.30% 46.61% 223ms 2.30% __strcmp_evex 1ms 0.01% 46.62% 223ms 2.30% alternateaxes 211ms 2.18% 48.79% 222ms 2.29% vertexmedian 81ms 0.84% 49.63% 218ms 2.25% WntCellCycleOdeSystem::EvaluateYDerivatives 218ms 2.25% 51.88% 218ms 2.25% boost::detail::sp_counted_base::release 27ms 0.28% 52.15% 216ms 2.23% N_VLinearSum 215ms 2.22% 54.37% 215ms 2.22% N_VWSqrSumLocal_Serial 18ms 0.19% 54.56% 210ms 2.16% Element::ResetIndex 6ms 0.062% 54.62% 207ms 2.13% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.021% 54.64% 203ms 2.09% Cell::GetCellProliferativeType 0 0% 54.64% 201ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 22ms 0.23% 54.87% 196ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.031% 54.90% 193ms 1.99% SUNMatScaleAddI 190ms 1.96% 56.86% 190ms 1.96% SUNMatScaleAddI_Dense 113ms 1.16% 58.02% 190ms 1.96% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 58.02% 190ms 1.96% std::_Vector_base::_M_allocate (inline) 5ms 0.052% 58.07% 188ms 1.94% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 58.07% 188ms 1.94% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 58.07% 182ms 1.88% Cell::GetMutationState 3ms 0.031% 58.10% 168ms 1.73% std::_Rb_tree::_Rb_tree (partial-inline) 12ms 0.12% 58.23% 165ms 1.70% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.041% 58.27% 165ms 1.70% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.01% 58.28% 160ms 1.65% TetrahedralMesh::RefreshJacobianCachedData 0 0% 58.28% 158ms 1.63% OffLatticeSimulation::ApplyBoundaries 7ms 0.072% 58.35% 154ms 1.59% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 58.35% 154ms 1.59% std::set::set (inline) 12ms 0.12% 58.47% 153ms 1.58% AbstractTetrahedralElement::CalculateJacobian 36ms 0.37% 58.85% 151ms 1.56% AbstractCellProperty::IsSame 19ms 0.2% 59.04% 150ms 1.55% std::_Rb_tree::_M_copy (inline) 12ms 0.12% 59.16% 150ms 1.55% std::vector::push_back (inline) 10ms 0.1% 59.27% 146ms 1.51% Element::MarkAsDeleted 5ms 0.052% 59.32% 146ms 1.51% SUNMatCopy 1ms 0.01% 59.33% 144ms 1.48% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.062% 59.39% 142ms 1.46% AbstractTetrahedralElement::CalculateInverseJacobian 138ms 1.42% 60.81% 141ms 1.45% SUNMatCopy_Dense 1ms 0.01% 60.82% 140ms 1.44% NodeLocationWriter::Visit 1ms 0.01% 60.84% 137ms 1.41% MeshBasedCellPopulation::GetDampingConstant 1ms 0.01% 60.85% 135ms 1.39% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.072% 60.92% 134ms 1.38% std::vector::_M_realloc_insert 61ms 0.63% 61.55% 131ms 1.35% std::_Rb_tree::_M_clone_node (inline) 10ms 0.1% 61.65% 123ms 1.27% std::num_put::_M_insert_float 23ms 0.24% 61.89% 117ms 1.21% AbstractTetrahedralElement::RefreshJacobian 0 0% 61.89% 116ms 1.20% Cell::HasCellProperty (inline) 3ms 0.031% 61.92% 115ms 1.19% CellPropertyCollection::HasProperty 115ms 1.19% 63.10% 115ms 1.19% incircle 18ms 0.19% 63.29% 115ms 1.19% std::type_info::operator== (inline) 1ms 0.01% 63.30% 113ms 1.16% CellProliferativeTypesWriter::VisitCell 15ms 0.15% 63.45% 110ms 1.13% N_VScale 34ms 0.35% 63.80% 109ms 1.12% N_VScale_Serial 80ms 0.82% 64.63% 109ms 1.12% malloc_consolidate 7ms 0.072% 64.70% 106ms 1.09% cvEwtSet 74ms 0.76% 65.46% 105ms 1.08% AbstractElement::GetNodeGlobalIndex 2ms 0.021% 65.48% 105ms 1.08% TetrahedralMesh::Clear 4ms 0.041% 65.53% 102ms 1.05% CVodeSetLinearSolver 102ms 1.05% 66.58% 102ms 1.05% std::_Rb_tree_insert_and_rebalance 0 0% 66.58% 100ms 1.03% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 66.58% 100ms 1.03% OutputFileHandler::OpenOutputFile 3ms 0.031% 66.61% 98ms 1.01% std::__cxx11::collate::do_transform 6ms 0.062% 66.67% 96ms 0.99% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.062% 66.73% 94ms 0.97% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 2ms 0.021% 66.75% 93ms 0.96% boost::numeric::ublas::vector_assign (inline) 0 0% 66.75% 92ms 0.95% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 66.75% 92ms 0.95% ___vsnprintf 12ms 0.12% 66.88% 92ms 0.95% __printf_buffer 0 0% 66.88% 92ms 0.95% __vsnprintf_internal (inline) 91ms 0.94% 67.81% 91ms 0.94% std::vector::size (inline) 8ms 0.082% 67.90% 87ms 0.9% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 67.90% 86ms 0.89% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 67.90% 86ms 0.89% std::_Rb_tree::_M_destroy_node (inline) 57ms 0.59% 68.48% 86ms 0.89% std::_Rb_tree::equal_range (inline) 0 0% 68.48% 86ms 0.89% std::__new_allocator::destroy (inline) 0 0% 68.48% 86ms 0.89% std::allocator_traits::destroy (inline) 5ms 0.052% 68.54% 85ms 0.88% N_VCloneEmpty_Serial 46ms 0.47% 69.01% 83ms 0.86% AbstractElement::GetNodeLocation 80ms 0.82% 69.84% 83ms 0.86% vertexsort 2ms 0.021% 69.86% 81ms 0.84% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 69.86% 80ms 0.82% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.01% 69.87% 79ms 0.81% AbstractTetrahedralElement::AbstractTetrahedralElement 51ms 0.53% 70.39% 79ms 0.81% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 45ms 0.46% 70.86% 78ms 0.8% Cylindrical2dMesh::GetVectorFromAtoB 4ms 0.041% 70.90% 78ms 0.8% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.021% 70.92% 77ms 0.79% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.052% 70.97% 77ms 0.79% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 76ms 0.78% 71.75% 76ms 0.78% std::_Rb_tree_increment 76ms 0.78% 72.54% 76ms 0.78% unlink_chunk 1ms 0.01% 72.55% 75ms 0.77% __printf_fp_l_buffer 0 0% 72.55% 75ms 0.77% __printf_fp_spec (inline) 6ms 0.062% 72.61% 73ms 0.75% std::_Rb_tree_const_iterator::operator++ (inline) 41ms 0.42% 73.03% 72ms 0.74% __printf_fp_buffer_1 0 0% 73.03% 71ms 0.73% Cell::SetCellProliferativeType 0 0% 73.03% 67ms 0.69% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 67ms 0.69% 73.72% 67ms 0.69% [libchaste_mesh.so] 24ms 0.25% 73.97% 67ms 0.69% boost::numeric::ublas::indexing_vector_assign 3ms 0.031% 74.00% 66ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 14ms 0.14% 74.14% 66ms 0.68% std::num_put::_M_insert_int 1ms 0.01% 74.15% 65ms 0.67% N_VClone 1ms 0.01% 74.16% 64ms 0.66% N_VClone_Serial 64ms 0.66% 74.82% 64ms 0.66% [libchaste_cell_based.so] 28ms 0.29% 75.11% 63ms 0.65% AbstractTetrahedralMesh::GetElement 7ms 0.072% 75.19% 63ms 0.65% SUNRpowerR 63ms 0.65% 75.84% 63ms 0.65% std::_Rb_tree_rebalance_for_erase 60ms 0.62% 76.45% 60ms 0.62% Node::GetIndex 4ms 0.041% 76.49% 60ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 17ms 0.18% 76.67% 56ms 0.58% N_VScaleAddMulti 2ms 0.021% 76.69% 56ms 0.58% Node::~Node 4ms 0.041% 76.73% 56ms 0.58% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 76.73% 56ms 0.58% tcache_get (inline) 56ms 0.58% 77.31% 56ms 0.58% tcache_get_n (inline) 5ms 0.052% 77.36% 55ms 0.57% __pow 10ms 0.1% 77.46% 53ms 0.55% std::__ostream_insert 2ms 0.021% 77.48% 53ms 0.55% std::vector::_M_default_append 0 0% 77.48% 53ms 0.55% std::vector::resize (inline) 6ms 0.062% 77.55% 52ms 0.54% Cylindrical2dMesh::CreateMirrorNodes 51ms 0.53% 78.07% 51ms 0.53% counterclockwise 4ms 0.041% 78.11% 50ms 0.52% __ieee754_pow_fma 0 0% 78.11% 50ms 0.52% std::basic_ofstream::basic_ofstream (inline) 6ms 0.062% 78.18% 49ms 0.51% CellLocationIndexWriter::VisitCell 3ms 0.031% 78.21% 49ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 49ms 0.51% 78.71% 49ms 0.51% N_VCopyOps 0 0% 78.71% 49ms 0.51% std::basic_ofstream::open (inline)