File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5064ms, 83.14% of 6091ms total Dropped 519 nodes (cum <= 30.45ms) flat flat% sum% cum cum% 0 0% 0% 6059ms 99.47% __libc_start_call_main 0 0% 0% 6059ms 99.47% __libc_start_main_impl 0 0% 0% 6059ms 99.47% _start 0 0% 0% 6045ms 99.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6045ms 99.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6045ms 99.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6045ms 99.24% main 0 0% 0% 6005ms 98.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6005ms 98.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6005ms 98.59% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.016% 0.016% 6003ms 98.56% AbstractCellBasedSimulation::Solve 0 0% 0.016% 2648ms 43.47% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.016% 0.033% 2274ms 37.33% MeshBasedCellPopulation::Update 1ms 0.016% 0.049% 2188ms 35.92% AbstractCellPopulation::WriteResultsToFiles 2ms 0.033% 0.082% 1154ms 18.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.016% 0.099% 1129ms 18.54% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.099% 1100ms 18.06% MutableMesh::ReMesh 0 0% 0.099% 1039ms 17.06% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.082% 0.18% 998ms 16.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 21ms 0.34% 0.53% 981ms 16.11% MeshBasedCellPopulation::SpringIterator::operator++ 88ms 1.44% 1.97% 780ms 12.81% TetrahedralMesh::EdgeIterator::operator++ 364ms 5.98% 7.95% 746ms 12.25% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.016% 7.96% 720ms 11.82% AbstractTwoBodyInteractionForce::AddForceContribution 166ms 2.73% 10.69% 710ms 11.66% __dynamic_cast 4ms 0.066% 10.75% 705ms 11.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 7ms 0.11% 10.87% 683ms 11.21% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.066% 10.93% 676ms 11.10% CellPopulationElementWriter::Visit 48ms 0.79% 11.72% 656ms 10.77% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.082% 11.80% 591ms 9.70% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.43% 12.23% 585ms 9.60% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.18% 12.41% 571ms 9.37% TetrahedralMesh::ImportFromMesher 3ms 0.049% 12.46% 557ms 9.14% AbstractCellProperty::IsSubType (inline) 0 0% 12.46% 482ms 7.91% std::ostream::operator<< (inline) 90ms 1.48% 13.94% 480ms 7.88% std::ostream::_M_insert 47ms 0.77% 14.71% 441ms 7.24% std::map::operator[] (partial-inline) 434ms 7.13% 21.84% 434ms 7.13% __strcmp_evex 21ms 0.34% 22.18% 422ms 6.93% std::_Rb_tree::find (inline) 1ms 0.016% 22.20% 418ms 6.86% triangulate 23ms 0.38% 22.57% 412ms 6.76% operator new 4ms 0.066% 22.64% 405ms 6.65% Cell::GetCellProliferativeType 0 0% 22.64% 389ms 6.39% std::set::count (inline) 189ms 3.10% 25.74% 388ms 6.37% __cxxabiv1::__si_class_type_info::__do_dyncast 128ms 2.10% 27.84% 386ms 6.34% __GI___libc_malloc 8ms 0.13% 27.98% 374ms 6.14% std::set::insert (inline) 0 0% 27.98% 373ms 6.12% delaunay 0 0% 27.98% 373ms 6.12% divconqdelaunay 21ms 0.34% 28.32% 371ms 6.09% std::__new_allocator::allocate (inline) 0 0% 28.32% 367ms 6.03% std::allocator_traits::allocate (inline) 3ms 0.049% 28.37% 366ms 6.01% LegacyCellProliferativeTypesWriter::VisitCell 9ms 0.15% 28.52% 366ms 6.01% std::_Rb_tree::_M_insert_unique 3ms 0.049% 28.57% 363ms 5.96% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.57% 359ms 5.89% std::_Rb_tree::lower_bound (inline) 0 0% 28.57% 359ms 5.89% std::map::lower_bound (inline) 35ms 0.57% 29.14% 350ms 5.75% std::_Rb_tree::~_Rb_tree (inline) 0 0% 29.14% 331ms 5.43% std::set::~set (inline) 0 0% 29.14% 312ms 5.12% std::_Rb_tree::_M_create_node (inline) 68ms 1.12% 30.26% 312ms 5.12% std::_Rb_tree::_M_erase 0 0% 30.26% 291ms 4.78% NodeLocationWriter::Visit 0 0% 30.26% 289ms 4.74% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 30.26% 284ms 4.66% std::_Rb_tree::_M_get_node (inline) 1ms 0.016% 30.27% 270ms 4.43% Cell::GetMutationState 12ms 0.2% 30.47% 270ms 4.43% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.033% 30.50% 267ms 4.38% Cell::ReadyToDivide 4ms 0.066% 30.57% 266ms 4.37% std::less::operator() (inline) 262ms 4.30% 34.87% 262ms 4.30% std::operator< (inline) 23ms 0.38% 35.25% 251ms 4.12% std::num_put::_M_insert_float 2ms 0.033% 35.28% 244ms 4.01% std::set::set (inline) 1ms 0.016% 35.30% 233ms 3.83% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 75ms 1.23% 36.53% 232ms 3.81% __GI___libc_free 0 0% 36.53% 231ms 3.79% AbstractCellBasedWriter::OpenOutputFileForAppend 6ms 0.099% 36.63% 230ms 3.78% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 36.63% 230ms 3.78% OutputFileHandler::OpenOutputFile 12ms 0.2% 36.82% 226ms 3.71% std::_Rb_tree::_M_insert_ (inline) 23ms 0.38% 37.20% 224ms 3.68% std::_Rb_tree::_M_copy (inline) 0 0% 37.20% 223ms 3.66% Element::Element 223ms 3.66% 40.86% 223ms 3.66% std::_Rb_tree::_S_right (inline) 0 0% 40.86% 219ms 3.60% std::_Rb_tree::_M_drop_node (inline) 2ms 0.033% 40.90% 218ms 3.58% MeshBasedCellPopulation::GetDampingConstant 1ms 0.016% 40.91% 215ms 3.53% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.15% 41.06% 207ms 3.40% divconqrecurse 7ms 0.11% 41.18% 201ms 3.30% std::__new_allocator::deallocate (inline) 0 0% 41.18% 198ms 3.25% std::allocator_traits::deallocate (inline) 3ms 0.049% 41.22% 197ms 3.23% std::__cxx11::collate::do_transform 54ms 0.89% 42.11% 195ms 3.20% std::_Rb_tree::_M_clone_node (inline) 123ms 2.02% 44.13% 194ms 3.19% _int_malloc 0 0% 44.13% 191ms 3.14% CellProliferativeTypesWriter::VisitCell 56ms 0.92% 45.05% 191ms 3.14% mergehulls 2ms 0.033% 45.08% 190ms 3.12% AbstractCellProperty::IsType (inline) 7ms 0.11% 45.20% 185ms 3.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.20% 185ms 3.04% ___vsnprintf 0 0% 45.20% 185ms 3.04% __vsnprintf_internal (inline) 26ms 0.43% 45.62% 183ms 3.00% __printf_buffer 0 0% 45.62% 181ms 2.97% Cell::HasCellProperty (inline) 3ms 0.049% 45.67% 181ms 2.97% CellPropertyCollection::HasProperty 9ms 0.15% 45.82% 178ms 2.92% TetrahedralMesh::Clear 7ms 0.11% 45.94% 174ms 2.86% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 45.94% 172ms 2.82% std::_Rb_tree::_M_put_node (inline) 134ms 2.20% 48.14% 157ms 2.58% _int_free 32ms 0.53% 48.66% 150ms 2.46% AbstractCellProperty::IsSame 6ms 0.099% 48.76% 150ms 2.46% MeshBasedCellPopulation::SpringsEnd (inline) 30ms 0.49% 49.25% 146ms 2.40% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.049% 49.30% 146ms 2.40% __printf_fp_l_buffer 0 0% 49.30% 146ms 2.40% __printf_fp_spec (inline) 3ms 0.049% 49.35% 143ms 2.35% Element::RegisterWithNodes (inline) 68ms 1.12% 50.47% 138ms 2.27% __printf_fp_buffer_1 2ms 0.033% 50.50% 136ms 2.23% Node::AddElement 40ms 0.66% 51.16% 131ms 2.15% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 51.16% 118ms 1.94% std::basic_ofstream::basic_ofstream (inline) 25ms 0.41% 51.57% 118ms 1.94% std::type_info::operator== (inline) 8ms 0.13% 51.70% 115ms 1.89% AbstractTetrahedralElement::CalculateJacobian 5ms 0.082% 51.78% 113ms 1.86% Node::~Node 0 0% 51.78% 112ms 1.84% std::basic_filebuf::open 0 0% 51.78% 112ms 1.84% std::basic_ofstream::open (inline) 2ms 0.033% 51.81% 108ms 1.77% alternateaxes 0 0% 51.81% 107ms 1.76% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.81% 106ms 1.74% AbstractCellBasedWriter::CloseFile 4ms 0.066% 51.88% 106ms 1.74% boost::numeric::ublas::vector_assign (inline) 0 0% 51.88% 106ms 1.74% std::basic_filebuf::close 0 0% 51.88% 106ms 1.74% std::basic_ofstream::close (inline) 95ms 1.56% 53.44% 105ms 1.72% vertexmedian 0 0% 53.44% 104ms 1.71% OutputFileHandler::CommonConstructor 0 0% 53.44% 104ms 1.71% OutputFileHandler::OutputFileHandler 84ms 1.38% 54.82% 104ms 1.71% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 54.82% 103ms 1.69% OutputFileHandler::MakeFoldersAndReturnFullPath 28ms 0.46% 55.28% 101ms 1.66% std::num_put::_M_insert_int 4ms 0.066% 55.34% 96ms 1.58% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.15% 55.49% 95ms 1.56% boost::detail::shared_count::~shared_count (inline) 0 0% 55.49% 95ms 1.56% boost::shared_ptr::~shared_ptr (inline) 34ms 0.56% 56.05% 95ms 1.56% std::__ostream_insert 0 0% 56.05% 93ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 0 0% 56.05% 92ms 1.51% FilesystemPermissions::SetFilePermissions (inline) 92ms 1.51% 57.56% 92ms 1.51% __GI_fchmodat 0 0% 57.56% 92ms 1.51% std::filesystem::permissions 89ms 1.46% 59.02% 89ms 1.46% [libchaste_cell_based.so] 11ms 0.18% 59.20% 88ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.033% 59.23% 87ms 1.43% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.066% 59.30% 85ms 1.40% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.25% 59.55% 85ms 1.40% AbstractTetrahedralElement::RefreshJacobian 0 0% 59.55% 85ms 1.40% _IO_new_fopen 0 0% 59.55% 85ms 1.40% __fopen_internal (inline) 0 0% 59.55% 85ms 1.40% std::__basic_file::open 84ms 1.38% 60.93% 84ms 1.38% incircle 0 0% 60.93% 83ms 1.36% std::_Vector_base::_M_allocate (inline) 2ms 0.033% 60.96% 83ms 1.36% std::vector::push_back (inline) 1ms 0.016% 60.98% 80ms 1.31% _IO_new_file_fopen 2ms 0.033% 61.01% 80ms 1.31% std::operator<< (inline) 2ms 0.033% 61.04% 79ms 1.30% std::basic_filebuf::overflow 0 0% 61.04% 78ms 1.28% __GI__IO_file_open 78ms 1.28% 62.32% 78ms 1.28% __GI___libc_write 74ms 1.21% 63.54% 78ms 1.28% boost::detail::sp_counted_base::release 14ms 0.23% 63.77% 78ms 1.28% std::vector::_M_realloc_insert 0 0% 63.77% 77ms 1.26% std::__basic_file::xsputn 0 0% 63.77% 77ms 1.26% std::basic_filebuf::_M_convert_to_external 0 0% 63.77% 77ms 1.26% std::basic_filebuf::_M_terminate_output 1ms 0.016% 63.78% 76ms 1.25% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.25% 64.03% 74ms 1.21% AbstractCellPopulation::Iterator::IsRealCell (inline) 24ms 0.39% 64.42% 72ms 1.18% boost::numeric::ublas::indexing_vector_assign 38ms 0.62% 65.05% 72ms 1.18% boost::shared_ptr::shared_ptr (inline) 70ms 1.15% 66.20% 70ms 1.15% __libc_open64 70ms 1.15% 67.35% 70ms 1.15% std::_Rb_tree_increment 69ms 1.13% 68.48% 69ms 1.13% std::_Rb_tree_insert_and_rebalance 65ms 1.07% 69.55% 65ms 1.07% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.099% 69.64% 65ms 1.07% std::_Rb_tree_const_iterator::operator++ (inline) 44ms 0.72% 70.37% 65ms 1.07% std::basic_filebuf::xsputn 0 0% 70.37% 64ms 1.05% Cell::GetCellId 4ms 0.066% 70.43% 63ms 1.03% TetrahedralMesh::EdgeIterator::GetNodeB 28ms 0.46% 70.89% 61ms 1.00% AbstractElement::GetNodeLocation 1ms 0.016% 70.91% 60ms 0.99% std::filesystem::status 60ms 0.99% 71.89% 60ms 0.99% std::vector::size (inline) 59ms 0.97% 72.86% 59ms 0.97% __GI___fstatat64 2ms 0.033% 72.89% 57ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 72.89% 56ms 0.92% tcache_get (inline) 56ms 0.92% 73.81% 56ms 0.92% tcache_get_n (inline) 0 0% 73.81% 55ms 0.9% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 37ms 0.61% 74.42% 54ms 0.89% malloc_consolidate 0 0% 74.42% 53ms 0.87% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.84% 75.26% 53ms 0.87% vertexsort 52ms 0.85% 76.11% 52ms 0.85% __memcpy_avx512_unaligned_erms 1ms 0.016% 76.13% 49ms 0.8% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.25% 76.37% 48ms 0.79% AbstractTetrahedralMesh::GetElement 0 0% 76.37% 47ms 0.77% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.37% 47ms 0.77% std::__new_allocator::destroy (inline) 0 0% 76.37% 47ms 0.77% std::allocator_traits::destroy (inline) 0 0% 76.37% 46ms 0.76% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 76.37% 46ms 0.76% std::filesystem::create_directory 33ms 0.54% 76.92% 45ms 0.74% AbstractElement::GetNodeGlobalIndex 6ms 0.099% 77.02% 45ms 0.74% CellPropertyCollection::AddProperty 45ms 0.74% 77.75% 45ms 0.74% counterclockwise 35ms 0.57% 78.33% 45ms 0.74% std::num_put::do_put 1ms 0.016% 78.35% 44ms 0.72% AbstractCentreBasedCellPopulation::CreateCellPair 24ms 0.39% 78.74% 43ms 0.71% std::basic_streambuf::xsputn 21ms 0.34% 79.08% 42ms 0.69% hack_digit 41ms 0.67% 79.76% 41ms 0.67% Node::GetIndex 0 0% 79.76% 38ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 38ms 0.62% 80.38% 38ms 0.62% [libstdc++.so.6.0.33] 0 0% 80.38% 38ms 0.62% std::vector::vector (inline) 0 0% 80.38% 37ms 0.61% BoundaryNodeWriter::Visit 0 0% 80.38% 37ms 0.61% CxxTest::RealWorldDescription::setUp 0 0% 80.38% 37ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.38% 37ms 0.61% PMPI_Init_thread 0 0% 80.38% 37ms 0.61% PetscInitialize 0 0% 80.38% 37ms 0.61% PetscSetup::setUpWorld 0 0% 80.38% 37ms 0.61% PetscSetupUtils::CommonSetup 0 0% 80.38% 37ms 0.61% PetscSetupUtils::InitialisePetsc 0 0% 80.38% 37ms 0.61% _dl_init 0 0% 80.38% 37ms 0.61% call_init (inline) 0 0% 80.38% 37ms 0.61% ompi_mpi_init 14ms 0.23% 80.61% 35ms 0.57% AbstractTetrahedralMesh::GetNumAllElements 0 0% 80.61% 35ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 80.61% 35ms 0.57% Node::ClearAppliedForce 0 0% 80.61% 35ms 0.57% Node::ConstructNodeAttributes (inline) 35ms 0.57% 81.19% 35ms 0.57% Node::rGetLocation 0 0% 81.19% 35ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 12ms 0.2% 81.38% 34ms 0.56% Determinant (inline) 33ms 0.54% 81.92% 34ms 0.56% boost::detail::shared_count::shared_count (inline) 20ms 0.33% 82.25% 34ms 0.56% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.016% 82.27% 33ms 0.54% 3ms 0.049% 82.32% 33ms 0.54% Element::~Element 23ms 0.38% 82.70% 33ms 0.54% TetrahedralMesh::SolveElementMapping 0 0% 82.70% 32ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 0 0% 82.70% 32ms 0.53% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 4ms 0.066% 82.76% 32ms 0.53% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 82.76% 32ms 0.53% std::_Vector_base::_Vector_base (inline) 14ms 0.23% 82.99% 31ms 0.51% AbstractCellCycleModel::GetAge 2ms 0.033% 83.02% 31ms 0.51% NodeAttributes::NodeAttributes 0 0% 83.02% 31ms 0.51% _dl_start_user 3ms 0.049% 83.07% 31ms 0.51% std::_Vector_base::_M_create_storage (inline) 4ms 0.066% 83.14% 31ms 0.51% std::__copy_move::__copy_m (inline) 0 0% 83.14% 31ms 0.51% std::__copy_move_a (inline) 0 0% 83.14% 31ms 0.51% std::__copy_move_a1 (inline) 0 0% 83.14% 31ms 0.51% std::__copy_move_a2 (inline) 0 0% 83.14% 31ms 0.51% std::__new_allocator::construct (inline) 0 0% 83.14% 31ms 0.51% std::allocator_traits::construct (inline) 0 0% 83.14% 31ms 0.51% std::copy (inline)