File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6464ms, 85.09% of 7597ms total Dropped 530 nodes (cum <= 37.98ms) flat flat% sum% cum cum% 0 0% 0% 7560ms 99.51% __libc_start_call_main 0 0% 0% 7560ms 99.51% __libc_start_main_impl 0 0% 0% 7560ms 99.51% _start 0 0% 0% 7545ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7545ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7545ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7545ms 99.32% main 0 0% 0% 7509ms 98.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7509ms 98.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7509ms 98.84% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7507ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0% 3236ms 42.60% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2821ms 37.13% MeshBasedCellPopulation::Update 0 0% 0.013% 2790ms 36.73% AbstractCellPopulation::WriteResultsToFiles 2ms 0.026% 0.039% 1473ms 19.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.053% 1417ms 18.65% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.066% 1361ms 17.91% MutableMesh::ReMesh 1ms 0.013% 0.079% 1317ms 17.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.066% 0.14% 1256ms 16.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.26% 0.41% 1208ms 15.90% MeshBasedCellPopulation::SpringIterator::operator++ 109ms 1.43% 1.84% 977ms 12.86% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 1.87% 900ms 11.85% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.026% 1.90% 880ms 11.58% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.14% 2.04% 875ms 11.52% CellPropertyCollection::GetPropertiesType (inline) 223ms 2.94% 4.98% 873ms 11.49% __dynamic_cast 9ms 0.12% 5.09% 816ms 10.74% CellPopulationElementWriter::Visit 385ms 5.07% 10.16% 803ms 10.57% std::_Rb_tree::_M_lower_bound (inline) 46ms 0.61% 10.77% 778ms 10.24% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.013% 10.78% 762ms 10.03% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.079% 10.86% 698ms 9.19% AbstractCellProperty::IsSubType (inline) 37ms 0.49% 11.35% 685ms 9.02% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.053% 11.40% 676ms 8.90% TetrahedralMesh::ImportFromMesher 95ms 1.25% 12.65% 653ms 8.60% std::ostream::_M_insert 0 0% 12.65% 653ms 8.60% std::ostream::operator<< (inline) 40ms 0.53% 13.18% 574ms 7.56% operator new 2ms 0.026% 13.20% 531ms 6.99% triangulate 10ms 0.13% 13.33% 525ms 6.91% std::set::insert (inline) 192ms 2.53% 15.86% 524ms 6.90% __GI___libc_malloc 7ms 0.092% 15.95% 515ms 6.78% std::_Rb_tree::_M_insert_unique 29ms 0.38% 16.34% 513ms 6.75% std::__new_allocator::allocate (inline) 510ms 6.71% 23.05% 510ms 6.71% __strcmp_avx2 0 0% 23.05% 509ms 6.70% std::allocator_traits::allocate (inline) 4ms 0.053% 23.10% 494ms 6.50% Cell::GetCellProliferativeType 4ms 0.053% 23.15% 488ms 6.42% LegacyCellProliferativeTypesWriter::VisitCell 18ms 0.24% 23.39% 485ms 6.38% std::_Rb_tree::find (inline) 222ms 2.92% 26.31% 475ms 6.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.31% 467ms 6.15% delaunay 1ms 0.013% 26.33% 465ms 6.12% divconqdelaunay 0 0% 26.33% 461ms 6.07% std::set::count (inline) 42ms 0.55% 26.88% 445ms 5.86% std::map::operator[] (partial-inline) 0 0% 26.88% 437ms 5.75% std::_Rb_tree::_M_create_node (inline) 0 0% 26.88% 417ms 5.49% std::_Rb_tree::_Alloc_node::operator() (inline) 34ms 0.45% 27.33% 411ms 5.41% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.026% 27.35% 402ms 5.29% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.35% 394ms 5.19% std::_Rb_tree::_M_get_node (inline) 0 0% 27.35% 378ms 4.98% std::set::~set (inline) 3ms 0.039% 27.39% 376ms 4.95% Cell::GetMutationState 1ms 0.013% 27.41% 373ms 4.91% NodeLocationWriter::Visit 72ms 0.95% 28.35% 373ms 4.91% std::_Rb_tree::_M_erase 25ms 0.33% 28.68% 366ms 4.82% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.68% 362ms 4.77% std::_Rb_tree::lower_bound (inline) 0 0% 28.68% 362ms 4.77% std::map::lower_bound (inline) 17ms 0.22% 28.91% 347ms 4.57% std::less::operator() (inline) 0 0% 28.91% 342ms 4.50% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.91% 340ms 4.48% AbstractCellBasedWriter::OpenOutputFileForAppend 20ms 0.26% 29.17% 339ms 4.46% std::num_put::_M_insert_float 1ms 0.013% 29.18% 334ms 4.40% OutputFileHandler::OpenOutputFile 330ms 4.34% 33.53% 330ms 4.34% std::operator< (inline) 5ms 0.066% 33.59% 326ms 4.29% std::set::set (inline) 18ms 0.24% 33.83% 325ms 4.28% std::_Rb_tree::_M_insert_ (inline) 2ms 0.026% 33.86% 299ms 3.94% Element::Element 114ms 1.50% 35.36% 299ms 3.94% __GI___libc_free 39ms 0.51% 35.87% 297ms 3.91% std::_Rb_tree::_M_copy (inline) 0 0% 35.87% 284ms 3.74% MeshBasedCellPopulation::GetDampingConstant 2ms 0.026% 35.90% 283ms 3.73% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.026% 35.92% 282ms 3.71% Cell::ReadyToDivide 0 0% 35.92% 282ms 3.71% std::_Rb_tree::_M_drop_node (inline) 10ms 0.13% 36.05% 272ms 3.58% std::__new_allocator::deallocate (inline) 6ms 0.079% 36.13% 271ms 3.57% std::__cxx11::collate::do_transform 11ms 0.14% 36.28% 266ms 3.50% divconqrecurse 0 0% 36.28% 261ms 3.44% std::allocator_traits::deallocate (inline) 167ms 2.20% 38.48% 258ms 3.40% _int_malloc 3ms 0.039% 38.52% 256ms 3.37% ___vsnprintf 57ms 0.75% 39.27% 254ms 3.34% std::_Rb_tree::_M_clone_node (inline) 0 0% 39.27% 253ms 3.33% __vsnprintf_internal (inline) 73ms 0.96% 40.23% 250ms 3.29% mergehulls 39ms 0.51% 40.74% 249ms 3.28% __printf_buffer 4ms 0.053% 40.79% 244ms 3.21% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 40.94% 230ms 3.03% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.12% 41.06% 223ms 2.94% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 41.06% 222ms 2.92% std::_Rb_tree::_M_put_node (inline) 6ms 0.079% 41.13% 221ms 2.91% AbstractCellProperty::IsType (inline) 7ms 0.092% 41.23% 217ms 2.86% CellPropertyCollection::HasProperty 0 0% 41.23% 214ms 2.82% Cell::HasCellProperty (inline) 209ms 2.75% 43.98% 209ms 2.75% std::_Rb_tree::_S_right (inline) 5ms 0.066% 44.04% 201ms 2.65% Element::RegisterWithNodes (inline) 3ms 0.039% 44.08% 193ms 2.54% Node::AddElement 2ms 0.026% 44.11% 191ms 2.51% AbstractPhaseBasedCellCycleModel::ReadyToDivide 16ms 0.21% 44.32% 186ms 2.45% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.013% 44.33% 186ms 2.45% __printf_fp_spec (inline) 6ms 0.079% 44.41% 185ms 2.44% __printf_fp_l_buffer 161ms 2.12% 46.53% 185ms 2.44% _int_free 69ms 0.91% 47.44% 183ms 2.41% std::_Rb_tree::_M_get_insert_unique_pos (inline) 90ms 1.18% 48.62% 175ms 2.30% __printf_fp_buffer_1 14ms 0.18% 48.81% 171ms 2.25% TetrahedralMesh::Clear 42ms 0.55% 49.36% 168ms 2.21% AbstractCellProperty::IsSame 42ms 0.55% 49.91% 168ms 2.21% TetrahedralMesh::EdgesEnd (partial-inline) 34ms 0.45% 50.36% 167ms 2.20% std::num_put::_M_insert_int 11ms 0.14% 50.51% 162ms 2.13% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.51% 162ms 2.13% std::basic_ofstream::basic_ofstream (inline) 5ms 0.066% 50.57% 154ms 2.03% boost::numeric::ublas::vector_assign (inline) 0 0% 50.57% 153ms 2.01% std::basic_ofstream::open (inline) 1ms 0.013% 50.59% 152ms 2.00% std::basic_filebuf::open 0 0% 50.59% 146ms 1.92% FilesystemPermissions::SetFilePermissions (inline) 146ms 1.92% 52.51% 146ms 1.92% __GI_fchmodat 0 0% 52.51% 146ms 1.92% std::filesystem::permissions 2ms 0.026% 52.53% 143ms 1.88% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 52.53% 142ms 1.87% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.026% 52.56% 138ms 1.82% OutputFileHandler::OutputFileHandler 0 0% 52.56% 137ms 1.80% AbstractCellBasedWriter::CloseFile 0 0% 52.56% 137ms 1.80% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.56% 137ms 1.80% std::basic_filebuf::close 0 0% 52.56% 137ms 1.80% std::basic_ofstream::close (inline) 15ms 0.2% 52.76% 135ms 1.78% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 52.76% 135ms 1.78% OutputFileHandler::CommonConstructor 11ms 0.14% 52.90% 131ms 1.72% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.90% 127ms 1.67% OutputFileHandler::MakeFoldersAndReturnFullPath 26ms 0.34% 53.24% 126ms 1.66% std::type_info::operator== (inline) 12ms 0.16% 53.40% 123ms 1.62% boost::detail::shared_count::~shared_count (inline) 0 0% 53.40% 123ms 1.62% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 53.42% 121ms 1.59% alternateaxes 112ms 1.47% 54.89% 118ms 1.55% vertexmedian 2ms 0.026% 54.92% 117ms 1.54% _IO_new_file_fopen 0 0% 54.92% 117ms 1.54% _IO_new_fopen 0 0% 54.92% 117ms 1.54% __fopen_internal (inline) 3ms 0.039% 54.96% 117ms 1.54% std::vector::push_back (inline) 79ms 1.04% 56.00% 116ms 1.53% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 56.01% 116ms 1.53% std::_Vector_base::_M_allocate (inline) 0 0% 56.01% 116ms 1.53% std::__basic_file::open 0 0% 56.01% 114ms 1.50% __GI__IO_file_open 14ms 0.18% 56.19% 112ms 1.47% AbstractTetrahedralElement::RefreshJacobian 110ms 1.45% 57.64% 110ms 1.45% boost::detail::sp_counted_base::release 15ms 0.2% 57.84% 110ms 1.45% std::vector::_M_realloc_insert 27ms 0.36% 58.19% 109ms 1.43% boost::numeric::ublas::indexing_vector_assign 2ms 0.026% 58.22% 108ms 1.42% std::basic_filebuf::overflow 0 0% 58.22% 107ms 1.41% std::basic_filebuf::_M_terminate_output 1ms 0.013% 58.23% 106ms 1.40% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 58.25% 105ms 1.38% std::__basic_file::xsputn 6ms 0.079% 58.33% 104ms 1.37% Node::~Node 102ms 1.34% 59.67% 104ms 1.37% __GI___libc_write 3ms 0.039% 59.71% 102ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 22ms 0.29% 60.00% 101ms 1.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 100ms 1.32% 61.31% 100ms 1.32% incircle 1ms 0.013% 61.33% 98ms 1.29% AbstractCellPopulation::Iterator::operator++ (inline) 96ms 1.26% 62.59% 98ms 1.29% __libc_open64 17ms 0.22% 62.81% 97ms 1.28% std::_Rb_tree_const_iterator::operator++ (inline) 96ms 1.26% 64.08% 96ms 1.26% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 46ms 0.61% 64.68% 94ms 1.24% boost::shared_ptr::shared_ptr (inline) 90ms 1.18% 65.87% 90ms 1.18% std::_Rb_tree_increment 89ms 1.17% 67.04% 89ms 1.17% std::_Rb_tree_insert_and_rebalance 43ms 0.57% 67.61% 89ms 1.17% std::__ostream_insert 63ms 0.83% 68.43% 86ms 1.13% std::basic_streambuf::xsputn 1ms 0.013% 68.45% 81ms 1.07% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 38ms 0.5% 68.95% 80ms 1.05% AbstractElement::GetNodeLocation 0 0% 68.95% 80ms 1.05% std::filesystem::create_directory 1ms 0.013% 68.96% 78ms 1.03% Cell::GetCellId 72ms 0.95% 69.91% 72ms 0.95% counterclockwise 47ms 0.62% 70.53% 71ms 0.93% malloc_consolidate 4ms 0.053% 70.58% 68ms 0.9% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 70.59% 67ms 0.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 46ms 0.61% 71.20% 65ms 0.86% std::basic_filebuf::xsputn 1ms 0.013% 71.21% 65ms 0.86% std::operator<< (inline) 4ms 0.053% 71.26% 64ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 71.26% 64ms 0.84% tcache_get (inline) 64ms 0.84% 72.11% 64ms 0.84% tcache_get_n (inline) 35ms 0.46% 72.57% 63ms 0.83% AbstractTetrahedralMesh::GetElement 5ms 0.066% 72.63% 63ms 0.83% CellPropertyCollection::AddProperty 63ms 0.83% 73.46% 63ms 0.83% [libchaste_cell_based.so] 52ms 0.68% 74.15% 63ms 0.83% std::num_put::do_put 58ms 0.76% 74.91% 62ms 0.82% vertexsort 61ms 0.8% 75.71% 61ms 0.8% __GI___fstatat64 1ms 0.013% 75.73% 61ms 0.8% std::filesystem::status 61ms 0.8% 76.53% 61ms 0.8% std::vector::size (inline) 0 0% 76.53% 60ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.53% 60ms 0.79% std::__new_allocator::destroy (inline) 0 0% 76.53% 60ms 0.79% std::allocator_traits::destroy (inline) 46ms 0.61% 77.14% 59ms 0.78% AbstractElement::GetNodeGlobalIndex 58ms 0.76% 77.90% 58ms 0.76% __memcpy_avx_unaligned_erms 56ms 0.74% 78.64% 56ms 0.74% [libchaste_mesh.so] 1ms 0.013% 78.65% 54ms 0.71% Node::ClearAppliedForce 0 0% 78.65% 54ms 0.71% std::vector::vector (inline) 0 0% 78.65% 53ms 0.7% Node::ConstructNodeAttributes (inline) 51ms 0.67% 79.32% 51ms 0.67% Node::GetIndex 51ms 0.67% 79.99% 51ms 0.67% boost::numeric::ublas::c_vector::operator() (inline) 37ms 0.49% 80.48% 51ms 0.67% hack_digit 0 0% 80.48% 51ms 0.67% std::_Vector_base::_Vector_base (inline) 30ms 0.39% 80.87% 50ms 0.66% boost::numeric::ublas::c_matrix::operator() (partial-inline) 4ms 0.053% 80.93% 50ms 0.66% std::__new_allocator::construct (inline) 0 0% 80.93% 50ms 0.66% std::allocator_traits::construct (inline) 5ms 0.066% 80.99% 49ms 0.64% TetrahedralMesh::EdgeIterator::GetNodeB 47ms 0.62% 81.61% 48ms 0.63% boost::detail::shared_count::shared_count (inline) 0 0% 81.61% 48ms 0.63% std::_Vector_base::_M_create_storage (inline) 0 0% 81.61% 47ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.61% 47ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 81.61% 47ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 47ms 0.62% 82.23% 47ms 0.62% __GI___mkdir 0 0% 82.23% 47ms 0.62% std::map::map (inline) 46ms 0.61% 82.84% 46ms 0.61% [libstdc++.so.6.0.33] 0 0% 82.84% 45ms 0.59% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.21% 83.05% 45ms 0.59% Determinant (inline) 44ms 0.58% 83.63% 44ms 0.58% boost::numeric::ublas::same_impl_ex 0 0% 83.63% 43ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.63% 43ms 0.57% std::_Rb_tree::_M_construct_node (inline) 0 0% 83.63% 42ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.55% 84.18% 42ms 0.55% Node::IsDeleted 18ms 0.24% 84.41% 41ms 0.54% AbstractCellCycleModel::GetAge 1ms 0.013% 84.43% 41ms 0.54% NodeAttributes::NodeAttributes 0 0% 84.43% 41ms 0.54% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 84.43% 41ms 0.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.039% 84.47% 41ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.47% 40ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 40ms 0.53% 84.99% 40ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 84.99% 40ms 0.53% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 5ms 0.066% 85.06% 40ms 0.53% std::_Rb_tree_header::_Rb_tree_header (inline) 2ms 0.026% 85.09% 39ms 0.51% std::_Vector_base::_M_deallocate (inline) 0 0% 85.09% 38ms 0.5% _dl_init 0 0% 85.09% 38ms 0.5% call_init (inline)