File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6802ms, 85.18% of 7985ms total Dropped 563 nodes (cum <= 39.92ms) flat flat% sum% cum cum% 0 0% 0% 7947ms 99.52% __libc_start_call_main 0 0% 0% 7947ms 99.52% __libc_start_main_impl 0 0% 0% 7947ms 99.52% _start 0 0% 0% 7929ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7929ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7929ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7929ms 99.30% main 0 0% 0% 7890ms 98.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7890ms 98.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7890ms 98.81% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7887ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3399ms 42.57% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.038% 2923ms 36.61% MeshBasedCellPopulation::Update 0 0% 0.038% 2917ms 36.53% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1565ms 19.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1514ms 18.96% MutableMesh::ReMesh 1ms 0.013% 0.05% 1411ms 17.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.05% 1358ms 17.01% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.063% 0.11% 1357ms 16.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.16% 0.28% 1176ms 14.73% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.05% 0.33% 959ms 12.01% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.013% 0.34% 954ms 11.95% AbstractTwoBodyInteractionForce::AddForceContribution 105ms 1.31% 1.65% 951ms 11.91% TetrahedralMesh::EdgeIterator::operator++ 443ms 5.55% 7.20% 942ms 11.80% std::_Rb_tree::_M_lower_bound (inline) 263ms 3.29% 10.49% 924ms 11.57% __dynamic_cast 5ms 0.063% 10.56% 916ms 11.47% CellPopulationElementWriter::Visit 12ms 0.15% 10.71% 880ms 11.02% CellPropertyCollection::GetPropertiesType (inline) 51ms 0.64% 11.35% 859ms 10.76% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 35ms 0.44% 11.78% 832ms 10.42% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.13% 11.91% 783ms 9.81% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.038% 11.95% 740ms 9.27% AbstractCellProperty::IsSubType (inline) 7ms 0.088% 12.04% 730ms 9.14% TetrahedralMesh::ImportFromMesher 53ms 0.66% 12.70% 633ms 7.93% std::map::operator[] (partial-inline) 4ms 0.05% 12.75% 593ms 7.43% triangulate 31ms 0.39% 13.14% 580ms 7.26% operator new 1ms 0.013% 13.15% 573ms 7.18% std::ostream::operator<< (inline) 103ms 1.29% 14.44% 572ms 7.16% std::ostream::_M_insert 556ms 6.96% 21.40% 556ms 6.96% __strcmp_avx2 176ms 2.20% 23.61% 545ms 6.83% __GI___libc_malloc 0 0% 23.61% 522ms 6.54% std::_Rb_tree::lower_bound (inline) 0 0% 23.61% 522ms 6.54% std::map::lower_bound (inline) 5ms 0.063% 23.67% 520ms 6.51% std::set::insert (inline) 0 0% 23.67% 517ms 6.47% delaunay 6ms 0.075% 23.74% 516ms 6.46% divconqdelaunay 3ms 0.038% 23.78% 515ms 6.45% std::_Rb_tree::_M_insert_unique 4ms 0.05% 23.83% 512ms 6.41% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.05% 23.88% 509ms 6.37% Cell::GetCellProliferativeType 28ms 0.35% 24.23% 508ms 6.36% std::__new_allocator::allocate (inline) 0 0% 24.23% 503ms 6.30% std::allocator_traits::allocate (inline) 210ms 2.63% 26.86% 475ms 5.95% __cxxabiv1::__si_class_type_info::__do_dyncast 20ms 0.25% 27.11% 472ms 5.91% std::_Rb_tree::find (inline) 0 0% 27.11% 460ms 5.76% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.11% 447ms 5.60% std::_Rb_tree::_M_create_node (inline) 45ms 0.56% 27.68% 437ms 5.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.68% 435ms 5.45% std::set::count (inline) 0 0% 27.68% 416ms 5.21% std::_Rb_tree::_M_get_node (inline) 0 0% 27.68% 414ms 5.18% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.68% 412ms 5.16% std::set::~set (inline) 79ms 0.99% 28.67% 384ms 4.81% std::_Rb_tree::_M_erase 3ms 0.038% 28.70% 372ms 4.66% Cell::GetMutationState 29ms 0.36% 29.07% 368ms 4.61% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 29.08% 345ms 4.32% NodeLocationWriter::Visit 3ms 0.038% 29.12% 341ms 4.27% std::set::set (inline) 1ms 0.013% 29.13% 334ms 4.18% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 22ms 0.28% 29.41% 334ms 4.18% std::_Rb_tree::_M_insert_ (inline) 331ms 4.15% 33.55% 331ms 4.15% std::_Rb_tree::_S_right (inline) 0 0% 33.55% 329ms 4.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.55% 326ms 4.08% OutputFileHandler::OpenOutputFile 91ms 1.14% 34.69% 313ms 3.92% __GI___libc_free 3ms 0.038% 34.73% 311ms 3.89% Element::Element 5ms 0.063% 34.79% 310ms 3.88% Cell::ReadyToDivide 26ms 0.33% 35.12% 309ms 3.87% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 35.13% 303ms 3.79% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 35.17% 302ms 3.78% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.088% 35.25% 302ms 3.78% std::less::operator() (inline) 26ms 0.33% 35.58% 301ms 3.77% std::num_put::_M_insert_float 8ms 0.1% 35.68% 299ms 3.74% AbstractCellPopulation::IsCellAttachedToLocationIndex 295ms 3.69% 39.37% 295ms 3.69% std::operator< (inline) 12ms 0.15% 39.52% 293ms 3.67% divconqrecurse 0 0% 39.52% 286ms 3.58% std::_Rb_tree::_M_drop_node (inline) 183ms 2.29% 41.82% 282ms 3.53% _int_malloc 4ms 0.05% 41.87% 278ms 3.48% std::__new_allocator::deallocate (inline) 0 0% 41.87% 275ms 3.44% std::allocator_traits::deallocate (inline) 78ms 0.98% 42.84% 274ms 3.43% std::_Rb_tree::_M_clone_node (inline) 68ms 0.85% 43.69% 268ms 3.36% mergehulls 2ms 0.025% 43.72% 262ms 3.28% AbstractCellProperty::IsType (inline) 0 0% 43.72% 258ms 3.23% Cell::HasCellProperty (inline) 1ms 0.013% 43.73% 258ms 3.23% CellPropertyCollection::HasProperty 7ms 0.088% 43.82% 254ms 3.18% std::__cxx11::collate::do_transform 2ms 0.025% 43.84% 239ms 2.99% ___vsnprintf 0 0% 43.84% 237ms 2.97% __vsnprintf_internal (inline) 29ms 0.36% 44.21% 236ms 2.96% __printf_buffer 0 0% 44.21% 227ms 2.84% std::_Rb_tree::_M_put_node (inline) 4ms 0.05% 44.26% 223ms 2.79% CellProliferativeTypesWriter::VisitCell 190ms 2.38% 46.64% 220ms 2.76% _int_free 6ms 0.075% 46.71% 218ms 2.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 46.85% 211ms 2.64% TetrahedralMesh::Clear 5ms 0.063% 46.91% 209ms 2.62% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 47.01% 207ms 2.59% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.088% 47.10% 205ms 2.57% Element::RegisterWithNodes (inline) 3ms 0.038% 47.14% 197ms 2.47% Node::AddElement 36ms 0.45% 47.59% 191ms 2.39% AbstractCellProperty::IsSame 8ms 0.1% 47.69% 191ms 2.39% __printf_fp_l_buffer 0 0% 47.69% 191ms 2.39% __printf_fp_spec (inline) 91ms 1.14% 48.83% 179ms 2.24% __printf_fp_buffer_1 70ms 0.88% 49.71% 179ms 2.24% std::_Rb_tree::_M_get_insert_unique_pos (inline) 12ms 0.15% 49.86% 177ms 2.22% AbstractTetrahedralElement::CalculateJacobian 0 0% 49.86% 161ms 2.02% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 49.87% 160ms 2.00% AbstractCellBasedWriter::CloseFile 0 0% 49.87% 160ms 2.00% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 49.87% 159ms 1.99% std::basic_filebuf::close 0 0% 49.87% 159ms 1.99% std::basic_ofstream::close (inline) 32ms 0.4% 50.27% 155ms 1.94% TetrahedralMesh::EdgesEnd (partial-inline) 30ms 0.38% 50.64% 155ms 1.94% std::type_info::operator== (inline) 5ms 0.063% 50.71% 154ms 1.93% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 50.71% 152ms 1.90% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.71% 149ms 1.87% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 50.72% 149ms 1.87% std::filesystem::permissions 146ms 1.83% 52.55% 146ms 1.83% __GI_fchmodat 1ms 0.013% 52.56% 145ms 1.82% std::basic_ofstream::open (inline) 2ms 0.025% 52.59% 144ms 1.80% std::basic_filebuf::open 1ms 0.013% 52.60% 143ms 1.79% OutputFileHandler::OutputFileHandler 2ms 0.025% 52.62% 142ms 1.78% OutputFileHandler::CommonConstructor 22ms 0.28% 52.90% 139ms 1.74% AbstractTetrahedralElement::RefreshJacobian 0 0% 52.90% 138ms 1.73% OutputFileHandler::MakeFoldersAndReturnFullPath 28ms 0.35% 53.25% 135ms 1.69% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.088% 53.34% 134ms 1.68% boost::numeric::ublas::vector_assign (inline) 8ms 0.1% 53.44% 133ms 1.67% Node::~Node 14ms 0.18% 53.61% 132ms 1.65% boost::detail::shared_count::~shared_count (inline) 0 0% 53.61% 132ms 1.65% boost::shared_ptr::~shared_ptr (inline) 127ms 1.59% 55.20% 127ms 1.59% incircle 3ms 0.038% 55.24% 125ms 1.57% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 55.25% 124ms 1.55% alternateaxes 41ms 0.51% 55.77% 123ms 1.54% std::__ostream_insert 33ms 0.41% 56.18% 123ms 1.54% std::num_put::_M_insert_int 111ms 1.39% 57.57% 122ms 1.53% vertexmedian 1ms 0.013% 57.58% 120ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.2% 57.78% 119ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 57.80% 118ms 1.48% AbstractTetrahedralElement::AbstractTetrahedralElement 88ms 1.10% 58.90% 115ms 1.44% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 54ms 0.68% 59.57% 114ms 1.43% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 59.59% 114ms 1.43% std::basic_filebuf::_M_terminate_output 1ms 0.013% 59.60% 113ms 1.42% std::basic_filebuf::_M_convert_to_external 0 0% 59.60% 113ms 1.42% std::basic_filebuf::overflow 0 0% 59.60% 112ms 1.40% std::__basic_file::xsputn 110ms 1.38% 60.98% 111ms 1.39% __GI___libc_write 0 0% 60.98% 109ms 1.37% _IO_new_fopen 0 0% 60.98% 109ms 1.37% __fopen_internal (inline) 0 0% 60.98% 109ms 1.37% std::__basic_file::open 106ms 1.33% 62.30% 108ms 1.35% boost::detail::sp_counted_base::release 1ms 0.013% 62.32% 107ms 1.34% _IO_new_file_fopen 0 0% 62.32% 106ms 1.33% __GI__IO_file_open 100ms 1.25% 63.57% 100ms 1.25% std::_Rb_tree_insert_and_rebalance 39ms 0.49% 64.06% 98ms 1.23% AbstractElement::GetNodeLocation 1ms 0.013% 64.07% 98ms 1.23% std::operator<< (inline) 34ms 0.43% 64.50% 94ms 1.18% boost::numeric::ublas::indexing_vector_assign 92ms 1.15% 65.65% 93ms 1.16% __libc_open64 91ms 1.14% 66.79% 91ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.038% 66.83% 89ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 66.84% 88ms 1.10% std::_Vector_base::_M_allocate (inline) 87ms 1.09% 67.93% 87ms 1.09% [libchaste_cell_based.so] 7ms 0.088% 68.02% 85ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 75ms 0.94% 68.95% 85ms 1.06% vertexsort 9ms 0.11% 69.07% 84ms 1.05% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.063% 69.13% 82ms 1.03% std::vector::push_back (inline) 0 0% 69.13% 80ms 1.00% tcache_get (inline) 80ms 1.00% 70.13% 80ms 1.00% tcache_get_n (inline) 57ms 0.71% 70.85% 78ms 0.98% malloc_consolidate 6ms 0.075% 70.92% 78ms 0.98% std::filesystem::status 77ms 0.96% 71.88% 77ms 0.96% std::_Rb_tree_increment 1ms 0.013% 71.90% 76ms 0.95% Cell::GetCellId 45ms 0.56% 72.46% 74ms 0.93% std::basic_filebuf::xsputn 9ms 0.11% 72.57% 74ms 0.93% std::vector::_M_realloc_insert 72ms 0.9% 73.48% 72ms 0.9% __GI___fstatat64 72ms 0.9% 74.38% 72ms 0.9% counterclockwise 0 0% 74.38% 69ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 69ms 0.86% 75.24% 69ms 0.86% Node::GetIndex 0 0% 75.24% 69ms 0.86% std::filesystem::create_directory 69ms 0.86% 76.11% 69ms 0.86% std::vector::size (inline) 48ms 0.6% 76.71% 68ms 0.85% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 76.72% 65ms 0.81% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.038% 76.76% 63ms 0.79% Node::ConstructNodeAttributes (inline) 63ms 0.79% 77.55% 63ms 0.79% __memcpy_avx_unaligned_erms 0 0% 77.55% 61ms 0.76% Node::ClearAppliedForce 55ms 0.69% 78.23% 60ms 0.75% boost::detail::shared_count::shared_count (inline) 0 0% 78.23% 59ms 0.74% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.23% 59ms 0.74% std::__new_allocator::destroy (inline) 0 0% 78.23% 59ms 0.74% std::allocator_traits::destroy (inline) 4ms 0.05% 78.28% 58ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 34ms 0.43% 78.71% 58ms 0.73% std::basic_streambuf::xsputn 56ms 0.7% 79.41% 56ms 0.7% [libchaste_mesh.so] 43ms 0.54% 79.95% 56ms 0.7% std::num_put::do_put 5ms 0.063% 80.01% 54ms 0.68% CellPropertyCollection::AddProperty 4ms 0.05% 80.06% 54ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeA 32ms 0.4% 80.46% 54ms 0.68% boost::numeric::ublas::c_matrix::operator() (partial-inline) 28ms 0.35% 80.81% 52ms 0.65% AbstractCellCycleModel::GetAge 5ms 0.063% 80.88% 52ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 80.88% 51ms 0.64% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 9ms 0.11% 80.99% 50ms 0.63% Inverse 50ms 0.63% 81.62% 50ms 0.63% [libstdc++.so.6.0.33] 0 0% 81.62% 49ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.05% 81.67% 49ms 0.61% NodeAttributes::NodeAttributes 6ms 0.075% 81.74% 49ms 0.61% std::_Vector_base::_M_deallocate (inline) 48ms 0.6% 82.34% 48ms 0.6% Node::rGetLocation 0 0% 82.34% 48ms 0.6% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.34% 48ms 0.6% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 15ms 0.19% 82.53% 47ms 0.59% Determinant (inline) 31ms 0.39% 82.92% 47ms 0.59% hack_digit 46ms 0.58% 83.49% 46ms 0.58% Node::IsDeleted 0 0% 83.49% 46ms 0.58% std::vector::vector (inline) 18ms 0.23% 83.72% 45ms 0.56% AbstractTetrahedralMesh::GetElement 33ms 0.41% 84.13% 43ms 0.54% writeedges 42ms 0.53% 84.66% 42ms 0.53% boost::numeric::ublas::same_impl_ex 0 0% 84.66% 41ms 0.51% _IO_new_fclose 41ms 0.51% 85.17% 41ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 85.17% 41ms 0.51% std::_Vector_base::_M_create_storage (inline) 0 0% 85.17% 41ms 0.51% std::_Vector_base::_Vector_base (inline) 0 0% 85.17% 41ms 0.51% std::__basic_file::close 0 0% 85.17% 40ms 0.5% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.17% 40ms 0.5% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.013% 85.18% 40ms 0.5% _IO_new_file_close_it 0 0% 85.18% 40ms 0.5% _dl_init 0 0% 85.18% 40ms 0.5% call_init (inline)