File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6458ms, 84.15% of 7674ms total Dropped 582 nodes (cum <= 38.37ms) flat flat% sum% cum cum% 0 0% 0% 7637ms 99.52% __libc_start_call_main 0 0% 0% 7637ms 99.52% __libc_start_main_impl 0 0% 0% 7637ms 99.52% _start 0 0% 0% 7622ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7622ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7622ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7622ms 99.32% main 0 0% 0% 7584ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7584ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7584ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7581ms 98.79% AbstractCellBasedSimulation::Solve 0 0% 0% 3260ms 42.48% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.026% 2806ms 36.57% MeshBasedCellPopulation::Update 0 0% 0.026% 2712ms 35.34% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.026% 1598ms 20.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.026% 1425ms 18.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.039% 1408ms 18.35% MutableMesh::ReMesh 5ms 0.065% 0.1% 1368ms 17.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.12% 1339ms 17.45% MeshBasedCellPopulation::UpdateNodePairs 19ms 0.25% 0.36% 1162ms 15.14% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.052% 0.42% 966ms 12.59% AbstractTwoBodyInteractionForce::AddForceContribution 110ms 1.43% 1.85% 943ms 12.29% TetrahedralMesh::EdgeIterator::operator++ 402ms 5.24% 7.09% 932ms 12.14% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.10% 888ms 11.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 6ms 0.078% 7.18% 880ms 11.47% CellPopulationElementWriter::Visit 7ms 0.091% 7.27% 874ms 11.39% CellPropertyCollection::GetPropertiesType (inline) 254ms 3.31% 10.58% 870ms 11.34% __dynamic_cast 53ms 0.69% 11.27% 853ms 11.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 28ms 0.36% 11.64% 746ms 9.72% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.039% 11.68% 744ms 9.70% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.091% 11.77% 734ms 9.56% TetrahedralMesh::ImportFromMesher 1ms 0.013% 11.78% 685ms 8.93% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.79% 628ms 8.18% std::ostream::operator<< (inline) 99ms 1.29% 13.08% 626ms 8.16% std::ostream::_M_insert 56ms 0.73% 13.81% 590ms 7.69% std::map::operator[] (partial-inline) 32ms 0.42% 14.23% 575ms 7.49% operator new 183ms 2.38% 16.61% 541ms 7.05% __GI___libc_malloc 28ms 0.36% 16.98% 530ms 6.91% std::__new_allocator::allocate (inline) 0 0% 16.98% 526ms 6.85% std::allocator_traits::allocate (inline) 1ms 0.013% 16.99% 524ms 6.83% triangulate 3ms 0.039% 17.03% 517ms 6.74% std::set::insert (inline) 6ms 0.078% 17.11% 514ms 6.70% std::_Rb_tree::_M_insert_unique 2ms 0.026% 17.14% 502ms 6.54% Cell::GetCellProliferativeType 493ms 6.42% 23.56% 493ms 6.42% __strcmp_avx2 0 0% 23.56% 483ms 6.29% std::_Rb_tree::lower_bound (inline) 0 0% 23.56% 483ms 6.29% std::map::lower_bound (inline) 15ms 0.2% 23.76% 474ms 6.18% std::_Rb_tree::find (inline) 5ms 0.065% 23.82% 467ms 6.09% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.82% 446ms 5.81% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.82% 440ms 5.73% std::_Rb_tree::_M_create_node (inline) 40ms 0.52% 24.34% 438ms 5.71% std::_Rb_tree::~_Rb_tree (inline) 0 0% 24.34% 438ms 5.71% std::set::count (inline) 0 0% 24.34% 437ms 5.69% delaunay 4ms 0.052% 24.39% 437ms 5.69% divconqdelaunay 203ms 2.65% 27.04% 429ms 5.59% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.04% 416ms 5.42% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.04% 411ms 5.36% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 27.05% 407ms 5.30% NodeLocationWriter::Visit 0 0% 27.05% 396ms 5.16% std::set::~set (inline) 88ms 1.15% 28.20% 395ms 5.15% std::_Rb_tree::_M_erase 27ms 0.35% 28.55% 392ms 5.11% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.026% 28.58% 376ms 4.90% Cell::GetMutationState 4ms 0.052% 28.63% 353ms 4.60% std::set::set (inline) 13ms 0.17% 28.80% 347ms 4.52% std::less::operator() (inline) 27ms 0.35% 29.15% 341ms 4.44% std::num_put::_M_insert_float 334ms 4.35% 33.50% 334ms 4.35% std::operator< (inline) 36ms 0.47% 33.97% 326ms 4.25% std::_Rb_tree::_M_copy (inline) 323ms 4.21% 38.18% 323ms 4.21% std::_Rb_tree::_S_right (inline) 1ms 0.013% 38.19% 318ms 4.14% MeshBasedCellPopulation::GetDampingConstant 2ms 0.026% 38.22% 317ms 4.13% AbstractCentreBasedCellPopulation::GetDampingConstant 102ms 1.33% 39.55% 315ms 4.10% __GI___libc_free 23ms 0.3% 39.85% 313ms 4.08% std::_Rb_tree::_M_insert_ (inline) 8ms 0.1% 39.95% 312ms 4.07% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.091% 40.04% 310ms 4.04% Cell::ReadyToDivide 6ms 0.078% 40.12% 310ms 4.04% Element::Element 69ms 0.9% 41.02% 286ms 3.73% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.02% 286ms 3.73% std::_Rb_tree::_M_drop_node (inline) 6ms 0.078% 41.10% 277ms 3.61% std::__cxx11::collate::do_transform 10ms 0.13% 41.23% 275ms 3.58% std::__new_allocator::deallocate (inline) 0 0% 41.23% 272ms 3.54% std::allocator_traits::deallocate (inline) 177ms 2.31% 43.54% 270ms 3.52% _int_malloc 2ms 0.026% 43.56% 263ms 3.43% ___vsnprintf 43ms 0.56% 44.12% 261ms 3.40% __printf_buffer 0 0% 44.12% 261ms 3.40% __vsnprintf_internal (inline) 12ms 0.16% 44.28% 260ms 3.39% divconqrecurse 1ms 0.013% 44.29% 240ms 3.13% CellProliferativeTypesWriter::VisitCell 69ms 0.9% 45.19% 238ms 3.10% mergehulls 1ms 0.013% 45.20% 231ms 3.01% AbstractCellProperty::IsType (inline) 0 0% 45.20% 228ms 2.97% std::_Rb_tree::_M_put_node (inline) 7ms 0.091% 45.30% 220ms 2.87% CellPropertyCollection::HasProperty 0 0% 45.30% 217ms 2.83% Cell::HasCellProperty (inline) 179ms 2.33% 47.63% 214ms 2.79% _int_free 24ms 0.31% 47.94% 210ms 2.74% TetrahedralMesh::Clear 7ms 0.091% 48.03% 209ms 2.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 12ms 0.16% 48.19% 199ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.039% 48.23% 199ms 2.59% Element::RegisterWithNodes (inline) 3ms 0.039% 48.27% 196ms 2.55% Node::AddElement 58ms 0.76% 49.02% 195ms 2.54% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.039% 49.06% 194ms 2.53% __printf_fp_spec (inline) 16ms 0.21% 49.27% 191ms 2.49% __printf_fp_l_buffer 54ms 0.7% 49.97% 178ms 2.32% AbstractCellProperty::IsSame 6ms 0.078% 50.05% 174ms 2.27% MeshBasedCellPopulation::SpringsEnd (inline) 94ms 1.22% 51.28% 170ms 2.22% __printf_fp_buffer_1 62ms 0.81% 52.08% 159ms 2.07% std::__ostream_insert 21ms 0.27% 52.36% 158ms 2.06% AbstractTetrahedralElement::CalculateJacobian 2ms 0.026% 52.38% 151ms 1.97% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 52.38% 148ms 1.93% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 52.40% 147ms 1.92% AbstractCellBasedWriter::CloseFile 0 0% 52.40% 147ms 1.92% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 52.41% 146ms 1.90% OutputFileHandler::OutputFileHandler 1ms 0.013% 52.42% 146ms 1.90% std::basic_ofstream::close (inline) 1ms 0.013% 52.44% 145ms 1.89% OutputFileHandler::CommonConstructor 31ms 0.4% 52.84% 145ms 1.89% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 52.85% 145ms 1.89% std::basic_filebuf::close 0 0% 52.85% 142ms 1.85% OutputFileHandler::OpenOutputFile 0 0% 52.85% 142ms 1.85% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 52.87% 140ms 1.82% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 52.88% 139ms 1.81% boost::numeric::ublas::vector_assign (inline) 0 0% 52.88% 136ms 1.77% std::basic_ofstream::open (inline) 1ms 0.013% 52.89% 134ms 1.75% std::basic_filebuf::open 36ms 0.47% 53.36% 129ms 1.68% std::num_put::_M_insert_int 4ms 0.052% 53.41% 129ms 1.68% std::operator<< (inline) 4ms 0.052% 53.47% 128ms 1.67% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.1% 53.57% 125ms 1.63% Node::~Node 0 0% 53.57% 125ms 1.63% TetrahedralMesh::RefreshJacobianCachedData 29ms 0.38% 53.95% 124ms 1.62% std::type_info::operator== (inline) 0 0% 53.95% 117ms 1.52% std::basic_filebuf::_M_terminate_output 3ms 0.039% 53.99% 117ms 1.52% std::basic_filebuf::overflow 2ms 0.026% 54.01% 116ms 1.51% AbstractTetrahedralElement::AbstractTetrahedralElement 14ms 0.18% 54.20% 116ms 1.51% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 54.20% 115ms 1.50% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 54.21% 114ms 1.49% std::basic_filebuf::_M_convert_to_external 14ms 0.18% 54.39% 113ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 9ms 0.12% 54.51% 113ms 1.47% boost::detail::shared_count::~shared_count (inline) 0 0% 54.51% 113ms 1.47% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 54.52% 113ms 1.47% std::__basic_file::xsputn 13ms 0.17% 54.69% 112ms 1.46% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.026% 54.72% 110ms 1.43% AbstractTetrahedralElement::CalculateInverseJacobian 110ms 1.43% 56.15% 110ms 1.43% std::_Rb_tree_increment 108ms 1.41% 57.56% 108ms 1.41% __GI___libc_write 0 0% 57.56% 107ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 72ms 0.94% 58.50% 106ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 33ms 0.43% 58.93% 105ms 1.37% boost::numeric::ublas::indexing_vector_assign 5ms 0.065% 58.99% 105ms 1.37% std::vector::push_back (inline) 104ms 1.36% 60.35% 104ms 1.36% std::_Rb_tree_insert_and_rebalance 101ms 1.32% 61.66% 101ms 1.32% incircle 99ms 1.29% 62.95% 100ms 1.30% boost::detail::sp_counted_base::release 9ms 0.12% 63.07% 98ms 1.28% AbstractTetrahedralElement::RefreshJacobian 6ms 0.078% 63.15% 98ms 1.28% std::vector::_M_realloc_insert 36ms 0.47% 63.62% 97ms 1.26% boost::shared_ptr::shared_ptr (inline) 95ms 1.24% 64.86% 95ms 1.24% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 64.86% 95ms 1.24% _IO_new_fopen 0 0% 64.86% 95ms 1.24% __fopen_internal (inline) 0 0% 64.86% 95ms 1.24% std::__basic_file::open 3ms 0.039% 64.89% 93ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 64.91% 93ms 1.21% _IO_new_file_fopen 1ms 0.013% 64.92% 92ms 1.20% alternateaxes 1ms 0.013% 64.93% 91ms 1.19% __GI__IO_file_open 58ms 0.76% 65.69% 91ms 1.19% std::basic_filebuf::xsputn 0 0% 65.69% 90ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 86ms 1.12% 66.81% 90ms 1.17% vertexmedian 89ms 1.16% 67.97% 89ms 1.16% [libchaste_cell_based.so] 62ms 0.81% 68.78% 84ms 1.09% std::basic_streambuf::xsputn 36ms 0.47% 69.25% 79ms 1.03% AbstractElement::GetNodeLocation 2ms 0.026% 69.27% 79ms 1.03% std::filesystem::status 78ms 1.02% 70.29% 78ms 1.02% __GI___fstatat64 78ms 1.02% 71.31% 78ms 1.02% __libc_open64 49ms 0.64% 71.94% 74ms 0.96% malloc_consolidate 4ms 0.052% 72.00% 73ms 0.95% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 72.01% 73ms 0.95% Cell::GetCellId 1ms 0.013% 72.02% 73ms 0.95% std::filesystem::create_directory 68ms 0.89% 72.91% 73ms 0.95% vertexsort 0 0% 72.91% 71ms 0.93% tcache_get (inline) 71ms 0.93% 73.83% 71ms 0.93% tcache_get_n (inline) 67ms 0.87% 74.71% 67ms 0.87% counterclockwise 49ms 0.64% 75.35% 64ms 0.83% AbstractElement::GetNodeGlobalIndex 5ms 0.065% 75.41% 64ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeA 11ms 0.14% 75.55% 61ms 0.79% CellPropertyCollection::AddProperty 6ms 0.078% 75.63% 61ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeB 57ms 0.74% 76.37% 61ms 0.79% boost::detail::shared_count::shared_count (inline) 59ms 0.77% 77.14% 59ms 0.77% __memcpy_avx_unaligned_erms 0 0% 77.14% 58ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.14% 58ms 0.76% std::__new_allocator::destroy (inline) 0 0% 77.14% 58ms 0.76% std::allocator_traits::destroy (inline) 47ms 0.61% 77.76% 57ms 0.74% std::num_put::do_put 0 0% 77.76% 55ms 0.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.76% 55ms 0.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.039% 77.80% 53ms 0.69% Node::ConstructNodeAttributes (inline) 36ms 0.47% 78.26% 51ms 0.66% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.026% 78.29% 51ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.29% 51ms 0.66% std::vector::vector (inline) 0 0% 78.29% 50ms 0.65% Node::ClearAppliedForce 27ms 0.35% 78.64% 49ms 0.64% AbstractCellCycleModel::GetAge 15ms 0.2% 78.84% 49ms 0.64% Determinant (inline) 49ms 0.64% 79.48% 49ms 0.64% [libchaste_mesh.so] 49ms 0.64% 80.11% 49ms 0.64% std::vector::size (inline) 48ms 0.63% 80.74% 48ms 0.63% Node::GetIndex 48ms 0.63% 81.37% 48ms 0.63% Node::IsDeleted 48ms 0.63% 81.99% 48ms 0.63% boost::shared_ptr::operator-> (inline) 32ms 0.42% 82.41% 48ms 0.63% hack_digit 1ms 0.013% 82.42% 47ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 82.42% 47ms 0.61% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 82.43% 46ms 0.6% BoundaryNodeWriter::Visit 46ms 0.6% 83.03% 46ms 0.6% boost::numeric::ublas::c_vector::operator() (partial-inline) 4ms 0.052% 83.09% 46ms 0.6% std::_Vector_base::_M_deallocate (inline) 0 0% 83.09% 45ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.09% 44ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.09% 44ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.09% 44ms 0.57% std::_Vector_base::_M_create_storage (inline) 0 0% 83.09% 44ms 0.57% std::map::map (inline) 0 0% 83.09% 43ms 0.56% std::map::~map (inline) 1ms 0.013% 83.10% 42ms 0.55% NodeAttributes::NodeAttributes 0 0% 83.10% 41ms 0.53% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 83.28% 41ms 0.53% boost::numeric::ublas::vector_norm_2::apply (inline) 28ms 0.36% 83.65% 40ms 0.52% writeedges 39ms 0.51% 84.15% 39ms 0.51% [libstdc++.so.6.0.33]