File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6556ms, 83.42% of 7859ms total Dropped 607 nodes (cum <= 39.30ms) flat flat% sum% cum cum% 0 0% 0% 7826ms 99.58% __libc_start_call_main 0 0% 0% 7826ms 99.58% __libc_start_main_impl 0 0% 0% 7826ms 99.58% _start 0 0% 0% 7812ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7812ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7812ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7812ms 99.40% main 0 0% 0% 7777ms 98.96% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7777ms 98.96% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7777ms 98.96% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7774ms 98.92% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3382ms 43.03% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.025% 2888ms 36.75% MeshBasedCellPopulation::Update 0 0% 0.025% 2872ms 36.54% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.051% 1513ms 19.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.064% 1449ms 18.44% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.089% 1387ms 17.65% MutableMesh::ReMesh 2ms 0.025% 0.11% 1383ms 17.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.14% 0.25% 1345ms 17.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.43% 1245ms 15.84% MeshBasedCellPopulation::SpringIterator::operator++ 103ms 1.31% 1.74% 1036ms 13.18% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.051% 1.79% 939ms 11.95% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 417ms 5.31% 7.10% 935ms 11.90% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.14% 7.24% 919ms 11.69% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.076% 7.32% 901ms 11.46% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.1% 7.42% 882ms 11.22% CellPopulationElementWriter::Visit 258ms 3.28% 10.70% 873ms 11.11% __dynamic_cast 1ms 0.013% 10.71% 785ms 9.99% MeshBasedCellPopulation::AcceptCellWriter 29ms 0.37% 11.08% 778ms 9.90% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.076% 11.16% 720ms 9.16% TetrahedralMesh::ImportFromMesher 28ms 0.36% 11.52% 714ms 9.09% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.051% 11.57% 695ms 8.84% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.58% 608ms 7.74% std::ostream::operator<< (inline) 83ms 1.06% 12.64% 606ms 7.71% std::ostream::_M_insert 60ms 0.76% 13.40% 570ms 7.25% std::map::operator[] (partial-inline) 45ms 0.57% 13.97% 559ms 7.11% operator new 4ms 0.051% 14.02% 558ms 7.10% std::set::insert (inline) 12ms 0.15% 14.17% 554ms 7.05% std::_Rb_tree::_M_insert_unique 4ms 0.051% 14.23% 547ms 6.96% Cell::GetCellProliferativeType 0 0% 14.23% 518ms 6.59% triangulate 18ms 0.23% 14.45% 516ms 6.57% std::_Rb_tree::find (inline) 158ms 2.01% 16.47% 515ms 6.55% __GI___libc_malloc 498ms 6.34% 22.80% 498ms 6.34% __strcmp_avx2 35ms 0.45% 23.25% 494ms 6.29% std::__new_allocator::allocate (inline) 0 0% 23.25% 490ms 6.23% std::allocator_traits::allocate (inline) 9ms 0.11% 23.36% 483ms 6.15% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.36% 478ms 6.08% std::set::count (inline) 3ms 0.038% 23.40% 470ms 5.98% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.40% 461ms 5.87% std::_Rb_tree::lower_bound (inline) 0 0% 23.40% 461ms 5.87% std::map::lower_bound (inline) 197ms 2.51% 25.91% 455ms 5.79% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.013% 25.92% 446ms 5.68% delaunay 4ms 0.051% 25.97% 444ms 5.65% divconqdelaunay 30ms 0.38% 26.35% 420ms 5.34% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.35% 410ms 5.22% std::_Rb_tree::_M_create_node (inline) 0 0% 26.35% 402ms 5.12% std::set::~set (inline) 0 0% 26.35% 394ms 5.01% NodeLocationWriter::Visit 0 0% 26.35% 389ms 4.95% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.025% 26.38% 384ms 4.89% Cell::GetMutationState 90ms 1.15% 27.52% 384ms 4.89% std::_Rb_tree::_M_erase 0 0% 27.52% 371ms 4.72% std::_Rb_tree::_M_get_node (inline) 10ms 0.13% 27.65% 364ms 4.63% std::less::operator() (inline) 354ms 4.50% 32.15% 354ms 4.50% std::operator< (inline) 16ms 0.2% 32.36% 344ms 4.38% std::num_put::_M_insert_float 2ms 0.025% 32.38% 340ms 4.33% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 32.40% 338ms 4.30% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.17% 32.56% 335ms 4.26% std::_Rb_tree::_M_insert_ (inline) 20ms 0.25% 32.82% 335ms 4.26% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.064% 32.88% 325ms 4.14% Cell::ReadyToDivide 17ms 0.22% 33.10% 313ms 3.98% AbstractCellPopulation::IsCellAttachedToLocationIndex 101ms 1.29% 34.38% 313ms 3.98% __GI___libc_free 308ms 3.92% 38.30% 308ms 3.92% std::_Rb_tree::_S_right (inline) 5ms 0.064% 38.36% 308ms 3.92% std::set::set (inline) 0 0% 38.36% 298ms 3.79% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.36% 297ms 3.78% AbstractCellBasedWriter::OpenOutputFileForAppend 28ms 0.36% 38.72% 292ms 3.72% std::_Rb_tree::_M_copy (inline) 0 0% 38.72% 289ms 3.68% OutputFileHandler::OpenOutputFile 6ms 0.076% 38.80% 287ms 3.65% Element::Element 198ms 2.52% 41.32% 287ms 3.65% _int_malloc 0 0% 41.32% 272ms 3.46% std::_Rb_tree::_M_drop_node (inline) 2ms 0.025% 41.34% 267ms 3.40% CellProliferativeTypesWriter::VisitCell 91ms 1.16% 42.50% 259ms 3.30% std::_Rb_tree::_M_clone_node (inline) 12ms 0.15% 42.65% 257ms 3.27% std::__new_allocator::deallocate (inline) 10ms 0.13% 42.78% 256ms 3.26% divconqrecurse 1ms 0.013% 42.79% 255ms 3.24% std::__cxx11::collate::do_transform 0 0% 42.79% 252ms 3.21% std::allocator_traits::deallocate (inline) 4ms 0.051% 42.84% 250ms 3.18% AbstractCellProperty::IsType (inline) 1ms 0.013% 42.86% 247ms 3.14% ___vsnprintf 0 0% 42.86% 246ms 3.13% __vsnprintf_internal (inline) 6ms 0.076% 42.93% 240ms 3.05% CellPropertyCollection::HasProperty 0 0% 42.93% 239ms 3.04% Cell::HasCellProperty (inline) 27ms 0.34% 43.28% 237ms 3.02% __printf_buffer 60ms 0.76% 44.04% 235ms 2.99% mergehulls 4ms 0.051% 44.09% 220ms 2.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 44.09% 219ms 2.79% std::_Rb_tree::_M_put_node (inline) 177ms 2.25% 46.34% 212ms 2.70% _int_free 5ms 0.064% 46.41% 211ms 2.68% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 77ms 0.98% 47.39% 207ms 2.63% std::_Rb_tree::_M_get_insert_unique_pos (inline) 22ms 0.28% 47.67% 206ms 2.62% TetrahedralMesh::Clear 6ms 0.076% 47.74% 193ms 2.46% Element::RegisterWithNodes (inline) 1ms 0.013% 47.75% 185ms 2.35% __printf_fp_spec (inline) 2ms 0.025% 47.78% 184ms 2.34% Node::AddElement 8ms 0.1% 47.88% 184ms 2.34% __printf_fp_l_buffer 58ms 0.74% 48.62% 183ms 2.33% AbstractCellProperty::IsSame 6ms 0.076% 48.70% 165ms 2.10% MeshBasedCellPopulation::SpringsEnd (inline) 55ms 0.7% 49.40% 164ms 2.09% TetrahedralMesh::EdgesEnd (partial-inline) 72ms 0.92% 50.31% 160ms 2.04% __printf_fp_buffer_1 3ms 0.038% 50.35% 152ms 1.93% boost::numeric::ublas::vector_assign (inline) 57ms 0.73% 51.08% 147ms 1.87% std::__ostream_insert 0 0% 51.08% 147ms 1.87% std::basic_ofstream::basic_ofstream (inline) 10ms 0.13% 51.20% 143ms 1.82% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 51.22% 142ms 1.81% std::basic_filebuf::open 0 0% 51.22% 142ms 1.81% std::basic_ofstream::open (inline) 1ms 0.013% 51.23% 139ms 1.77% OutputFileHandler::OutputFileHandler 0 0% 51.23% 138ms 1.76% OutputFileHandler::CommonConstructor 1ms 0.013% 51.24% 136ms 1.73% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.13% 51.37% 135ms 1.72% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 51.38% 132ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.38% 127ms 1.62% AbstractCellBasedWriter::CloseFile 0 0% 51.38% 127ms 1.62% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.38% 127ms 1.62% std::basic_filebuf::close 0 0% 51.38% 127ms 1.62% std::basic_ofstream::close (inline) 126ms 1.60% 52.98% 126ms 1.60% std::_Rb_tree_increment 26ms 0.33% 53.31% 125ms 1.59% std::type_info::operator== (inline) 0 0% 53.31% 124ms 1.58% TetrahedralMesh::RefreshJacobianCachedData 33ms 0.42% 53.73% 124ms 1.58% std::num_put::_M_insert_int 4ms 0.051% 53.79% 121ms 1.54% Node::~Node 40ms 0.51% 54.29% 120ms 1.53% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 54.31% 120ms 1.53% std::_Vector_base::_M_allocate (inline) 4ms 0.051% 54.36% 119ms 1.51% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 54.37% 118ms 1.50% std::operator<< (inline) 10ms 0.13% 54.50% 117ms 1.49% boost::detail::shared_count::~shared_count (inline) 0 0% 54.50% 117ms 1.49% boost::shared_ptr::~shared_ptr (inline) 3ms 0.038% 54.54% 116ms 1.48% std::vector::push_back (inline) 15ms 0.19% 54.73% 115ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 31ms 0.39% 55.12% 114ms 1.45% boost::numeric::ublas::indexing_vector_assign 0 0% 55.12% 113ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 113ms 1.44% 56.56% 113ms 1.44% std::_Rb_tree_insert_and_rebalance 112ms 1.43% 57.98% 112ms 1.43% incircle 111ms 1.41% 59.40% 111ms 1.41% [libchaste_cell_based.so] 18ms 0.23% 59.63% 110ms 1.40% AbstractTetrahedralElement::RefreshJacobian 0 0% 59.63% 110ms 1.40% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.038% 59.66% 110ms 1.40% std::filesystem::permissions 2ms 0.025% 59.69% 109ms 1.39% alternateaxes 0 0% 59.69% 109ms 1.39% std::__basic_file::open 1ms 0.013% 59.70% 108ms 1.37% _IO_new_fopen 0 0% 59.70% 107ms 1.36% __fopen_internal (inline) 101ms 1.29% 60.99% 107ms 1.36% vertexmedian 14ms 0.18% 61.17% 106ms 1.35% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 61.17% 106ms 1.35% _IO_new_file_fopen 106ms 1.35% 62.51% 106ms 1.35% __GI_fchmodat 7ms 0.089% 62.60% 106ms 1.35% std::vector::_M_realloc_insert 4ms 0.051% 62.65% 104ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 62.67% 104ms 1.32% __GI__IO_file_open 102ms 1.30% 63.96% 104ms 1.32% boost::detail::sp_counted_base::release 56ms 0.71% 64.68% 94ms 1.20% std::basic_streambuf::xsputn 3ms 0.038% 64.72% 93ms 1.18% std::basic_filebuf::overflow 0 0% 64.72% 92ms 1.17% std::basic_filebuf::_M_terminate_output 90ms 1.15% 65.86% 91ms 1.16% __libc_open64 1ms 0.013% 65.87% 90ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 65.87% 90ms 1.15% std::__basic_file::xsputn 0 0% 65.87% 90ms 1.15% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 65.89% 89ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 89ms 1.13% 67.02% 89ms 1.13% __GI___libc_write 84ms 1.07% 68.09% 84ms 1.07% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 59ms 0.75% 68.84% 82ms 1.04% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 81ms 1.03% 69.87% 81ms 1.03% __memcpy_avx_unaligned_erms 56ms 0.71% 70.58% 81ms 1.03% std::basic_filebuf::xsputn 77ms 0.98% 71.56% 80ms 1.02% boost::detail::shared_count::shared_count (inline) 34ms 0.43% 71.99% 79ms 1.01% AbstractElement::GetNodeLocation 68ms 0.87% 72.86% 78ms 0.99% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 72.87% 78ms 0.99% Cell::GetCellId 0 0% 72.87% 77ms 0.98% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 72.88% 77ms 0.98% std::filesystem::create_directory 55ms 0.7% 73.58% 76ms 0.97% malloc_consolidate 9ms 0.11% 73.70% 74ms 0.94% CellPropertyCollection::AddProperty 73ms 0.93% 74.63% 73ms 0.93% Node::GetIndex 2ms 0.025% 74.65% 72ms 0.92% AbstractCellPopulation::GetLocationIndexUsingCell 61ms 0.78% 75.43% 70ms 0.89% std::num_put::do_put 61ms 0.78% 76.21% 70ms 0.89% vertexsort 3ms 0.038% 76.24% 68ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 76.24% 65ms 0.83% tcache_get (inline) 65ms 0.83% 77.07% 65ms 0.83% tcache_get_n (inline) 4ms 0.051% 77.12% 64ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 5ms 0.064% 77.19% 63ms 0.8% Node::ConstructNodeAttributes (inline) 0 0% 77.19% 62ms 0.79% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 62ms 0.79% 77.97% 62ms 0.79% [libchaste_mesh.so] 62ms 0.79% 78.76% 62ms 0.79% counterclockwise 0 0% 78.76% 60ms 0.76% Node::ClearAppliedForce 0 0% 78.76% 58ms 0.74% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 2ms 0.025% 78.79% 58ms 0.74% std::filesystem::status 56ms 0.71% 79.50% 56ms 0.71% __GI___fstatat64 28ms 0.36% 79.86% 55ms 0.7% AbstractCellCycleModel::GetAge 0 0% 79.86% 55ms 0.7% AbstractCentreBasedCellPopulation::CreateCellPair 35ms 0.45% 80.30% 53ms 0.67% hack_digit 0 0% 80.30% 53ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.30% 53ms 0.67% std::__new_allocator::destroy (inline) 0 0% 80.30% 53ms 0.67% std::allocator_traits::destroy (inline) 52ms 0.66% 80.96% 52ms 0.66% std::vector::size (inline) 30ms 0.38% 81.35% 51ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 81.35% 50ms 0.64% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.35% 50ms 0.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.35% 49ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.051% 81.40% 49ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.40% 48ms 0.61% std::vector::vector (inline) 47ms 0.6% 82.00% 47ms 0.6% boost::shared_ptr::operator-> (inline) 2ms 0.025% 82.02% 46ms 0.59% BoundaryNodeWriter::Visit 1ms 0.013% 82.03% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.03% 44ms 0.56% std::_Vector_base::_Vector_base (inline) 0 0% 82.03% 44ms 0.56% std::__new_allocator::construct (inline) 0 0% 82.03% 44ms 0.56% std::allocator_traits::construct (inline) 23ms 0.29% 82.33% 43ms 0.55% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 82.33% 43ms 0.55% std::_Vector_base::_M_create_storage (inline) 42ms 0.53% 82.86% 42ms 0.53% boost::numeric::ublas::c_vector::operator() 4ms 0.051% 82.91% 41ms 0.52% NodeAttributes::NodeAttributes 40ms 0.51% 83.42% 40ms 0.51% Node::rGetLocation