File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5143ms, 84.09% of 6116ms total Dropped 532 nodes (cum <= 30.58ms) flat flat% sum% cum cum% 0 0% 0% 6089ms 99.56% __libc_start_call_main 0 0% 0% 6089ms 99.56% __libc_start_main_impl 0 0% 0% 6089ms 99.56% _start 0 0% 0% 6075ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6075ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6075ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6075ms 99.33% main 0 0% 0% 6034ms 98.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6034ms 98.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6034ms 98.66% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6032ms 98.63% AbstractCellBasedSimulation::Solve 0 0% 0% 2635ms 43.08% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.033% 0.033% 2280ms 37.28% MeshBasedCellPopulation::Update 1ms 0.016% 0.049% 2229ms 36.45% AbstractCellPopulation::WriteResultsToFiles 2ms 0.033% 0.082% 1159ms 18.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.082% 1121ms 18.33% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.098% 1110ms 18.15% MutableMesh::ReMesh 0 0% 0.098% 1040ms 17.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.049% 0.15% 991ms 16.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.25% 0.39% 961ms 15.71% MeshBasedCellPopulation::SpringIterator::operator++ 104ms 1.70% 2.09% 778ms 12.72% TetrahedralMesh::EdgeIterator::operator++ 327ms 5.35% 7.44% 730ms 11.94% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.033% 7.47% 720ms 11.77% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.065% 7.54% 715ms 11.69% CellPopulationElementWriter::Visit 204ms 3.34% 10.87% 704ms 11.51% __dynamic_cast 3ms 0.049% 10.92% 703ms 11.49% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.065% 10.99% 643ms 10.51% CellPropertyCollection::GetPropertiesType (inline) 42ms 0.69% 11.67% 639ms 10.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 17ms 0.28% 11.95% 585ms 9.57% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.098% 12.05% 570ms 9.32% MeshBasedCellPopulation::AcceptCellWriter 1ms 0.016% 12.07% 541ms 8.85% AbstractCellProperty::IsSubType (inline) 10ms 0.16% 12.23% 528ms 8.63% TetrahedralMesh::ImportFromMesher 0 0% 12.23% 476ms 7.78% std::ostream::operator<< (inline) 84ms 1.37% 13.60% 475ms 7.77% std::ostream::_M_insert 53ms 0.87% 14.47% 469ms 7.67% std::map::operator[] (partial-inline) 2ms 0.033% 14.50% 457ms 7.47% triangulate 0 0% 14.50% 414ms 6.77% delaunay 1ms 0.016% 14.52% 414ms 6.77% divconqdelaunay 411ms 6.72% 21.24% 411ms 6.72% __strcmp_evex 25ms 0.41% 21.65% 408ms 6.67% operator new 4ms 0.065% 21.71% 391ms 6.39% Cell::GetCellProliferativeType 22ms 0.36% 22.07% 390ms 6.38% std::_Rb_tree::find (inline) 131ms 2.14% 24.22% 380ms 6.21% __GI___libc_malloc 0 0% 24.22% 380ms 6.21% std::_Rb_tree::lower_bound (inline) 0 0% 24.22% 380ms 6.21% std::map::lower_bound (inline) 4ms 0.065% 24.28% 373ms 6.10% LegacyCellProliferativeTypesWriter::VisitCell 9ms 0.15% 24.43% 372ms 6.08% std::set::insert (inline) 25ms 0.41% 24.84% 371ms 6.07% std::__new_allocator::allocate (inline) 0 0% 24.84% 367ms 6.00% std::allocator_traits::allocate (inline) 38ms 0.62% 25.46% 364ms 5.95% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.065% 25.52% 363ms 5.94% std::_Rb_tree::_M_insert_unique 0 0% 25.52% 352ms 5.76% std::set::count (inline) 165ms 2.70% 28.22% 345ms 5.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.22% 343ms 5.61% std::set::~set (inline) 2ms 0.033% 28.25% 338ms 5.53% AbstractCellBasedSimulation::DoCellBirth 60ms 0.98% 29.23% 322ms 5.26% std::_Rb_tree::_M_erase 0 0% 29.23% 306ms 5.00% std::_Rb_tree::_M_create_node (inline) 0 0% 29.23% 289ms 4.73% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.23% 282ms 4.61% std::_Rb_tree::_M_get_node (inline) 1ms 0.016% 29.25% 274ms 4.48% NodeLocationWriter::Visit 15ms 0.25% 29.50% 274ms 4.48% std::_Rb_tree::_Rb_tree (partial-inline) 10ms 0.16% 29.66% 266ms 4.35% std::less::operator() (inline) 3ms 0.049% 29.71% 262ms 4.28% Cell::GetMutationState 256ms 4.19% 33.89% 256ms 4.19% std::operator< (inline) 0 0% 33.89% 252ms 4.12% std::_Rb_tree::_M_drop_node (inline) 75ms 1.23% 35.12% 249ms 4.07% __GI___libc_free 1ms 0.016% 35.14% 246ms 4.02% std::set::set (inline) 6ms 0.098% 35.24% 240ms 3.92% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.2% 35.43% 240ms 3.92% std::num_put::_M_insert_float 0 0% 35.43% 238ms 3.89% Cell::ReadyToDivide 5ms 0.082% 35.51% 236ms 3.86% divconqrecurse 231ms 3.78% 39.29% 231ms 3.78% std::_Rb_tree::_S_right (inline) 8ms 0.13% 39.42% 228ms 3.73% std::__new_allocator::deallocate (inline) 0 0% 39.42% 227ms 3.71% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 39.42% 227ms 3.71% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 32ms 0.52% 39.94% 225ms 3.68% std::_Rb_tree::_M_copy (inline) 0 0% 39.94% 224ms 3.66% OutputFileHandler::OpenOutputFile 63ms 1.03% 40.97% 223ms 3.65% mergehulls 0 0% 40.97% 222ms 3.63% std::allocator_traits::deallocate (inline) 2ms 0.033% 41.01% 219ms 3.58% Element::Element 5ms 0.082% 41.09% 212ms 3.47% std::_Rb_tree::_M_insert_ (inline) 0 0% 41.09% 207ms 3.38% std::_Rb_tree::_M_put_node (inline) 2ms 0.033% 41.12% 205ms 3.35% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 41.12% 205ms 3.35% MeshBasedCellPopulation::GetDampingConstant 124ms 2.03% 43.15% 198ms 3.24% _int_malloc 5ms 0.082% 43.23% 197ms 3.22% std::__cxx11::collate::do_transform 3ms 0.049% 43.28% 189ms 3.09% AbstractCellProperty::IsType (inline) 3ms 0.049% 43.33% 188ms 3.07% CellPropertyCollection::HasProperty 3ms 0.049% 43.38% 188ms 3.07% ___vsnprintf 0 0% 43.38% 186ms 3.04% Cell::HasCellProperty (inline) 41ms 0.67% 44.05% 186ms 3.04% std::_Rb_tree::_M_clone_node (inline) 22ms 0.36% 44.41% 185ms 3.02% __printf_buffer 0 0% 44.41% 185ms 3.02% __vsnprintf_internal (inline) 145ms 2.37% 46.78% 174ms 2.84% _int_free 0 0% 46.78% 166ms 2.71% CellProliferativeTypesWriter::VisitCell 8ms 0.13% 46.91% 163ms 2.67% TetrahedralMesh::Clear 1ms 0.016% 46.93% 154ms 2.52% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.15% 47.07% 154ms 2.52% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.065% 47.14% 152ms 2.49% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.016% 47.16% 150ms 2.45% __printf_fp_spec (inline) 7ms 0.11% 47.27% 149ms 2.44% __printf_fp_l_buffer 51ms 0.83% 48.10% 147ms 2.40% std::_Rb_tree::_M_get_insert_unique_pos (inline) 31ms 0.51% 48.61% 146ms 2.39% AbstractCellProperty::IsSame 68ms 1.11% 49.72% 136ms 2.22% __printf_fp_buffer_1 4ms 0.065% 49.79% 133ms 2.17% Element::RegisterWithNodes (inline) 14ms 0.23% 50.02% 128ms 2.09% AbstractTetrahedralElement::CalculateJacobian 3ms 0.049% 50.07% 128ms 2.09% Node::AddElement 27ms 0.44% 50.51% 126ms 2.06% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.51% 120ms 1.96% OutputFileHandler::CommonConstructor 0 0% 50.51% 120ms 1.96% OutputFileHandler::OutputFileHandler 1ms 0.016% 50.52% 118ms 1.93% std::basic_filebuf::close 1ms 0.016% 50.54% 118ms 1.93% std::basic_ofstream::close (inline) 0 0% 50.54% 117ms 1.91% AbstractCellBasedWriter::CloseFile 0 0% 50.54% 117ms 1.91% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.54% 117ms 1.91% OutputFileHandler::MakeFoldersAndReturnFullPath 25ms 0.41% 50.95% 115ms 1.88% std::type_info::operator== (inline) 2ms 0.033% 50.98% 113ms 1.85% alternateaxes 104ms 1.70% 52.68% 111ms 1.81% vertexmedian 21ms 0.34% 53.02% 108ms 1.77% std::num_put::_M_insert_int 0 0% 53.02% 104ms 1.70% std::basic_ofstream::basic_ofstream (inline) 6ms 0.098% 53.12% 102ms 1.67% Node::~Node 0 0% 53.12% 101ms 1.65% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.065% 53.19% 101ms 1.65% boost::numeric::ublas::vector_assign (inline) 2ms 0.033% 53.22% 101ms 1.65% std::basic_filebuf::open 0 0% 53.22% 101ms 1.65% std::basic_ofstream::open (inline) 7ms 0.11% 53.34% 100ms 1.64% boost::detail::shared_count::~shared_count (inline) 0 0% 53.34% 100ms 1.64% boost::shared_ptr::~shared_ptr (inline) 100ms 1.64% 54.97% 100ms 1.64% incircle 5ms 0.082% 55.05% 98ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.065% 55.12% 98ms 1.60% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.098% 55.22% 94ms 1.54% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 55.22% 94ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 61ms 1% 56.21% 94ms 1.54% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 37ms 0.6% 56.82% 93ms 1.52% std::__ostream_insert 1ms 0.016% 56.83% 93ms 1.52% std::filesystem::permissions 10ms 0.16% 57.00% 91ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 91ms 1.49% 58.49% 91ms 1.49% __GI_fchmodat 0 0% 58.49% 89ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.049% 58.53% 89ms 1.46% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 58.53% 87ms 1.42% std::basic_filebuf::_M_terminate_output 0 0% 58.53% 87ms 1.42% std::basic_filebuf::overflow 1ms 0.016% 58.55% 86ms 1.41% std::_Vector_base::_M_allocate (inline) 0 0% 58.55% 86ms 1.41% std::__basic_file::xsputn 0 0% 58.55% 86ms 1.41% std::basic_filebuf::_M_convert_to_external 83ms 1.36% 59.91% 84ms 1.37% __GI___libc_write 81ms 1.32% 61.23% 83ms 1.36% boost::detail::sp_counted_base::release 82ms 1.34% 62.57% 82ms 1.34% [libchaste_cell_based.so] 13ms 0.21% 62.79% 81ms 1.32% AbstractTetrahedralElement::RefreshJacobian 6ms 0.098% 62.88% 77ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 33ms 0.54% 63.42% 75ms 1.23% boost::shared_ptr::shared_ptr (inline) 0 0% 63.42% 75ms 1.23% std::operator<< (inline) 4ms 0.065% 63.49% 74ms 1.21% std::vector::push_back (inline) 73ms 1.19% 64.68% 73ms 1.19% std::_Rb_tree_insert_and_rebalance 72ms 1.18% 65.86% 72ms 1.18% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.016% 65.88% 72ms 1.18% std::__basic_file::open 2ms 0.033% 65.91% 71ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 65.91% 71ms 1.16% _IO_new_fopen 0 0% 65.91% 71ms 1.16% __fopen_internal (inline) 0 0% 65.91% 69ms 1.13% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 69ms 1.13% 67.04% 69ms 1.13% __GI___fstatat64 39ms 0.64% 67.67% 69ms 1.13% std::basic_filebuf::xsputn 1ms 0.016% 67.69% 69ms 1.13% std::filesystem::create_directory 0 0% 67.69% 68ms 1.11% _IO_new_file_fopen 0 0% 67.69% 68ms 1.11% __GI__IO_file_open 0 0% 67.69% 68ms 1.11% std::filesystem::status 3ms 0.049% 67.74% 67ms 1.10% TetrahedralMesh::EdgeIterator::GetNodeB 6ms 0.098% 67.84% 66ms 1.08% std::vector::_M_realloc_insert 45ms 0.74% 68.57% 64ms 1.05% malloc_consolidate 0 0% 68.57% 63ms 1.03% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 68.57% 63ms 1.03% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 68.57% 63ms 1.03% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 30ms 0.49% 69.06% 62ms 1.01% AbstractElement::GetNodeLocation 22ms 0.36% 69.42% 62ms 1.01% boost::numeric::ublas::indexing_vector_assign 46ms 0.75% 70.18% 61ms 1% AbstractElement::GetNodeGlobalIndex 60ms 0.98% 71.16% 60ms 0.98% counterclockwise 56ms 0.92% 72.07% 60ms 0.98% vertexsort 58ms 0.95% 73.02% 58ms 0.95% std::vector::size (inline) 57ms 0.93% 73.95% 57ms 0.93% __libc_open64 33ms 0.54% 74.49% 57ms 0.93% std::basic_streambuf::xsputn 56ms 0.92% 75.41% 56ms 0.92% Node::GetIndex 55ms 0.9% 76.31% 55ms 0.9% __memcpy_avx512_unaligned_erms 53ms 0.87% 77.17% 53ms 0.87% std::_Rb_tree_increment 1ms 0.016% 77.19% 51ms 0.83% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.033% 77.22% 50ms 0.82% Cell::GetCellId 0 0% 77.22% 50ms 0.82% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.016% 77.24% 49ms 0.8% BoundaryNodeWriter::Visit 0 0% 77.24% 47ms 0.77% tcache_get (inline) 47ms 0.77% 78.01% 47ms 0.77% tcache_get_n (inline) 0 0% 78.01% 46ms 0.75% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 46ms 0.75% 78.76% 46ms 0.75% [libstdc++.so.6.0.33] 0 0% 78.76% 46ms 0.75% boost::numeric::ublas::norm_2 (inline) 21ms 0.34% 79.10% 46ms 0.75% boost::numeric::ublas::vector_norm_2::apply (inline) 15ms 0.25% 79.35% 45ms 0.74% AbstractTetrahedralMesh::GetElement 0 0% 79.35% 45ms 0.74% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.35% 45ms 0.74% std::__new_allocator::destroy (inline) 0 0% 79.35% 45ms 0.74% std::allocator_traits::destroy (inline) 32ms 0.52% 79.87% 45ms 0.74% std::num_put::do_put 0 0% 79.87% 43ms 0.7% Node::ClearAppliedForce 1ms 0.016% 79.89% 43ms 0.7% Node::ConstructNodeAttributes (inline) 23ms 0.38% 80.26% 43ms 0.7% hack_digit 0 0% 80.26% 42ms 0.69% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 42ms 0.69% 80.95% 42ms 0.69% boost::detail::shared_count::shared_count (inline) 3ms 0.049% 81.00% 41ms 0.67% CellPropertyCollection::AddProperty 9ms 0.15% 81.15% 41ms 0.67% TetrahedralMesh::EdgeIterator::GetNodeA 41ms 0.67% 81.82% 41ms 0.67% [libchaste_mesh.so] 14ms 0.23% 82.05% 38ms 0.62% Determinant (inline) 0 0% 82.05% 37ms 0.6% CxxTest::RealWorldDescription::setUp 0 0% 82.05% 37ms 0.6% PMPI_Init_thread 0 0% 82.05% 37ms 0.6% PetscInitialize 0 0% 82.05% 37ms 0.6% PetscSetup::setUpWorld 0 0% 82.05% 37ms 0.6% PetscSetupUtils::CommonSetup 0 0% 82.05% 37ms 0.6% PetscSetupUtils::InitialisePetsc 0 0% 82.05% 37ms 0.6% ompi_mpi_init 0 0% 82.05% 37ms 0.6% std::vector::vector (inline) 1ms 0.016% 82.06% 36ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.06% 35ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 25ms 0.41% 82.47% 35ms 0.57% boost::numeric::ublas::c_matrix::operator() 0 0% 82.47% 35ms 0.57% std::_Vector_base::_Vector_base (inline) 0 0% 82.47% 34ms 0.56% std::_Vector_base::_M_create_storage (inline) 1ms 0.016% 82.49% 33ms 0.54% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 82.49% 33ms 0.54% NodeAttributes::NodeAttributes 0 0% 82.49% 32ms 0.52% 32ms 0.52% 83.01% 32ms 0.52% __GI___mkdir 32ms 0.52% 83.53% 32ms 0.52% boost::numeric::ublas::same_impl_ex 32ms 0.52% 84.06% 32ms 0.52% boost::shared_ptr::operator-> (inline) 0 0% 84.06% 32ms 0.52% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.033% 84.09% 32ms 0.52% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 84.09% 31ms 0.51% _dl_init 0 0% 84.09% 31ms 0.51% call_init (inline) 0 0% 84.09% 31ms 0.51% std::map::find (inline)