File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6876ms, 84.78% of 8110ms total Dropped 602 nodes (cum <= 40.55ms) flat flat% sum% cum cum% 0 0% 0% 8071ms 99.52% __libc_start_call_main 0 0% 0% 8071ms 99.52% __libc_start_main_impl 0 0% 0% 8071ms 99.52% _start 0 0% 0% 8054ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8054ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8054ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8054ms 99.31% main 0 0% 0% 8011ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 8011ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 8011ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 8006ms 98.72% AbstractCellBasedSimulation::Solve 0 0% 0% 3496ms 43.11% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.037% 0.037% 2995ms 36.93% MeshBasedCellPopulation::Update 2ms 0.025% 0.062% 2962ms 36.52% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.074% 1544ms 19.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.037% 0.11% 1473ms 18.16% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.12% 1458ms 17.98% MutableMesh::ReMesh 0 0% 0.12% 1378ms 16.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.037% 0.16% 1320ms 16.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.36% 1251ms 15.43% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.074% 0.43% 1019ms 12.56% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 111ms 1.37% 1.80% 1013ms 12.49% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 1.84% 971ms 11.97% CellPropertyCollection::GetPropertiesType (inline) 432ms 5.33% 7.16% 968ms 11.94% std::_Rb_tree::_M_lower_bound (inline) 290ms 3.58% 10.74% 966ms 11.91% __dynamic_cast 13ms 0.16% 10.90% 919ms 11.33% CellPopulationElementWriter::Visit 0 0% 10.90% 888ms 10.95% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.049% 10.95% 839ms 10.35% MeshBasedCellPopulation::AcceptCellWriter 36ms 0.44% 11.39% 794ms 9.79% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.049% 11.44% 790ms 9.74% AbstractCellProperty::IsSubType (inline) 25ms 0.31% 11.75% 764ms 9.42% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.86% 700ms 8.63% TetrahedralMesh::ImportFromMesher 53ms 0.65% 12.52% 612ms 7.55% std::map::operator[] (partial-inline) 37ms 0.46% 12.97% 606ms 7.47% operator new 2ms 0.025% 13.00% 573ms 7.07% triangulate 571ms 7.04% 20.04% 571ms 7.04% __strcmp_avx2 3ms 0.037% 20.07% 559ms 6.89% Cell::GetCellProliferativeType 197ms 2.43% 22.50% 557ms 6.87% __GI___libc_malloc 0 0% 22.50% 551ms 6.79% std::ostream::operator<< (inline) 91ms 1.12% 23.63% 549ms 6.77% std::ostream::_M_insert 24ms 0.3% 23.92% 543ms 6.70% std::__new_allocator::allocate (inline) 0 0% 23.92% 539ms 6.65% std::allocator_traits::allocate (inline) 9ms 0.11% 24.03% 530ms 6.54% std::set::insert (inline) 11ms 0.14% 24.17% 521ms 6.42% std::_Rb_tree::_M_insert_unique 6ms 0.074% 24.24% 514ms 6.34% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.24% 510ms 6.29% std::_Rb_tree::lower_bound (inline) 0 0% 24.24% 510ms 6.29% std::map::lower_bound (inline) 0 0% 24.24% 500ms 6.17% delaunay 16ms 0.2% 24.44% 499ms 6.15% std::_Rb_tree::find (inline) 0 0% 24.44% 498ms 6.14% divconqdelaunay 3ms 0.037% 24.48% 488ms 6.02% AbstractCellBasedSimulation::DoCellBirth 205ms 2.53% 27.00% 480ms 5.92% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.00% 451ms 5.56% std::set::count (inline) 0 0% 27.00% 436ms 5.38% std::_Rb_tree::_M_create_node (inline) 37ms 0.46% 27.46% 436ms 5.38% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.46% 415ms 5.12% std::set::~set (inline) 0 0% 27.46% 407ms 5.02% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.46% 406ms 5.01% std::_Rb_tree::_M_get_node (inline) 3ms 0.037% 27.50% 402ms 4.96% Cell::GetMutationState 21ms 0.26% 27.76% 397ms 4.90% std::_Rb_tree::_Rb_tree (partial-inline) 86ms 1.06% 28.82% 394ms 4.86% std::_Rb_tree::_M_erase 12ms 0.15% 28.96% 363ms 4.48% std::less::operator() (inline) 351ms 4.33% 33.29% 351ms 4.33% std::operator< (inline) 2ms 0.025% 33.32% 350ms 4.32% std::set::set (inline) 0 0% 33.32% 345ms 4.25% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 11ms 0.14% 33.45% 345ms 4.25% Cell::ReadyToDivide 0 0% 33.45% 344ms 4.24% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.45% 342ms 4.22% OutputFileHandler::OpenOutputFile 4ms 0.049% 33.50% 340ms 4.19% MeshBasedCellPopulation::GetDampingConstant 8ms 0.099% 33.60% 335ms 4.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 33.60% 335ms 4.13% AbstractCentreBasedCellPopulation::GetDampingConstant 51ms 0.63% 34.23% 335ms 4.13% std::_Rb_tree::_M_copy (inline) 330ms 4.07% 38.30% 330ms 4.07% std::_Rb_tree::_S_right (inline) 1ms 0.012% 38.31% 322ms 3.97% NodeLocationWriter::Visit 96ms 1.18% 39.49% 319ms 3.93% __GI___libc_free 22ms 0.27% 39.77% 313ms 3.86% std::_Rb_tree::_M_insert_ (inline) 8ms 0.099% 39.86% 293ms 3.61% divconqrecurse 2ms 0.025% 39.89% 289ms 3.56% CellProliferativeTypesWriter::VisitCell 1ms 0.012% 39.90% 287ms 3.54% Element::Element 0 0% 39.90% 287ms 3.54% std::_Rb_tree::_M_drop_node (inline) 10ms 0.12% 40.02% 287ms 3.54% std::__new_allocator::deallocate (inline) 188ms 2.32% 42.34% 281ms 3.46% _int_malloc 0 0% 42.34% 281ms 3.46% std::allocator_traits::deallocate (inline) 79ms 0.97% 43.32% 275ms 3.39% mergehulls 66ms 0.81% 44.13% 275ms 3.39% std::_Rb_tree::_M_clone_node (inline) 32ms 0.39% 44.53% 270ms 3.33% std::num_put::_M_insert_float 2ms 0.025% 44.55% 268ms 3.30% AbstractCellProperty::IsType (inline) 3ms 0.037% 44.59% 258ms 3.18% CellPropertyCollection::HasProperty 0 0% 44.59% 257ms 3.17% Cell::HasCellProperty (inline) 0 0% 44.59% 233ms 2.87% std::_Rb_tree::_M_put_node (inline) 184ms 2.27% 46.86% 223ms 2.75% _int_free 3ms 0.037% 46.89% 220ms 2.71% AbstractPhaseBasedCellCycleModel::ReadyToDivide 10ms 0.12% 47.02% 213ms 2.63% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.11% 47.13% 209ms 2.58% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.086% 47.21% 208ms 2.56% std::__cxx11::collate::do_transform 11ms 0.14% 47.35% 203ms 2.50% TetrahedralMesh::Clear 61ms 0.75% 48.10% 197ms 2.43% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 48.10% 191ms 2.36% ___vsnprintf 1ms 0.012% 48.11% 191ms 2.36% __vsnprintf_internal (inline) 44ms 0.54% 48.66% 187ms 2.31% AbstractCellProperty::IsSame 27ms 0.33% 48.99% 186ms 2.29% __printf_buffer 5ms 0.062% 49.05% 182ms 2.24% Element::RegisterWithNodes (inline) 37ms 0.46% 49.51% 180ms 2.22% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.012% 49.52% 172ms 2.12% Node::AddElement 0 0% 49.52% 169ms 2.08% std::basic_ofstream::basic_ofstream (inline) 13ms 0.16% 49.68% 166ms 2.05% AbstractTetrahedralElement::CalculateJacobian 1ms 0.012% 49.69% 165ms 2.03% std::basic_filebuf::open 0 0% 49.69% 165ms 2.03% std::basic_ofstream::open (inline) 0 0% 49.69% 159ms 1.96% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.12% 49.82% 151ms 1.86% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 49.82% 147ms 1.81% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.012% 49.83% 147ms 1.81% std::filesystem::permissions 146ms 1.80% 51.63% 146ms 1.80% __GI_fchmodat 6ms 0.074% 51.70% 146ms 1.80% __printf_fp_l_buffer 0 0% 51.70% 146ms 1.80% __printf_fp_spec (inline) 30ms 0.37% 52.07% 143ms 1.76% std::type_info::operator== (inline) 1ms 0.012% 52.08% 142ms 1.75% AbstractCellBasedWriter::CloseFile 0 0% 52.08% 142ms 1.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.08% 141ms 1.74% std::basic_filebuf::close 0 0% 52.08% 141ms 1.74% std::basic_ofstream::close (inline) 2ms 0.025% 52.11% 139ms 1.71% OutputFileHandler::CommonConstructor 0 0% 52.11% 139ms 1.71% OutputFileHandler::OutputFileHandler 3ms 0.037% 52.15% 139ms 1.71% boost::numeric::ublas::vector_assign (inline) 87ms 1.07% 53.22% 137ms 1.69% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 68ms 0.84% 54.06% 137ms 1.69% __printf_fp_buffer_1 6ms 0.074% 54.13% 137ms 1.69% boost::numeric::ublas::c_vector::c_vector (inline) 137ms 1.69% 55.82% 137ms 1.69% incircle 0 0% 55.82% 136ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 55.82% 133ms 1.64% std::_Vector_base::_M_allocate (inline) 13ms 0.16% 55.98% 131ms 1.62% boost::detail::shared_count::~shared_count (inline) 0 0% 55.98% 131ms 1.62% boost::shared_ptr::~shared_ptr (inline) 1ms 0.012% 55.99% 131ms 1.62% std::__basic_file::open 0 0% 55.99% 130ms 1.60% _IO_new_fopen 1ms 0.012% 56.00% 130ms 1.60% __fopen_internal (inline) 0 0% 56.00% 129ms 1.59% _IO_new_file_fopen 56ms 0.69% 56.70% 129ms 1.59% std::__ostream_insert 0 0% 56.70% 128ms 1.58% __GI__IO_file_open 2ms 0.025% 56.72% 127ms 1.57% alternateaxes 12ms 0.15% 56.87% 126ms 1.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.062% 56.93% 126ms 1.55% Node::~Node 112ms 1.38% 58.31% 125ms 1.54% vertexmedian 32ms 0.39% 58.71% 122ms 1.50% std::num_put::_M_insert_int 19ms 0.23% 58.94% 117ms 1.44% AbstractTetrahedralElement::RefreshJacobian 9ms 0.11% 59.05% 113ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.049% 59.10% 113ms 1.39% std::vector::push_back (inline) 0 0% 59.10% 111ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 59.10% 111ms 1.37% std::operator<< (inline) 105ms 1.29% 60.39% 107ms 1.32% __libc_open64 107ms 1.32% 61.71% 107ms 1.32% std::_Rb_tree_increment 99ms 1.22% 62.93% 106ms 1.31% boost::detail::sp_counted_base::release 5ms 0.062% 63.00% 105ms 1.29% AbstractTetrahedralElement::AbstractTetrahedralElement 37ms 0.46% 63.45% 105ms 1.29% boost::numeric::ublas::indexing_vector_assign 5ms 0.062% 63.51% 105ms 1.29% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.012% 63.53% 105ms 1.29% std::basic_filebuf::_M_convert_to_external 0 0% 63.53% 105ms 1.29% std::basic_filebuf::_M_terminate_output 0 0% 63.53% 105ms 1.29% std::basic_filebuf::overflow 104ms 1.28% 64.81% 104ms 1.28% [libchaste_cell_based.so] 104ms 1.28% 66.09% 104ms 1.28% __GI___libc_write 0 0% 66.09% 104ms 1.28% std::__basic_file::xsputn 7ms 0.086% 66.18% 102ms 1.26% std::vector::_M_realloc_insert 3ms 0.037% 66.21% 100ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 43ms 0.53% 66.74% 98ms 1.21% boost::shared_ptr::shared_ptr (inline) 97ms 1.20% 67.94% 97ms 1.20% std::_Rb_tree_insert_and_rebalance 94ms 1.16% 69.10% 94ms 1.16% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.012% 69.11% 89ms 1.10% Cell::GetCellId 2ms 0.025% 69.14% 86ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 69.14% 84ms 1.04% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 69.15% 84ms 1.04% std::filesystem::create_directory 56ms 0.69% 69.84% 83ms 1.02% malloc_consolidate 0 0% 69.84% 82ms 1.01% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.32% 70.16% 82ms 1.01% AbstractElement::GetNodeLocation 82ms 1.01% 71.17% 82ms 1.01% Node::GetIndex 8ms 0.099% 71.27% 82ms 1.01% TetrahedralMesh::EdgeIterator::GetNodeA 76ms 0.94% 72.21% 76ms 0.94% std::vector::size (inline) 63ms 0.78% 72.98% 74ms 0.91% AbstractElement::GetNodeGlobalIndex 47ms 0.58% 73.56% 74ms 0.91% std::basic_filebuf::xsputn 2ms 0.025% 73.59% 72ms 0.89% std::filesystem::status 71ms 0.88% 74.46% 71ms 0.88% __GI___fstatat64 0 0% 74.46% 71ms 0.88% tcache_get (inline) 71ms 0.88% 75.34% 71ms 0.88% tcache_get_n (inline) 66ms 0.81% 76.15% 71ms 0.88% vertexsort 9ms 0.11% 76.26% 69ms 0.85% CellPropertyCollection::AddProperty 9ms 0.11% 76.37% 63ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 62ms 0.76% 77.14% 62ms 0.76% __memcpy_avx_unaligned_erms 39ms 0.48% 77.62% 62ms 0.76% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 77.62% 62ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.62% 62ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 77.62% 61ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 61ms 0.75% 78.37% 61ms 0.75% counterclockwise 0 0% 78.37% 61ms 0.75% std::vector::vector (inline) 1ms 0.012% 78.38% 59ms 0.73% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 78.38% 56ms 0.69% std::_Vector_base::_Vector_base (inline) 40ms 0.49% 78.88% 56ms 0.69% std::basic_streambuf::xsputn 0 0% 78.88% 55ms 0.68% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 54ms 0.67% 79.54% 55ms 0.68% boost::detail::shared_count::shared_count (inline) 0 0% 79.54% 54ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.012% 79.56% 54ms 0.67% std::_Vector_base::_M_create_storage (inline) 0 0% 79.56% 54ms 0.67% std::__new_allocator::destroy (inline) 0 0% 79.56% 54ms 0.67% std::allocator_traits::destroy (inline) 43ms 0.53% 80.09% 54ms 0.67% std::num_put::do_put 21ms 0.26% 80.35% 52ms 0.64% AbstractTetrahedralMesh::GetNumAllElements 18ms 0.22% 80.57% 51ms 0.63% Determinant (inline) 0 0% 80.57% 51ms 0.63% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 1ms 0.012% 80.58% 51ms 0.63% Node::ConstructNodeAttributes (inline) 0 0% 80.58% 50ms 0.62% Node::ClearAppliedForce 32ms 0.39% 80.97% 49ms 0.6% AbstractTetrahedralMesh::GetElement 49ms 0.6% 81.58% 49ms 0.6% Node::rGetLocation 2ms 0.025% 81.60% 49ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.037% 81.64% 49ms 0.6% std::_Vector_base::_M_deallocate (inline) 0 0% 81.64% 49ms 0.6% std::map::map (inline) 49ms 0.6% 82.24% 49ms 0.6% std::ostream::sentry::sentry 48ms 0.59% 82.84% 48ms 0.59% [libchaste_mesh.so] 0 0% 82.84% 48ms 0.59% boost::numeric::ublas::norm_2 (inline) 18ms 0.22% 83.06% 48ms 0.59% boost::numeric::ublas::vector_norm_2::apply (inline) 32ms 0.39% 83.45% 47ms 0.58% writeedges 0 0% 83.45% 46ms 0.57% std::map::find (inline) 0 0% 83.45% 44ms 0.54% BoundaryNodeWriter::Visit 18ms 0.22% 83.67% 43ms 0.53% AbstractCellCycleModel::GetAge 6ms 0.074% 83.75% 43ms 0.53% Inverse 43ms 0.53% 84.28% 43ms 0.53% Node::IsDeleted 41ms 0.51% 84.78% 41ms 0.51% [libstdc++.so.6.0.33] 0 0% 84.78% 41ms 0.51% _dl_init 0 0% 84.78% 41ms 0.51% call_init (inline)