File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6689ms, 85.13% of 7857ms total Dropped 584 nodes (cum <= 39.28ms) flat flat% sum% cum cum% 0 0% 0% 7816ms 99.48% __libc_start_call_main 0 0% 0% 7816ms 99.48% __libc_start_main_impl 0 0% 0% 7816ms 99.48% _start 0 0% 0% 7802ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7802ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7802ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7802ms 99.30% main 0 0% 0% 7761ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7761ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7761ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7759ms 98.75% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3353ms 42.68% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 3081ms 39.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.013% 2837ms 36.11% MeshBasedCellPopulation::Update 0 0% 0.013% 1403ms 17.86% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.025% 1375ms 17.50% MutableMesh::ReMesh 0 0% 0.025% 1315ms 16.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 28ms 0.36% 0.38% 1236ms 15.73% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.38% 1172ms 14.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.14% 0.52% 1140ms 14.51% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.064% 0.59% 1122ms 14.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.59% 1036ms 13.19% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 128ms 1.63% 2.21% 1001ms 12.74% TetrahedralMesh::EdgeIterator::operator++ 457ms 5.82% 8.03% 957ms 12.18% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 8.04% 933ms 11.87% CellPopulationElementWriter::Visit 9ms 0.11% 8.16% 926ms 11.79% AbstractCellProperty::IsSubType (inline) 274ms 3.49% 11.65% 924ms 11.76% __dynamic_cast 5ms 0.064% 11.71% 887ms 11.29% MeshBasedCellPopulation::AcceptCellWriter 37ms 0.47% 12.18% 737ms 9.38% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.051% 12.23% 715ms 9.10% Cell::GetCellProliferativeType 4ms 0.051% 12.28% 707ms 9.00% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.1% 12.38% 695ms 8.85% TetrahedralMesh::ImportFromMesher 38ms 0.48% 12.87% 610ms 7.76% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 52ms 0.66% 13.53% 583ms 7.42% std::map::operator[] (partial-inline) 3ms 0.038% 13.57% 579ms 7.37% std::ostream::operator<< (inline) 89ms 1.13% 14.70% 574ms 7.31% std::ostream::_M_insert 44ms 0.56% 15.26% 540ms 6.87% operator new 9ms 0.11% 15.37% 523ms 6.66% std::set::insert (inline) 5ms 0.064% 15.44% 521ms 6.63% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.1% 15.54% 514ms 6.54% std::_Rb_tree::_M_insert_unique 18ms 0.23% 15.77% 511ms 6.50% std::_Rb_tree::find (inline) 4ms 0.051% 15.82% 506ms 6.44% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 15.83% 506ms 6.44% triangulate 151ms 1.92% 17.75% 491ms 6.25% __GI___libc_malloc 40ms 0.51% 18.26% 488ms 6.21% std::__new_allocator::allocate (inline) 0 0% 18.26% 487ms 6.20% std::_Rb_tree::lower_bound (inline) 0 0% 18.26% 487ms 6.20% std::map::lower_bound (inline) 0 0% 18.26% 483ms 6.15% std::allocator_traits::allocate (inline) 204ms 2.60% 20.86% 480ms 6.11% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 20.86% 470ms 5.98% std::set::count (inline) 5ms 0.064% 20.92% 463ms 5.89% Cell::GetMutationState 441ms 5.61% 26.54% 441ms 5.61% __strcmp_avx2 0 0% 26.54% 441ms 5.61% delaunay 2ms 0.025% 26.56% 440ms 5.60% divconqdelaunay 0 0% 26.56% 408ms 5.19% std::_Rb_tree::_M_create_node (inline) 35ms 0.45% 27.01% 395ms 5.03% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.01% 387ms 4.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.01% 381ms 4.85% std::_Rb_tree::_M_get_node (inline) 27ms 0.34% 27.35% 375ms 4.77% std::_Rb_tree::_Rb_tree (partial-inline) 19ms 0.24% 27.59% 374ms 4.76% Cell::ReadyToDivide 0 0% 27.59% 370ms 4.71% std::set::~set (inline) 78ms 0.99% 28.59% 356ms 4.53% std::_Rb_tree::_M_erase 16ms 0.2% 28.79% 349ms 4.44% std::less::operator() (inline) 2ms 0.025% 28.82% 345ms 4.39% std::set::set (inline) 1ms 0.013% 28.83% 344ms 4.38% NodeLocationWriter::Visit 23ms 0.29% 29.12% 342ms 4.35% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 29.16% 338ms 4.30% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 29.18% 335ms 4.26% AbstractCentreBasedCellPopulation::GetDampingConstant 333ms 4.24% 33.42% 333ms 4.24% std::operator< (inline) 0 0% 33.42% 330ms 4.20% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.42% 330ms 4.20% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 33.45% 324ms 4.12% CellProliferativeTypesWriter::VisitCell 0 0% 33.45% 324ms 4.12% OutputFileHandler::OpenOutputFile 37ms 0.47% 33.92% 318ms 4.05% std::_Rb_tree::_M_copy (inline) 9ms 0.11% 34.03% 315ms 4.01% AbstractCellPopulation::IsCellAttachedToLocationIndex 109ms 1.39% 35.42% 312ms 3.97% __GI___libc_free 27ms 0.34% 35.76% 301ms 3.83% std::num_put::_M_insert_float 287ms 3.65% 39.42% 287ms 3.65% std::_Rb_tree::_S_right (inline) 6ms 0.076% 39.49% 280ms 3.56% Element::Element 97ms 1.23% 40.73% 275ms 3.50% std::_Rb_tree::_M_clone_node (inline) 11ms 0.14% 40.87% 266ms 3.39% std::__new_allocator::deallocate (inline) 181ms 2.30% 43.17% 264ms 3.36% _int_malloc 0 0% 43.17% 262ms 3.33% std::allocator_traits::deallocate (inline) 0 0% 43.17% 256ms 3.26% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 43.18% 244ms 3.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.11% 43.30% 240ms 3.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 43.40% 240ms 3.05% divconqrecurse 59ms 0.75% 44.15% 223ms 2.84% mergehulls 5ms 0.064% 44.22% 215ms 2.74% std::__cxx11::collate::do_transform 0 0% 44.22% 212ms 2.70% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 44.25% 207ms 2.63% ___vsnprintf 0 0% 44.25% 204ms 2.60% __vsnprintf_internal (inline) 171ms 2.18% 46.43% 203ms 2.58% _int_free 8ms 0.1% 46.53% 199ms 2.53% CellPropertyCollection::HasProperty 3ms 0.038% 46.57% 199ms 2.53% Element::RegisterWithNodes (inline) 24ms 0.31% 46.88% 199ms 2.53% __printf_buffer 0 0% 46.88% 196ms 2.49% Cell::HasCellProperty (inline) 5ms 0.064% 46.94% 196ms 2.49% Node::AddElement 14ms 0.18% 47.12% 185ms 2.35% TetrahedralMesh::Clear 13ms 0.17% 47.28% 180ms 2.29% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 47.28% 170ms 2.16% OutputFileHandler::CommonConstructor 0 0% 47.28% 170ms 2.16% OutputFileHandler::OutputFileHandler 0 0% 47.28% 167ms 2.13% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 47.28% 166ms 2.11% std::basic_ofstream::basic_ofstream (inline) 53ms 0.67% 47.96% 164ms 2.09% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 47.97% 163ms 2.07% __printf_fp_spec (inline) 5ms 0.064% 48.03% 162ms 2.06% __printf_fp_l_buffer 0 0% 48.03% 161ms 2.05% AbstractCellBasedWriter::CloseFile 0 0% 48.03% 161ms 2.05% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 48.05% 161ms 2.05% std::basic_ofstream::close (inline) 0 0% 48.05% 160ms 2.04% std::basic_filebuf::close 1ms 0.013% 48.06% 160ms 2.04% std::basic_ofstream::open (inline) 0 0% 48.06% 159ms 2.02% std::basic_filebuf::open 9ms 0.11% 48.17% 156ms 1.99% AbstractTetrahedralElement::CalculateJacobian 10ms 0.13% 48.30% 156ms 1.99% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 48.30% 154ms 1.96% TetrahedralMesh::RefreshJacobianCachedData 77ms 0.98% 49.28% 153ms 1.95% __printf_fp_buffer_1 151ms 1.92% 51.20% 151ms 1.92% std::_Rb_tree_increment 6ms 0.076% 51.28% 144ms 1.83% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.076% 51.36% 143ms 1.82% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 51.39% 143ms 1.82% boost::numeric::ublas::vector_assign (inline) 59ms 0.75% 52.14% 142ms 1.81% std::__ostream_insert 33ms 0.42% 52.56% 139ms 1.77% TetrahedralMesh::EdgesEnd (partial-inline) 82ms 1.04% 53.61% 133ms 1.69% AbstractCellProperty::IsType (partial-inline) 0 0% 53.61% 133ms 1.69% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 53.62% 132ms 1.68% std::filesystem::permissions 131ms 1.67% 55.29% 131ms 1.67% __GI_fchmodat 5ms 0.064% 55.35% 128ms 1.63% std::vector::push_back (inline) 0 0% 55.35% 124ms 1.58% _IO_new_fopen 0 0% 55.35% 124ms 1.58% __fopen_internal (inline) 0 0% 55.35% 124ms 1.58% std::__basic_file::open 0 0% 55.35% 123ms 1.57% alternateaxes 111ms 1.41% 56.76% 122ms 1.55% vertexmedian 0 0% 56.76% 121ms 1.54% std::basic_filebuf::_M_terminate_output 2ms 0.025% 56.79% 121ms 1.54% std::basic_filebuf::overflow 11ms 0.14% 56.93% 121ms 1.54% std::vector::_M_realloc_insert 2ms 0.025% 56.96% 120ms 1.53% _IO_new_file_fopen 0 0% 56.96% 119ms 1.51% std::__basic_file::xsputn 0 0% 56.96% 119ms 1.51% std::basic_filebuf::_M_convert_to_external 116ms 1.48% 58.43% 118ms 1.50% __GI___libc_write 36ms 0.46% 58.89% 118ms 1.50% std::num_put::_M_insert_int 1ms 0.013% 58.90% 117ms 1.49% __GI__IO_file_open 15ms 0.19% 59.09% 115ms 1.46% AbstractTetrahedralElement::RefreshJacobian 10ms 0.13% 59.22% 115ms 1.46% MeshBasedCellPopulation::SpringIterator::SpringIterator 115ms 1.46% 60.68% 115ms 1.46% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 60.71% 113ms 1.44% std::operator<< (inline) 111ms 1.41% 62.12% 111ms 1.41% incircle 5ms 0.064% 62.19% 110ms 1.40% Node::~Node 16ms 0.2% 62.39% 108ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (partial-inline) 76ms 0.97% 63.36% 106ms 1.35% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 63.38% 104ms 1.32% std::_Vector_base::_M_allocate (inline) 27ms 0.34% 63.73% 103ms 1.31% boost::numeric::ublas::indexing_vector_assign 0 0% 63.73% 100ms 1.27% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 1.27% 65.00% 100ms 1.27% __libc_open64 4ms 0.051% 65.05% 98ms 1.25% std::filesystem::status 12ms 0.15% 65.20% 97ms 1.23% boost::detail::shared_count::~shared_count (inline) 0 0% 65.20% 97ms 1.23% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 65.22% 94ms 1.20% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 94ms 1.20% 66.41% 94ms 1.20% __GI___fstatat64 0 0% 66.41% 93ms 1.18% std::filesystem::create_directory 5ms 0.064% 66.48% 89ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 38ms 0.48% 66.96% 86ms 1.09% boost::shared_ptr::shared_ptr (inline) 68ms 0.87% 67.82% 86ms 1.09% std::basic_streambuf::xsputn 42ms 0.53% 68.36% 85ms 1.08% AbstractElement::GetNodeLocation 83ms 1.06% 69.42% 83ms 1.06% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 82ms 1.04% 70.46% 83ms 1.06% boost::detail::sp_counted_base::release 0 0% 70.46% 82ms 1.04% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 70.47% 79ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 79ms 1.01% 71.48% 79ms 1.01% [libchaste_cell_based.so] 3ms 0.038% 71.52% 76ms 0.97% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.45% 71.96% 75ms 0.95% std::basic_filebuf::xsputn 6ms 0.076% 72.04% 74ms 0.94% CellPropertyCollection::AddProperty 0 0% 72.04% 74ms 0.94% tcache_get (inline) 74ms 0.94% 72.98% 74ms 0.94% tcache_get_n (inline) 49ms 0.62% 73.60% 71ms 0.9% std::num_put::do_put 70ms 0.89% 74.49% 70ms 0.89% Node::GetIndex 49ms 0.62% 75.12% 69ms 0.88% malloc_consolidate 58ms 0.74% 75.86% 67ms 0.85% AbstractElement::GetNodeGlobalIndex 0 0% 75.86% 67ms 0.85% Cell::GetCellId 61ms 0.78% 76.63% 67ms 0.85% vertexsort 3ms 0.038% 76.67% 63ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.67% 61ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.67% 61ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 42ms 0.53% 77.21% 60ms 0.76% CellPropertyCollection::GetProperty 1ms 0.013% 77.22% 56ms 0.71% BoundaryNodeWriter::Visit 33ms 0.42% 77.64% 55ms 0.7% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.025% 77.66% 53ms 0.67% Node::ConstructNodeAttributes (inline) 53ms 0.67% 78.34% 53ms 0.67% __memcpy_avx_unaligned_erms 1ms 0.013% 78.35% 52ms 0.66% Node::ClearAppliedForce 51ms 0.65% 79.00% 51ms 0.65% CellProperty::GetTypeId 51ms 0.65% 79.65% 51ms 0.65% counterclockwise 31ms 0.39% 80.04% 50ms 0.64% AbstractTetrahedralMesh::GetElement 0 0% 80.04% 50ms 0.64% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.025% 80.07% 50ms 0.64% std::_Vector_base::_M_deallocate (inline) 0 0% 80.07% 49ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 49ms 0.62% 80.69% 49ms 0.62% boost::numeric::ublas::c_vector::operator() 22ms 0.28% 80.97% 48ms 0.61% Determinant (inline) 48ms 0.61% 81.58% 48ms 0.61% [libchaste_mesh.so] 47ms 0.6% 82.18% 48ms 0.61% boost::detail::shared_count::shared_count (inline) 47ms 0.6% 82.78% 47ms 0.6% boost::shared_ptr::operator-> (inline) 1ms 0.013% 82.79% 45ms 0.57% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 82.79% 45ms 0.57% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 82.97% 45ms 0.57% boost::numeric::ublas::vector_norm_2::apply (inline) 31ms 0.39% 83.37% 45ms 0.57% hack_digit 0 0% 83.37% 44ms 0.56% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.025% 83.39% 44ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.39% 44ms 0.56% std::__new_allocator::destroy (inline) 0 0% 83.39% 44ms 0.56% std::allocator_traits::destroy (inline) 43ms 0.55% 83.94% 43ms 0.55% boost::numeric::ublas::same_impl_ex 43ms 0.55% 84.49% 43ms 0.55% std::vector::size (inline) 42ms 0.53% 85.02% 42ms 0.53% std::ostream::sentry::sentry 9ms 0.11% 85.13% 41ms 0.52% Inverse 0 0% 85.13% 40ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.13% 40ms 0.51% _dl_init 0 0% 85.13% 40ms 0.51% _dl_start_user 0 0% 85.13% 40ms 0.51% call_init (inline)