File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6656ms, 84.83% of 7846ms total Dropped 577 nodes (cum <= 39.23ms) flat flat% sum% cum cum% 0 0% 0% 7809ms 99.53% __libc_start_call_main 0 0% 0% 7809ms 99.53% __libc_start_main_impl 0 0% 0% 7809ms 99.53% _start 0 0% 0% 7792ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7792ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7792ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7792ms 99.31% main 0 0% 0% 7754ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7754ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7754ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7751ms 98.79% AbstractCellBasedSimulation::Solve 0 0% 0% 3401ms 43.35% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2955ms 37.66% MeshBasedCellPopulation::Update 1ms 0.013% 0.025% 2816ms 35.89% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.038% 1525ms 19.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.051% 1520ms 19.37% MutableMesh::ReMesh 0 0% 0.051% 1381ms 17.60% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.051% 1358ms 17.31% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.038% 0.089% 1307ms 16.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.27% 1198ms 15.27% MeshBasedCellPopulation::SpringIterator::operator++ 97ms 1.24% 1.50% 969ms 12.35% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.013% 1.52% 926ms 11.80% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 455ms 5.80% 7.32% 926ms 11.80% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.32% 921ms 11.74% AbstractTwoBodyInteractionForce::AddForceContribution 259ms 3.30% 10.62% 879ms 11.20% __dynamic_cast 6ms 0.076% 10.69% 871ms 11.10% CellPopulationElementWriter::Visit 6ms 0.076% 10.77% 860ms 10.96% CellPropertyCollection::GetPropertiesType (inline) 49ms 0.62% 11.39% 820ms 10.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.038% 11.43% 779ms 9.93% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 11.81% 745ms 9.50% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 11.90% 729ms 9.29% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.94% 681ms 8.68% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 11.97% 606ms 7.72% triangulate 43ms 0.55% 12.52% 594ms 7.57% operator new 48ms 0.61% 13.13% 578ms 7.37% std::map::operator[] (partial-inline) 105ms 1.34% 14.47% 557ms 7.10% std::ostream::_M_insert 0 0% 14.47% 557ms 7.10% std::ostream::operator<< (inline) 193ms 2.46% 16.93% 547ms 6.97% __GI___libc_malloc 0 0% 16.93% 533ms 6.79% delaunay 4ms 0.051% 16.98% 533ms 6.79% divconqdelaunay 7ms 0.089% 17.07% 529ms 6.74% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.22% 17.28% 522ms 6.65% std::__new_allocator::allocate (inline) 0 0% 17.28% 519ms 6.61% std::allocator_traits::allocate (inline) 7ms 0.089% 17.37% 505ms 6.44% std::set::insert (inline) 24ms 0.31% 17.68% 500ms 6.37% std::_Rb_tree::find (inline) 11ms 0.14% 17.82% 498ms 6.35% std::_Rb_tree::_M_insert_unique 487ms 6.21% 24.02% 487ms 6.21% __strcmp_avx2 0 0% 24.02% 479ms 6.11% std::_Rb_tree::lower_bound (inline) 0 0% 24.02% 479ms 6.11% std::map::lower_bound (inline) 3ms 0.038% 24.06% 476ms 6.07% Cell::GetCellProliferativeType 215ms 2.74% 26.80% 475ms 6.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.80% 464ms 5.91% std::set::count (inline) 3ms 0.038% 26.84% 433ms 5.52% AbstractCellBasedSimulation::DoCellBirth 37ms 0.47% 27.31% 430ms 5.48% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.31% 422ms 5.38% std::_Rb_tree::_M_create_node (inline) 0 0% 27.31% 397ms 5.06% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.31% 394ms 5.02% std::set::~set (inline) 78ms 0.99% 28.31% 388ms 4.95% std::_Rb_tree::_M_erase 0 0% 28.31% 387ms 4.93% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 28.32% 374ms 4.77% Cell::GetMutationState 0 0% 28.32% 368ms 4.69% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.32% 366ms 4.66% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.32% 362ms 4.61% OutputFileHandler::OpenOutputFile 25ms 0.32% 28.64% 348ms 4.44% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.089% 28.73% 346ms 4.41% std::less::operator() (inline) 339ms 4.32% 33.05% 340ms 4.33% std::operator< (inline) 76ms 0.97% 34.02% 328ms 4.18% __GI___libc_free 2ms 0.025% 34.04% 316ms 4.03% std::set::set (inline) 6ms 0.076% 34.12% 311ms 3.96% Element::Element 0 0% 34.12% 311ms 3.96% NodeLocationWriter::Visit 24ms 0.31% 34.43% 309ms 3.94% std::_Rb_tree::_M_insert_ (inline) 6ms 0.076% 34.50% 305ms 3.89% Cell::ReadyToDivide 0 0% 34.50% 299ms 3.81% std::_Rb_tree::_M_drop_node (inline) 5ms 0.064% 34.57% 298ms 3.80% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 34.62% 292ms 3.72% AbstractCentreBasedCellPopulation::GetDampingConstant 39ms 0.5% 35.11% 289ms 3.68% std::_Rb_tree::_M_copy (inline) 6ms 0.076% 35.19% 285ms 3.63% divconqrecurse 9ms 0.11% 35.30% 285ms 3.63% std::__new_allocator::deallocate (inline) 0 0% 35.30% 284ms 3.62% std::allocator_traits::deallocate (inline) 23ms 0.29% 35.60% 284ms 3.62% std::num_put::_M_insert_float 6ms 0.076% 35.67% 279ms 3.56% AbstractCellPopulation::IsCellAttachedToLocationIndex 166ms 2.12% 37.79% 267ms 3.40% _int_malloc 66ms 0.84% 38.63% 265ms 3.38% mergehulls 7ms 0.089% 38.72% 263ms 3.35% AbstractCellProperty::IsType (inline) 6ms 0.076% 38.80% 259ms 3.30% CellPropertyCollection::HasProperty 0 0% 38.80% 257ms 3.28% Cell::HasCellProperty (inline) 251ms 3.20% 42.00% 251ms 3.20% std::_Rb_tree::_S_right (inline) 213ms 2.71% 44.71% 248ms 3.16% _int_free 56ms 0.71% 45.42% 245ms 3.12% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.42% 244ms 3.11% std::_Rb_tree::_M_put_node (inline) 6ms 0.076% 45.50% 228ms 2.91% std::__cxx11::collate::do_transform 1ms 0.013% 45.51% 218ms 2.78% ___vsnprintf 0 0% 45.51% 217ms 2.77% __vsnprintf_internal (inline) 3ms 0.038% 45.55% 214ms 2.73% CellProliferativeTypesWriter::VisitCell 31ms 0.4% 45.95% 214ms 2.73% __printf_buffer 10ms 0.13% 46.07% 201ms 2.56% TetrahedralMesh::Clear 10ms 0.13% 46.20% 197ms 2.51% MeshBasedCellPopulation::SpringsEnd (inline) 53ms 0.68% 46.88% 194ms 2.47% AbstractCellProperty::IsSame 4ms 0.051% 46.93% 193ms 2.46% Element::RegisterWithNodes (inline) 2ms 0.025% 46.95% 192ms 2.45% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.064% 47.02% 190ms 2.42% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.064% 47.08% 181ms 2.31% Node::AddElement 13ms 0.17% 47.25% 180ms 2.29% AbstractTetrahedralElement::CalculateJacobian 62ms 0.79% 48.04% 178ms 2.27% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 48.04% 178ms 2.27% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 48.05% 173ms 2.20% std::basic_ofstream::open (inline) 1ms 0.013% 48.06% 172ms 2.19% std::basic_filebuf::open 4ms 0.051% 48.11% 168ms 2.14% __printf_fp_l_buffer 0 0% 48.11% 168ms 2.14% __printf_fp_spec (inline) 0 0% 48.11% 160ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 28ms 0.36% 48.47% 158ms 2.01% TetrahedralMesh::EdgesEnd (partial-inline) 91ms 1.16% 49.63% 158ms 2.01% __printf_fp_buffer_1 0 0% 49.63% 157ms 2.00% FilesystemPermissions::SetFilePermissions (inline) 157ms 2.00% 51.63% 157ms 2.00% __GI_fchmodat 0 0% 51.63% 157ms 2.00% std::filesystem::permissions 2ms 0.025% 51.66% 153ms 1.95% alternateaxes 137ms 1.75% 53.40% 151ms 1.92% vertexmedian 5ms 0.064% 53.47% 150ms 1.91% AbstractTetrahedralElement::CalculateInverseJacobian 33ms 0.42% 53.89% 141ms 1.80% std::type_info::operator== (inline) 0 0% 53.89% 139ms 1.77% OutputFileHandler::CommonConstructor 0 0% 53.89% 139ms 1.77% OutputFileHandler::OutputFileHandler 97ms 1.24% 55.12% 136ms 1.73% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 55.12% 135ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 55.12% 133ms 1.70% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 55.12% 132ms 1.68% _IO_new_fopen 0 0% 55.12% 132ms 1.68% __fopen_internal (inline) 0 0% 55.12% 132ms 1.68% std::_Vector_base::_M_allocate (inline) 0 0% 55.12% 132ms 1.68% std::__basic_file::open 0 0% 55.12% 131ms 1.67% AbstractCellBasedWriter::CloseFile 1ms 0.013% 55.14% 131ms 1.67% std::basic_ofstream::close (inline) 2ms 0.025% 55.16% 130ms 1.66% std::basic_filebuf::close 1ms 0.013% 55.17% 128ms 1.63% _IO_new_file_fopen 10ms 0.13% 55.30% 127ms 1.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.089% 55.39% 127ms 1.62% boost::detail::shared_count::~shared_count (inline) 0 0% 55.39% 127ms 1.62% boost::shared_ptr::~shared_ptr (inline) 16ms 0.2% 55.60% 126ms 1.61% AbstractTetrahedralElement::RefreshJacobian 0 0% 55.60% 126ms 1.61% __GI__IO_file_open 4ms 0.051% 55.65% 125ms 1.59% boost::numeric::ublas::vector_assign (inline) 34ms 0.43% 56.08% 125ms 1.59% std::num_put::_M_insert_int 3ms 0.038% 56.12% 124ms 1.58% AbstractTetrahedralElement::AbstractTetrahedralElement 124ms 1.58% 57.70% 124ms 1.58% incircle 39ms 0.5% 58.20% 121ms 1.54% std::__ostream_insert 4ms 0.051% 58.25% 117ms 1.49% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 58.27% 116ms 1.48% Node::~Node 1ms 0.013% 58.28% 112ms 1.43% std::vector::push_back (inline) 109ms 1.39% 59.67% 110ms 1.40% __libc_open64 101ms 1.29% 60.96% 110ms 1.40% boost::detail::sp_counted_base::release 108ms 1.38% 62.34% 108ms 1.38% [libchaste_cell_based.so] 8ms 0.1% 62.44% 106ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 13ms 0.17% 62.61% 105ms 1.34% std::vector::_M_realloc_insert 0 0% 62.61% 103ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 51ms 0.65% 63.26% 102ms 1.30% boost::shared_ptr::shared_ptr (inline) 101ms 1.29% 64.54% 101ms 1.29% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 43ms 0.55% 65.09% 99ms 1.26% AbstractElement::GetNodeLocation 12ms 0.15% 65.24% 99ms 1.26% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 65.27% 98ms 1.25% std::basic_filebuf::overflow 0 0% 65.27% 97ms 1.24% std::basic_filebuf::_M_terminate_output 2ms 0.025% 65.29% 96ms 1.22% std::__basic_file::xsputn 0 0% 65.29% 96ms 1.22% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 65.32% 96ms 1.22% std::operator<< (inline) 94ms 1.20% 66.52% 94ms 1.20% __GI___libc_write 27ms 0.34% 66.86% 90ms 1.15% boost::numeric::ublas::indexing_vector_assign 58ms 0.74% 67.60% 89ms 1.13% std::basic_filebuf::xsputn 2ms 0.025% 67.63% 85ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.038% 67.67% 84ms 1.07% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 83ms 1.06% 68.72% 83ms 1.06% counterclockwise 83ms 1.06% 69.78% 83ms 1.06% std::_Rb_tree_increment 2ms 0.025% 69.81% 82ms 1.05% Cell::GetCellId 54ms 0.69% 70.49% 81ms 1.03% malloc_consolidate 71ms 0.9% 71.40% 81ms 1.03% vertexsort 80ms 1.02% 72.42% 80ms 1.02% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 72.44% 77ms 0.98% TetrahedralMesh::EdgeIterator::GetNodeB 74ms 0.94% 73.39% 74ms 0.94% std::vector::size (inline) 73ms 0.93% 74.32% 73ms 0.93% __GI___fstatat64 0 0% 74.32% 73ms 0.93% std::filesystem::status 0 0% 74.32% 73ms 0.93% tcache_get (inline) 73ms 0.93% 75.25% 73ms 0.93% tcache_get_n (inline) 4ms 0.051% 75.30% 72ms 0.92% CellPropertyCollection::AddProperty 0 0% 75.30% 71ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 75.30% 71ms 0.9% std::filesystem::create_directory 4ms 0.051% 75.35% 70ms 0.89% AbstractCellPopulation::GetLocationIndexUsingCell 53ms 0.68% 76.03% 66ms 0.84% AbstractElement::GetNodeGlobalIndex 64ms 0.82% 76.84% 64ms 0.82% __memcpy_avx_unaligned_erms 0 0% 76.84% 63ms 0.8% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.84% 63ms 0.8% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 61ms 0.78% 77.62% 61ms 0.78% Node::GetIndex 13ms 0.17% 77.78% 60ms 0.76% Determinant (inline) 42ms 0.54% 78.32% 60ms 0.76% std::basic_streambuf::xsputn 43ms 0.55% 78.87% 59ms 0.75% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 78.87% 59ms 0.75% std::vector::vector (inline) 0 0% 78.87% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.87% 55ms 0.7% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.87% 55ms 0.7% std::__new_allocator::destroy (inline) 0 0% 78.87% 55ms 0.7% std::allocator_traits::destroy (inline) 26ms 0.33% 79.20% 54ms 0.69% AbstractTetrahedralMesh::GetElement 54ms 0.69% 79.89% 54ms 0.69% [libstdc++.so.6.0.33] 0 0% 79.89% 54ms 0.69% std::_Vector_base::_Vector_base (inline) 0 0% 79.89% 53ms 0.68% AbstractCentreBasedCellPopulation::CreateCellPair 3ms 0.038% 79.93% 53ms 0.68% Node::ClearAppliedForce 1ms 0.013% 79.94% 53ms 0.68% std::_Vector_base::_M_create_storage (inline) 45ms 0.57% 80.51% 53ms 0.68% std::num_put::do_put 1ms 0.013% 80.53% 51ms 0.65% Node::ConstructNodeAttributes (inline) 0 0% 80.53% 51ms 0.65% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 47ms 0.6% 81.12% 51ms 0.65% boost::detail::shared_count::shared_count (inline) 4ms 0.051% 81.18% 51ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.18% 48ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.18% 47ms 0.6% boost::numeric::ublas::norm_2 (inline) 18ms 0.23% 81.40% 47ms 0.6% boost::numeric::ublas::vector_norm_2::apply (inline) 27ms 0.34% 81.75% 47ms 0.6% hack_digit 46ms 0.59% 82.33% 46ms 0.59% [libchaste_mesh.so] 45ms 0.57% 82.91% 45ms 0.57% Node::IsDeleted 44ms 0.56% 83.47% 44ms 0.56% boost::numeric::ublas::same_impl_ex 44ms 0.56% 84.03% 44ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 84.03% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 4ms 0.051% 84.08% 43ms 0.55% std::_Vector_base::_M_deallocate (inline) 12ms 0.15% 84.23% 42ms 0.54% Inverse 42ms 0.54% 84.77% 42ms 0.54% Node::rGetLocation 5ms 0.064% 84.83% 40ms 0.51% std::__copy_move::__copy_m (inline) 0 0% 84.83% 40ms 0.51% std::__copy_move_a (inline) 0 0% 84.83% 40ms 0.51% std::__copy_move_a1 (inline) 0 0% 84.83% 40ms 0.51% std::__copy_move_a2 (inline) 0 0% 84.83% 40ms 0.51% std::copy (inline)