File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6657ms, 84.79% of 7851ms total Dropped 576 nodes (cum <= 39.26ms) flat flat% sum% cum cum% 0 0% 0% 7816ms 99.55% __libc_start_call_main 0 0% 0% 7816ms 99.55% __libc_start_main_impl 0 0% 0% 7816ms 99.55% _start 0 0% 0% 7802ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7802ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7802ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7802ms 99.38% main 0 0% 0% 7762ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7762ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7762ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 2ms 0.025% 0.025% 7760ms 98.84% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.038% 3408ms 43.41% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.064% 2929ms 37.31% MeshBasedCellPopulation::Update 1ms 0.013% 0.076% 2808ms 35.77% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.076% 1531ms 19.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.089% 1467ms 18.69% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.11% 1417ms 18.05% MutableMesh::ReMesh 1ms 0.013% 0.13% 1392ms 17.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.089% 0.22% 1333ms 16.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.17% 0.38% 1297ms 16.52% MeshBasedCellPopulation::SpringIterator::operator++ 110ms 1.40% 1.78% 1071ms 13.64% TetrahedralMesh::EdgeIterator::operator++ 467ms 5.95% 7.73% 1049ms 13.36% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.1% 7.83% 916ms 11.67% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.051% 7.88% 909ms 11.58% AbstractTwoBodyInteractionForce::AddForceContribution 262ms 3.34% 11.22% 904ms 11.51% __dynamic_cast 10ms 0.13% 11.35% 901ms 11.48% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.13% 11.48% 892ms 11.36% CellPopulationElementWriter::Visit 31ms 0.39% 11.87% 802ms 10.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 29ms 0.37% 12.24% 783ms 9.97% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.064% 12.30% 759ms 9.67% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.13% 12.43% 730ms 9.30% TetrahedralMesh::ImportFromMesher 5ms 0.064% 12.50% 707ms 9.01% AbstractCellProperty::IsSubType (inline) 59ms 0.75% 13.25% 632ms 8.05% std::map::operator[] (partial-inline) 1ms 0.013% 13.26% 616ms 7.85% std::ostream::operator<< (inline) 97ms 1.24% 14.49% 614ms 7.82% std::ostream::_M_insert 45ms 0.57% 15.07% 585ms 7.45% operator new 29ms 0.37% 15.44% 569ms 7.25% std::_Rb_tree::find (inline) 5ms 0.064% 15.50% 535ms 6.81% Cell::GetCellProliferativeType 0 0% 15.50% 533ms 6.79% std::_Rb_tree::lower_bound (inline) 0 0% 15.50% 533ms 6.79% std::map::lower_bound (inline) 201ms 2.56% 18.06% 532ms 6.78% __GI___libc_malloc 0 0% 18.06% 524ms 6.67% triangulate 0 0% 18.06% 517ms 6.59% std::set::count (inline) 34ms 0.43% 18.49% 513ms 6.53% std::__new_allocator::allocate (inline) 0 0% 18.49% 509ms 6.48% std::allocator_traits::allocate (inline) 4ms 0.051% 18.55% 504ms 6.42% std::set::insert (inline) 12ms 0.15% 18.70% 500ms 6.37% std::_Rb_tree::_M_insert_unique 498ms 6.34% 25.04% 498ms 6.34% __strcmp_avx2 221ms 2.81% 27.86% 480ms 6.11% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.025% 27.88% 466ms 5.94% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 27.89% 464ms 5.91% delaunay 3ms 0.038% 27.93% 463ms 5.90% divconqdelaunay 3ms 0.038% 27.97% 443ms 5.64% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 27.97% 423ms 5.39% std::_Rb_tree::_M_create_node (inline) 0 0% 27.97% 401ms 5.11% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.36% 28.33% 387ms 4.93% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.33% 382ms 4.87% Cell::GetMutationState 0 0% 28.33% 382ms 4.87% std::_Rb_tree::_M_get_node (inline) 12ms 0.15% 28.48% 362ms 4.61% std::less::operator() (inline) 22ms 0.28% 28.76% 361ms 4.60% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.76% 361ms 4.60% std::set::~set (inline) 79ms 1.01% 29.77% 356ms 4.53% std::_Rb_tree::_M_erase 353ms 4.50% 34.26% 353ms 4.50% std::_Rb_tree::_S_right (inline) 1ms 0.013% 34.28% 351ms 4.47% NodeLocationWriter::Visit 350ms 4.46% 38.73% 350ms 4.46% std::operator< (inline) 2ms 0.025% 38.76% 337ms 4.29% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 38.78% 335ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.051% 38.84% 334ms 4.25% std::set::set (inline) 18ms 0.23% 39.07% 328ms 4.18% std::num_put::_M_insert_float 6ms 0.076% 39.14% 315ms 4.01% Cell::ReadyToDivide 8ms 0.1% 39.24% 314ms 4.00% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 39.27% 305ms 3.88% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.27% 301ms 3.83% AbstractCellBasedWriter::OpenOutputFileForAppend 14ms 0.18% 39.45% 298ms 3.80% std::_Rb_tree::_M_insert_ (inline) 0 0% 39.45% 296ms 3.77% OutputFileHandler::OpenOutputFile 27ms 0.34% 39.79% 296ms 3.77% std::_Rb_tree::_M_copy (inline) 3ms 0.038% 39.83% 292ms 3.72% Element::Element 108ms 1.38% 41.20% 289ms 3.68% __GI___libc_free 2ms 0.025% 41.23% 274ms 3.49% CellProliferativeTypesWriter::VisitCell 65ms 0.83% 42.06% 265ms 3.38% std::_Rb_tree::_M_clone_node (inline) 179ms 2.28% 44.34% 264ms 3.36% _int_malloc 0 0% 44.34% 256ms 3.26% std::_Rb_tree::_M_drop_node (inline) 4ms 0.051% 44.39% 252ms 3.21% std::__cxx11::collate::do_transform 11ms 0.14% 44.53% 251ms 3.20% divconqrecurse 7ms 0.089% 44.62% 248ms 3.16% std::__new_allocator::deallocate (inline) 0 0% 44.62% 244ms 3.11% std::allocator_traits::deallocate (inline) 2ms 0.025% 44.64% 238ms 3.03% ___vsnprintf 0 0% 44.64% 236ms 3.01% __vsnprintf_internal (inline) 63ms 0.8% 45.45% 235ms 2.99% mergehulls 38ms 0.48% 45.93% 233ms 2.97% __printf_buffer 3ms 0.038% 45.97% 205ms 2.61% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.97% 204ms 2.60% std::_Rb_tree::_M_put_node (inline) 4ms 0.051% 46.02% 203ms 2.59% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.25% 46.27% 203ms 2.59% TetrahedralMesh::Clear 0 0% 46.27% 201ms 2.56% AbstractCellProperty::IsType (inline) 9ms 0.11% 46.39% 200ms 2.55% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.051% 46.44% 198ms 2.52% CellPropertyCollection::HasProperty 0 0% 46.44% 197ms 2.51% Cell::HasCellProperty (inline) 78ms 0.99% 47.43% 190ms 2.42% std::_Rb_tree::_M_get_insert_unique_pos (inline) 143ms 1.82% 49.25% 181ms 2.31% _int_free 49ms 0.62% 49.88% 176ms 2.24% TetrahedralMesh::EdgesEnd (partial-inline) 14ms 0.18% 50.06% 174ms 2.22% AbstractTetrahedralElement::CalculateJacobian 6ms 0.076% 50.13% 173ms 2.20% __printf_fp_l_buffer 0 0% 50.13% 173ms 2.20% __printf_fp_spec (inline) 3ms 0.038% 50.17% 167ms 2.13% Element::RegisterWithNodes (inline) 2ms 0.025% 50.20% 161ms 2.05% Node::AddElement 83ms 1.06% 51.25% 159ms 2.03% __printf_fp_buffer_1 41ms 0.52% 51.78% 151ms 1.92% AbstractCellProperty::IsSame 0 0% 51.78% 140ms 1.78% OutputFileHandler::CommonConstructor 0 0% 51.78% 140ms 1.78% OutputFileHandler::OutputFileHandler 0 0% 51.78% 139ms 1.77% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.78% 137ms 1.75% TetrahedralMesh::RefreshJacobianCachedData 19ms 0.24% 52.02% 134ms 1.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 52.02% 134ms 1.71% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 52.02% 134ms 1.71% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 52.03% 134ms 1.71% std::filesystem::permissions 133ms 1.69% 53.73% 133ms 1.69% __GI_fchmodat 0 0% 53.73% 133ms 1.69% std::basic_ofstream::open (inline) 0 0% 53.73% 132ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 53.74% 132ms 1.68% std::basic_filebuf::open 38ms 0.48% 54.22% 132ms 1.68% std::num_put::_M_insert_int 5ms 0.064% 54.29% 131ms 1.67% boost::numeric::ublas::vector_assign (inline) 6ms 0.076% 54.36% 128ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 54.38% 128ms 1.63% std::_Vector_base::_M_allocate (inline) 3ms 0.038% 54.41% 127ms 1.62% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.2% 54.62% 126ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.025% 54.64% 126ms 1.60% alternateaxes 5ms 0.064% 54.71% 125ms 1.59% AbstractTetrahedralElement::CalculateInverseJacobian 60ms 0.76% 55.47% 125ms 1.59% std::__ostream_insert 8ms 0.1% 55.57% 125ms 1.59% std::vector::push_back (inline) 7ms 0.089% 55.66% 123ms 1.57% Node::~Node 115ms 1.46% 57.13% 122ms 1.55% vertexmedian 20ms 0.25% 57.38% 121ms 1.54% AbstractTetrahedralElement::RefreshJacobian 11ms 0.14% 57.52% 119ms 1.52% boost::detail::shared_count::~shared_count (inline) 0 0% 57.52% 119ms 1.52% boost::shared_ptr::~shared_ptr (inline) 0 0% 57.52% 118ms 1.50% AbstractCellPopulation::CloseRoundRobinWritersFiles 9ms 0.11% 57.64% 117ms 1.49% std::_Rb_tree_const_iterator::operator++ (inline) 117ms 1.49% 59.13% 117ms 1.49% std::_Rb_tree_increment 1ms 0.013% 59.14% 116ms 1.48% AbstractCellBasedWriter::CloseFile 2ms 0.025% 59.16% 115ms 1.46% std::basic_ofstream::close (inline) 12ms 0.15% 59.32% 115ms 1.46% std::vector::_M_realloc_insert 0 0% 59.32% 113ms 1.44% std::basic_filebuf::close 20ms 0.25% 59.57% 110ms 1.40% std::type_info::operator== (inline) 65ms 0.83% 60.40% 106ms 1.35% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 46ms 0.59% 60.99% 104ms 1.32% boost::shared_ptr::shared_ptr (inline) 103ms 1.31% 62.30% 103ms 1.31% boost::detail::sp_counted_base::release 0 0% 62.30% 99ms 1.26% std::__basic_file::open 0 0% 62.30% 98ms 1.25% _IO_new_fopen 0 0% 62.30% 98ms 1.25% __fopen_internal (inline) 2ms 0.025% 62.32% 98ms 1.25% std::operator<< (inline) 1ms 0.013% 62.34% 96ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.27% 62.60% 95ms 1.21% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 62.62% 94ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 62.63% 94ms 1.20% _IO_new_file_fopen 94ms 1.20% 63.83% 94ms 1.20% incircle 92ms 1.17% 65.00% 92ms 1.17% [libchaste_cell_based.so] 1ms 0.013% 65.01% 90ms 1.15% __GI__IO_file_open 3ms 0.038% 65.05% 90ms 1.15% std::__basic_file::xsputn 0 0% 65.05% 90ms 1.15% std::basic_filebuf::_M_convert_to_external 0 0% 65.05% 90ms 1.15% std::basic_filebuf::_M_terminate_output 0 0% 65.05% 90ms 1.15% std::basic_filebuf::overflow 89ms 1.13% 66.18% 89ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 89ms 1.13% 67.32% 89ms 1.13% std::_Rb_tree_insert_and_rebalance 85ms 1.08% 68.40% 86ms 1.10% __GI___libc_write 44ms 0.56% 68.96% 84ms 1.07% AbstractElement::GetNodeLocation 3ms 0.038% 69.00% 81ms 1.03% AbstractCellPopulation::GetLocationIndexUsingCell 80ms 1.02% 70.02% 80ms 1.02% __libc_open64 58ms 0.74% 70.76% 80ms 1.02% std::basic_streambuf::xsputn 76ms 0.97% 71.72% 76ms 0.97% counterclockwise 69ms 0.88% 72.60% 75ms 0.96% vertexsort 64ms 0.82% 73.42% 74ms 0.94% AbstractElement::GetNodeGlobalIndex 74ms 0.94% 74.36% 74ms 0.94% Node::GetIndex 1ms 0.013% 74.37% 73ms 0.93% std::filesystem::status 72ms 0.92% 75.29% 72ms 0.92% __GI___fstatat64 53ms 0.68% 75.96% 72ms 0.92% malloc_consolidate 0 0% 75.96% 68ms 0.87% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 75.98% 68ms 0.87% std::filesystem::create_directory 41ms 0.52% 76.50% 66ms 0.84% std::basic_filebuf::xsputn 61ms 0.78% 77.28% 61ms 0.78% std::vector::size (inline) 0 0% 77.28% 60ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.28% 60ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 49ms 0.62% 77.90% 60ms 0.76% std::num_put::do_put 2ms 0.025% 77.93% 59ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 59ms 0.75% 78.68% 59ms 0.75% [libchaste_mesh.so] 59ms 0.75% 79.43% 59ms 0.75% __memcpy_avx_unaligned_erms 6ms 0.076% 79.51% 58ms 0.74% CellPropertyCollection::AddProperty 58ms 0.74% 80.24% 58ms 0.74% boost::detail::shared_count::shared_count (inline) 58ms 0.74% 80.98% 58ms 0.74% boost::numeric::ublas::c_vector::operator() 0 0% 80.98% 57ms 0.73% tcache_get (inline) 57ms 0.73% 81.71% 57ms 0.73% tcache_get_n (inline) 0 0% 81.71% 56ms 0.71% std::vector::vector (inline) 31ms 0.39% 82.10% 55ms 0.7% AbstractTetrahedralMesh::GetElement 1ms 0.013% 82.12% 55ms 0.7% Cell::GetCellId 0 0% 82.12% 54ms 0.69% Node::ClearAppliedForce 0 0% 82.12% 54ms 0.69% Node::ConstructNodeAttributes (inline) 0 0% 82.12% 53ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 0.68% 82.79% 53ms 0.68% [libstdc++.so.6.0.33] 25ms 0.32% 83.11% 52ms 0.66% hack_digit 0 0% 83.11% 52ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.11% 52ms 0.66% std::__new_allocator::destroy (inline) 0 0% 83.11% 52ms 0.66% std::allocator_traits::destroy (inline) 22ms 0.28% 83.39% 51ms 0.65% Determinant (inline) 0 0% 83.39% 47ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 83.39% 46ms 0.59% std::_Vector_base::_M_create_storage (inline) 1ms 0.013% 83.40% 45ms 0.57% BoundaryNodeWriter::Visit 45ms 0.57% 83.98% 45ms 0.57% boost::shared_ptr::operator-> (inline) 27ms 0.34% 84.32% 44ms 0.56% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 84.32% 44ms 0.56% boost::numeric::ublas::norm_2 (inline) 13ms 0.17% 84.49% 44ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.49% 43ms 0.55% std::map::find (inline) 15ms 0.19% 84.68% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 0 0% 84.68% 42ms 0.53% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.038% 84.72% 42ms 0.53% std::_Rb_tree_header::_Rb_tree_header (inline) 3ms 0.038% 84.75% 42ms 0.53% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 84.77% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 84.77% 42ms 0.53% std::allocator_traits::construct (inline) 0 0% 84.77% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.77% 40ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 2ms 0.025% 84.79% 40ms 0.51% std::_Rb_tree::_M_emplace_hint_unique