File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6849ms, 85.81% of 7982ms total Dropped 570 nodes (cum <= 39.91ms) flat flat% sum% cum cum% 0 0% 0% 7947ms 99.56% __libc_start_call_main 0 0% 0% 7947ms 99.56% __libc_start_main_impl 0 0% 0% 7947ms 99.56% _start 0 0% 0% 7933ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7933ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7933ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7933ms 99.39% main 0 0% 0% 7897ms 98.94% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7897ms 98.94% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7897ms 98.94% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7894ms 98.90% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3376ms 42.30% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2991ms 37.47% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.05% 2889ms 36.19% MeshBasedCellPopulation::Update 1ms 0.013% 0.063% 1519ms 19.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.063% 1476ms 18.49% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.063% 1367ms 17.13% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.075% 1359ms 17.03% MutableMesh::ReMesh 3ms 0.038% 0.11% 1320ms 16.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.29% 1281ms 16.05% MeshBasedCellPopulation::SpringIterator::operator++ 108ms 1.35% 1.64% 1058ms 13.25% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.063% 1.70% 1009ms 12.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 13ms 0.16% 1.87% 978ms 12.25% CellPropertyCollection::GetPropertiesType (inline) 417ms 5.22% 7.09% 976ms 12.23% std::_Rb_tree::_M_lower_bound (inline) 303ms 3.80% 10.89% 936ms 11.73% __dynamic_cast 9ms 0.11% 11.00% 924ms 11.58% CellPopulationElementWriter::Visit 5ms 0.063% 11.06% 885ms 11.09% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.013% 11.07% 848ms 10.62% MeshBasedCellPopulation::AcceptCellWriter 33ms 0.41% 11.49% 777ms 9.73% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.038% 11.53% 766ms 9.60% AbstractCellProperty::IsSubType (inline) 28ms 0.35% 11.88% 745ms 9.33% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.063% 11.94% 719ms 9.01% TetrahedralMesh::ImportFromMesher 1ms 0.013% 11.95% 642ms 8.04% std::ostream::operator<< (inline) 94ms 1.18% 13.13% 641ms 8.03% std::ostream::_M_insert 56ms 0.7% 13.83% 580ms 7.27% std::map::operator[] (partial-inline) 7ms 0.088% 13.92% 579ms 7.25% Cell::GetCellProliferativeType 30ms 0.38% 14.29% 557ms 6.98% std::_Rb_tree::find (inline) 39ms 0.49% 14.78% 553ms 6.93% operator new 6ms 0.075% 14.86% 542ms 6.79% std::set::insert (inline) 20ms 0.25% 15.11% 536ms 6.72% std::_Rb_tree::_M_insert_unique 4ms 0.05% 15.16% 522ms 6.54% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 15.16% 514ms 6.44% std::set::count (inline) 513ms 6.43% 21.59% 513ms 6.43% __strcmp_avx2 159ms 1.99% 23.58% 510ms 6.39% __GI___libc_malloc 41ms 0.51% 24.09% 506ms 6.34% std::__new_allocator::allocate (inline) 0 0% 24.09% 503ms 6.30% std::allocator_traits::allocate (inline) 0 0% 24.09% 486ms 6.09% triangulate 0 0% 24.09% 482ms 6.04% std::_Rb_tree::lower_bound (inline) 0 0% 24.09% 482ms 6.04% std::map::lower_bound (inline) 6ms 0.075% 24.17% 476ms 5.96% AbstractCellBasedSimulation::DoCellBirth 211ms 2.64% 26.81% 437ms 5.47% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.81% 429ms 5.37% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 26.82% 414ms 5.19% delaunay 3ms 0.038% 26.86% 412ms 5.16% divconqdelaunay 0 0% 26.86% 412ms 5.16% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.025% 26.89% 402ms 5.04% NodeLocationWriter::Visit 3ms 0.038% 26.92% 399ms 5.00% Cell::GetMutationState 9ms 0.11% 27.04% 395ms 4.95% std::less::operator() (inline) 386ms 4.84% 31.87% 386ms 4.84% std::operator< (inline) 0 0% 31.87% 385ms 4.82% std::_Rb_tree::_M_get_node (inline) 28ms 0.35% 32.22% 383ms 4.80% std::_Rb_tree::~_Rb_tree (inline) 22ms 0.28% 32.50% 369ms 4.62% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 32.51% 352ms 4.41% MeshBasedCellPopulation::GetDampingConstant 81ms 1.01% 33.53% 352ms 4.41% std::_Rb_tree::_M_erase 4ms 0.05% 33.58% 351ms 4.40% AbstractCentreBasedCellPopulation::GetDampingConstant 32ms 0.4% 33.98% 351ms 4.40% std::num_put::_M_insert_float 0 0% 33.98% 350ms 4.38% std::set::~set (inline) 2ms 0.025% 34.00% 336ms 4.21% std::set::set (inline) 38ms 0.48% 34.48% 322ms 4.03% std::_Rb_tree::_M_copy (inline) 319ms 4.00% 38.47% 319ms 4.00% std::_Rb_tree::_S_right (inline) 1ms 0.013% 38.49% 318ms 3.98% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.49% 318ms 3.98% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.05% 38.54% 316ms 3.96% Cell::ReadyToDivide 0 0% 38.54% 314ms 3.93% OutputFileHandler::OpenOutputFile 18ms 0.23% 38.76% 314ms 3.93% std::_Rb_tree::_M_insert_ (inline) 4ms 0.05% 38.81% 308ms 3.86% Element::Element 11ms 0.14% 38.95% 307ms 3.85% AbstractCellPopulation::IsCellAttachedToLocationIndex 117ms 1.47% 40.42% 304ms 3.81% __GI___libc_free 4ms 0.05% 40.47% 285ms 3.57% CellProliferativeTypesWriter::VisitCell 91ms 1.14% 41.61% 283ms 3.55% std::_Rb_tree::_M_clone_node (inline) 187ms 2.34% 43.95% 279ms 3.50% _int_malloc 4ms 0.05% 44.00% 266ms 3.33% std::__cxx11::collate::do_transform 13ms 0.16% 44.16% 258ms 3.23% std::__new_allocator::deallocate (inline) 4ms 0.05% 44.21% 253ms 3.17% ___vsnprintf 0 0% 44.21% 253ms 3.17% std::allocator_traits::deallocate (inline) 1ms 0.013% 44.22% 249ms 3.12% __vsnprintf_internal (inline) 0 0% 44.22% 249ms 3.12% std::_Rb_tree::_M_drop_node (inline) 24ms 0.3% 44.53% 243ms 3.04% __printf_buffer 2ms 0.025% 44.55% 240ms 3.01% AbstractCellProperty::IsType (inline) 10ms 0.13% 44.68% 239ms 2.99% divconqrecurse 83ms 1.04% 45.72% 226ms 2.83% mergehulls 0 0% 45.72% 225ms 2.82% Cell::HasCellProperty (inline) 6ms 0.075% 45.79% 225ms 2.82% CellPropertyCollection::HasProperty 1ms 0.013% 45.80% 208ms 2.61% __printf_fp_spec (inline) 1ms 0.013% 45.82% 207ms 2.59% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 45.95% 207ms 2.59% __printf_fp_l_buffer 8ms 0.1% 46.05% 204ms 2.56% Element::RegisterWithNodes (inline) 11ms 0.14% 46.19% 203ms 2.54% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 72ms 0.9% 47.09% 202ms 2.53% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 47.09% 202ms 2.53% std::_Rb_tree::_M_put_node (inline) 1ms 0.013% 47.11% 195ms 2.44% Node::AddElement 20ms 0.25% 47.36% 195ms 2.44% TetrahedralMesh::Clear 123ms 1.54% 48.90% 192ms 2.41% __printf_fp_buffer_1 156ms 1.95% 50.85% 185ms 2.32% _int_free 35ms 0.44% 51.29% 175ms 2.19% AbstractCellProperty::IsSame 11ms 0.14% 51.43% 170ms 2.13% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.25% 51.68% 168ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 6ms 0.075% 51.75% 154ms 1.93% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.75% 153ms 1.92% std::basic_ofstream::basic_ofstream (inline) 2ms 0.025% 51.78% 148ms 1.85% std::basic_filebuf::open 0 0% 51.78% 148ms 1.85% std::basic_ofstream::open (inline) 56ms 0.7% 52.48% 144ms 1.80% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 52.49% 143ms 1.79% TetrahedralMesh::RefreshJacobianCachedData 21ms 0.26% 52.76% 140ms 1.75% std::type_info::operator== (inline) 7ms 0.088% 52.84% 138ms 1.73% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.05% 52.89% 138ms 1.73% boost::numeric::ublas::vector_assign (inline) 7ms 0.088% 52.98% 135ms 1.69% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.98% 135ms 1.69% OutputFileHandler::CommonConstructor 0 0% 52.98% 135ms 1.69% OutputFileHandler::OutputFileHandler 60ms 0.75% 53.73% 134ms 1.68% std::__ostream_insert 0 0% 53.73% 132ms 1.65% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 53.73% 131ms 1.64% AbstractCellBasedWriter::CloseFile 1ms 0.013% 53.75% 130ms 1.63% std::basic_filebuf::close 0 0% 53.75% 130ms 1.63% std::basic_ofstream::close (inline) 0 0% 53.75% 129ms 1.62% OutputFileHandler::MakeFoldersAndReturnFullPath 32ms 0.4% 54.15% 129ms 1.62% std::num_put::_M_insert_int 0 0% 54.15% 123ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 123ms 1.54% 55.69% 123ms 1.54% __GI_fchmodat 0 0% 55.69% 123ms 1.54% std::filesystem::permissions 2ms 0.025% 55.71% 122ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.19% 55.90% 119ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 55.91% 119ms 1.49% std::_Vector_base::_M_allocate (inline) 23ms 0.29% 56.20% 118ms 1.48% MeshBasedCellPopulation::SpringIterator::SpringIterator 18ms 0.23% 56.43% 117ms 1.47% AbstractTetrahedralElement::RefreshJacobian 6ms 0.075% 56.50% 116ms 1.45% std::vector::push_back (inline) 11ms 0.14% 56.64% 111ms 1.39% boost::detail::shared_count::~shared_count (inline) 0 0% 56.64% 111ms 1.39% boost::shared_ptr::~shared_ptr (inline) 12ms 0.15% 56.79% 111ms 1.39% std::_Rb_tree_const_iterator::operator++ (inline) 109ms 1.37% 58.16% 109ms 1.37% std::_Rb_tree_increment 3ms 0.038% 58.19% 108ms 1.35% std::operator<< (inline) 3ms 0.038% 58.23% 107ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.025% 58.26% 107ms 1.34% alternateaxes 0 0% 58.26% 107ms 1.34% std::__basic_file::open 1ms 0.013% 58.27% 105ms 1.32% _IO_new_fopen 0 0% 58.27% 104ms 1.30% __fopen_internal (inline) 43ms 0.54% 58.81% 104ms 1.30% boost::shared_ptr::shared_ptr (inline) 6ms 0.075% 58.88% 104ms 1.30% std::vector::_M_realloc_insert 96ms 1.20% 60.09% 104ms 1.30% vertexmedian 23ms 0.29% 60.37% 103ms 1.29% boost::numeric::ublas::indexing_vector_assign 6ms 0.075% 60.45% 101ms 1.27% Node::~Node 4ms 0.05% 60.50% 100ms 1.25% _IO_new_file_fopen 95ms 1.19% 61.69% 96ms 1.20% boost::detail::sp_counted_base::release 0 0% 61.69% 95ms 1.19% __GI__IO_file_open 36ms 0.45% 62.14% 93ms 1.17% AbstractTetrahedralMesh::GetNumAllElements 20ms 0.25% 62.39% 93ms 1.17% TetrahedralMesh::EdgeIterator::GetNodeB 3ms 0.038% 62.43% 92ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 90ms 1.13% 63.56% 91ms 1.14% __GI___libc_write 0 0% 63.56% 90ms 1.13% std::__basic_file::xsputn 0 0% 63.56% 90ms 1.13% std::basic_filebuf::_M_convert_to_external 0 0% 63.56% 90ms 1.13% std::basic_filebuf::_M_terminate_output 0 0% 63.56% 90ms 1.13% std::basic_filebuf::overflow 1ms 0.013% 63.57% 88ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 88ms 1.10% 64.67% 88ms 1.10% std::_Rb_tree_insert_and_rebalance 88ms 1.10% 65.77% 88ms 1.10% std::vector::size (inline) 87ms 1.09% 66.86% 87ms 1.09% Node::GetIndex 87ms 1.09% 67.95% 87ms 1.09% __libc_open64 87ms 1.09% 69.04% 87ms 1.09% incircle 65ms 0.81% 69.86% 85ms 1.06% malloc_consolidate 34ms 0.43% 70.28% 83ms 1.04% AbstractElement::GetNodeLocation 0 0% 70.28% 83ms 1.04% Cell::GetCellId 56ms 0.7% 70.98% 81ms 1.01% std::basic_filebuf::xsputn 0 0% 70.98% 79ms 0.99% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.1% 71.08% 73ms 0.91% CellPropertyCollection::AddProperty 60ms 0.75% 71.84% 72ms 0.9% AbstractElement::GetNodeGlobalIndex 69ms 0.86% 72.70% 69ms 0.86% [libchaste_cell_based.so] 68ms 0.85% 73.55% 68ms 0.85% __memcpy_avx_unaligned_erms 48ms 0.6% 74.15% 67ms 0.84% std::basic_streambuf::xsputn 59ms 0.74% 74.89% 67ms 0.84% std::num_put::do_put 5ms 0.063% 74.96% 65ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 74.96% 63ms 0.79% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 63ms 0.79% 75.75% 63ms 0.79% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 63ms 0.79% 76.53% 63ms 0.79% __GI___fstatat64 0 0% 76.53% 63ms 0.79% std::filesystem::create_directory 1ms 0.013% 76.55% 63ms 0.79% std::filesystem::status 0 0% 76.55% 63ms 0.79% tcache_get (inline) 63ms 0.79% 77.34% 63ms 0.79% tcache_get_n (inline) 2ms 0.025% 77.36% 62ms 0.78% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 60ms 0.75% 78.11% 61ms 0.76% boost::detail::shared_count::shared_count (inline) 0 0% 78.11% 61ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.11% 61ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 35ms 0.44% 78.55% 60ms 0.75% boost::numeric::ublas::c_matrix::operator() (partial-inline) 34ms 0.43% 78.98% 57ms 0.71% AbstractTetrahedralMesh::GetElement 57ms 0.71% 79.69% 57ms 0.71% counterclockwise 55ms 0.69% 80.38% 55ms 0.69% [libstdc++.so.6.0.33] 55ms 0.69% 81.07% 55ms 0.69% boost::shared_ptr::operator-> (inline) 53ms 0.66% 81.73% 53ms 0.66% Node::IsDeleted 53ms 0.66% 82.40% 53ms 0.66% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.40% 53ms 0.66% std::vector::vector (inline) 48ms 0.6% 83.00% 51ms 0.64% vertexsort 4ms 0.05% 83.05% 50ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 83.05% 50ms 0.63% std::_Vector_base::_Vector_base (inline) 6ms 0.075% 83.12% 49ms 0.61% Node::ConstructNodeAttributes (inline) 1ms 0.013% 83.14% 49ms 0.61% std::_Vector_base::_M_create_storage (inline) 3ms 0.038% 83.17% 48ms 0.6% Node::ClearAppliedForce 0 0% 83.17% 47ms 0.59% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.038% 83.21% 47ms 0.59% std::__new_allocator::construct (inline) 0 0% 83.21% 47ms 0.59% std::__new_allocator::destroy (inline) 0 0% 83.21% 47ms 0.59% std::allocator_traits::construct (inline) 0 0% 83.21% 47ms 0.59% std::allocator_traits::destroy (inline) 1ms 0.013% 83.22% 45ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 12ms 0.15% 83.38% 45ms 0.56% Inverse 0 0% 83.38% 44ms 0.55% std::_Rb_tree::_M_construct_node (inline) 17ms 0.21% 83.59% 43ms 0.54% AbstractCellCycleModel::GetAge 28ms 0.35% 83.94% 43ms 0.54% hack_digit 43ms 0.54% 84.48% 43ms 0.54% std::ostream::sentry::sentry 14ms 0.18% 84.65% 42ms 0.53% Determinant (inline) 42ms 0.53% 85.18% 42ms 0.53% [libchaste_mesh.so] 0 0% 85.18% 42ms 0.53% boost::numeric::ublas::norm_2 (inline) 8ms 0.1% 85.28% 42ms 0.53% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.025% 85.30% 42ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 0 0% 85.30% 41ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 40ms 0.5% 85.81% 40ms 0.5% Node::rGetLocation 0 0% 85.81% 40ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)