File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6732ms, 83.80% of 8033ms total Dropped 573 nodes (cum <= 40.16ms) flat flat% sum% cum cum% 0 0% 0% 7997ms 99.55% __libc_start_call_main 0 0% 0% 7997ms 99.55% __libc_start_main_impl 0 0% 0% 7997ms 99.55% _start 0 0% 0% 7979ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7979ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7979ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7979ms 99.33% main 0 0% 0% 7938ms 98.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7938ms 98.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7938ms 98.82% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7935ms 98.78% AbstractCellBasedSimulation::Solve 1ms 0.012% 0.012% 3436ms 42.77% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.025% 2976ms 37.05% MeshBasedCellPopulation::Update 0 0% 0.025% 2905ms 36.16% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.037% 1583ms 19.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.037% 0.075% 1476ms 18.37% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.075% 1450ms 18.05% MutableMesh::ReMesh 0 0% 0.075% 1424ms 17.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.037% 0.11% 1371ms 17.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 30ms 0.37% 0.49% 1271ms 15.82% MeshBasedCellPopulation::SpringIterator::operator++ 101ms 1.26% 1.74% 1006ms 12.52% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.05% 1.79% 956ms 11.90% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.05% 1.84% 927ms 11.54% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 238ms 2.96% 4.81% 918ms 11.43% __dynamic_cast 422ms 5.25% 10.06% 908ms 11.30% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.14% 10.20% 906ms 11.28% CellPopulationElementWriter::Visit 10ms 0.12% 10.32% 878ms 10.93% CellPropertyCollection::GetPropertiesType (inline) 46ms 0.57% 10.89% 843ms 10.49% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.05% 10.94% 778ms 9.69% MeshBasedCellPopulation::AcceptCellWriter 29ms 0.36% 11.30% 753ms 9.37% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 11.45% 743ms 9.25% TetrahedralMesh::ImportFromMesher 2ms 0.025% 11.48% 699ms 8.70% AbstractCellProperty::IsSubType (inline) 0 0% 11.48% 634ms 7.89% std::ostream::operator<< (inline) 106ms 1.32% 12.80% 630ms 7.84% std::ostream::_M_insert 73ms 0.91% 13.71% 561ms 6.98% std::map::operator[] (partial-inline) 36ms 0.45% 14.15% 560ms 6.97% operator new 555ms 6.91% 21.06% 555ms 6.91% __strcmp_avx2 1ms 0.012% 21.08% 538ms 6.70% triangulate 18ms 0.22% 21.30% 520ms 6.47% std::_Rb_tree::find (inline) 7ms 0.087% 21.39% 519ms 6.46% Cell::GetCellProliferativeType 11ms 0.14% 21.52% 516ms 6.42% std::set::insert (inline) 166ms 2.07% 23.59% 507ms 6.31% __GI___libc_malloc 8ms 0.1% 23.69% 505ms 6.29% std::_Rb_tree::_M_insert_unique 26ms 0.32% 24.01% 503ms 6.26% std::__new_allocator::allocate (inline) 4ms 0.05% 24.06% 499ms 6.21% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.06% 497ms 6.19% std::allocator_traits::allocate (inline) 216ms 2.69% 26.75% 482ms 6.00% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.75% 474ms 5.90% delaunay 1ms 0.012% 26.76% 473ms 5.89% divconqdelaunay 0 0% 26.76% 470ms 5.85% std::set::count (inline) 40ms 0.5% 27.26% 450ms 5.60% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.05% 27.31% 445ms 5.54% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.31% 435ms 5.42% std::_Rb_tree::lower_bound (inline) 0 0% 27.31% 435ms 5.42% std::map::lower_bound (inline) 0 0% 27.31% 424ms 5.28% std::_Rb_tree::_M_create_node (inline) 0 0% 27.31% 420ms 5.23% std::set::~set (inline) 83ms 1.03% 28.35% 407ms 5.07% std::_Rb_tree::_M_erase 0 0% 28.35% 399ms 4.97% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.35% 385ms 4.79% std::_Rb_tree::_M_get_node (inline) 1ms 0.012% 28.36% 367ms 4.57% NodeLocationWriter::Visit 2ms 0.025% 28.38% 362ms 4.51% Cell::GetMutationState 17ms 0.21% 28.59% 346ms 4.31% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.075% 28.67% 345ms 4.29% std::less::operator() (inline) 339ms 4.22% 32.89% 339ms 4.22% std::operator< (inline) 0 0% 32.89% 329ms 4.10% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 32.89% 329ms 4.10% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 3ms 0.037% 32.93% 327ms 4.07% MeshBasedCellPopulation::GetDampingConstant 1ms 0.012% 32.94% 326ms 4.06% OutputFileHandler::OpenOutputFile 0 0% 32.94% 324ms 4.03% AbstractCentreBasedCellPopulation::GetDampingConstant 30ms 0.37% 33.31% 319ms 3.97% std::num_put::_M_insert_float 4ms 0.05% 33.36% 314ms 3.91% Cell::ReadyToDivide 19ms 0.24% 33.60% 313ms 3.90% std::_Rb_tree::_M_insert_ (inline) 5ms 0.062% 33.66% 311ms 3.87% std::set::set (inline) 0 0% 33.66% 306ms 3.81% std::_Rb_tree::_M_drop_node (inline) 83ms 1.03% 34.69% 295ms 3.67% __GI___libc_free 5ms 0.062% 34.76% 293ms 3.65% Element::Element 34ms 0.42% 35.18% 293ms 3.65% std::_Rb_tree::_M_copy (inline) 15ms 0.19% 35.37% 284ms 3.54% std::__new_allocator::deallocate (inline) 0 0% 35.37% 282ms 3.51% std::allocator_traits::deallocate (inline) 5ms 0.062% 35.43% 278ms 3.46% divconqrecurse 72ms 0.9% 36.33% 266ms 3.31% mergehulls 266ms 3.31% 39.64% 266ms 3.31% std::_Rb_tree::_S_right (inline) 3ms 0.037% 39.67% 263ms 3.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 169ms 2.10% 41.78% 252ms 3.14% _int_malloc 69ms 0.86% 42.64% 252ms 3.14% std::_Rb_tree::_M_clone_node (inline) 7ms 0.087% 42.72% 251ms 3.12% std::__cxx11::collate::do_transform 0 0% 42.72% 246ms 3.06% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 42.75% 245ms 3.05% AbstractCellProperty::IsType (inline) 5ms 0.062% 42.81% 245ms 3.05% CellPropertyCollection::HasProperty 0 0% 42.81% 243ms 3.03% Cell::HasCellProperty (inline) 1ms 0.012% 42.82% 234ms 2.91% CellProliferativeTypesWriter::VisitCell 2ms 0.025% 42.85% 232ms 2.89% ___vsnprintf 0 0% 42.85% 230ms 2.86% __vsnprintf_internal (inline) 31ms 0.39% 43.23% 228ms 2.84% __printf_buffer 11ms 0.14% 43.37% 215ms 2.68% TetrahedralMesh::Clear 185ms 2.30% 45.67% 211ms 2.63% _int_free 5ms 0.062% 45.74% 210ms 2.61% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.075% 45.81% 206ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.062% 45.87% 203ms 2.53% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 51ms 0.63% 46.51% 189ms 2.35% TetrahedralMesh::EdgesEnd (partial-inline) 6ms 0.075% 46.58% 187ms 2.33% __printf_fp_l_buffer 0 0% 46.58% 187ms 2.33% __printf_fp_spec (inline) 70ms 0.87% 47.45% 184ms 2.29% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.087% 47.54% 183ms 2.28% Element::RegisterWithNodes (inline) 44ms 0.55% 48.09% 181ms 2.25% AbstractCellProperty::IsSame 90ms 1.12% 49.21% 179ms 2.23% __printf_fp_buffer_1 5ms 0.062% 49.27% 173ms 2.15% Node::AddElement 8ms 0.1% 49.37% 163ms 2.03% AbstractTetrahedralElement::CalculateJacobian 1ms 0.012% 49.38% 153ms 1.90% TetrahedralMesh::RefreshJacobianCachedData 0 0% 49.38% 153ms 1.90% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.38% 149ms 1.85% std::basic_filebuf::open 0 0% 49.38% 149ms 1.85% std::basic_ofstream::open (inline) 0 0% 49.38% 148ms 1.84% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 49.38% 147ms 1.83% AbstractCellBasedWriter::CloseFile 0 0% 49.38% 147ms 1.83% std::basic_filebuf::close 0 0% 49.38% 147ms 1.83% std::basic_ofstream::close (inline) 0 0% 49.38% 143ms 1.78% OutputFileHandler::CommonConstructor 0 0% 49.38% 143ms 1.78% OutputFileHandler::OutputFileHandler 37ms 0.46% 49.84% 143ms 1.78% std::num_put::_M_insert_int 10ms 0.12% 49.97% 142ms 1.77% AbstractTetrahedralElement::CalculateInverseJacobian 56ms 0.7% 50.67% 141ms 1.76% std::__ostream_insert 0 0% 50.67% 139ms 1.73% FilesystemPermissions::SetFilePermissions (inline) 139ms 1.73% 52.40% 139ms 1.73% __GI_fchmodat 0 0% 52.40% 139ms 1.73% std::filesystem::permissions 1ms 0.012% 52.41% 138ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.062% 52.47% 138ms 1.72% boost::numeric::ublas::vector_assign (inline) 7ms 0.087% 52.56% 137ms 1.71% boost::detail::shared_count::~shared_count (inline) 0 0% 52.56% 137ms 1.71% boost::shared_ptr::~shared_ptr (inline) 33ms 0.41% 52.97% 137ms 1.71% std::type_info::operator== (inline) 21ms 0.26% 53.23% 134ms 1.67% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.062% 53.29% 134ms 1.67% Node::~Node 131ms 1.63% 54.92% 131ms 1.63% incircle 94ms 1.17% 56.09% 130ms 1.62% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 4ms 0.05% 56.14% 129ms 1.61% boost::numeric::ublas::c_vector::c_vector (inline) 24ms 0.3% 56.44% 125ms 1.56% AbstractTetrahedralElement::RefreshJacobian 0 0% 56.44% 121ms 1.51% _IO_new_fopen 0 0% 56.44% 121ms 1.51% __fopen_internal (inline) 0 0% 56.44% 121ms 1.51% std::__basic_file::open 111ms 1.38% 57.82% 120ms 1.49% boost::detail::sp_counted_base::release 2ms 0.025% 57.85% 119ms 1.48% _IO_new_file_fopen 9ms 0.11% 57.96% 116ms 1.44% std::vector::push_back (inline) 0 0% 57.96% 115ms 1.43% __GI__IO_file_open 1ms 0.012% 57.97% 113ms 1.41% std::_Vector_base::_M_allocate (inline) 112ms 1.39% 59.37% 112ms 1.39% [libchaste_cell_based.so] 7ms 0.087% 59.45% 111ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.012% 59.47% 111ms 1.38% std::operator<< (inline) 3ms 0.037% 59.50% 110ms 1.37% alternateaxes 14ms 0.17% 59.68% 107ms 1.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 107ms 1.33% 61.01% 107ms 1.33% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 101ms 1.26% 62.27% 107ms 1.33% vertexmedian 2ms 0.025% 62.29% 103ms 1.28% std::basic_filebuf::_M_terminate_output 0 0% 62.29% 102ms 1.27% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.012% 62.31% 102ms 1.27% std::basic_filebuf::overflow 9ms 0.11% 62.42% 102ms 1.27% std::vector::_M_realloc_insert 0 0% 62.42% 101ms 1.26% std::__basic_file::xsputn 0 0% 62.42% 101ms 1.26% std::basic_filebuf::_M_convert_to_external 99ms 1.23% 63.65% 99ms 1.23% __GI___libc_write 70ms 0.87% 64.52% 99ms 1.23% std::basic_filebuf::xsputn 96ms 1.20% 65.72% 98ms 1.22% __libc_open64 43ms 0.54% 66.25% 97ms 1.21% boost::shared_ptr::shared_ptr (inline) 6ms 0.075% 66.33% 97ms 1.21% std::_Rb_tree_const_iterator::operator++ (inline) 94ms 1.17% 67.50% 94ms 1.17% std::_Rb_tree_increment 29ms 0.36% 67.86% 93ms 1.16% boost::numeric::ublas::indexing_vector_assign 40ms 0.5% 68.36% 92ms 1.15% AbstractElement::GetNodeLocation 89ms 1.11% 69.46% 89ms 1.11% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 69.48% 88ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 4ms 0.05% 69.53% 84ms 1.05% TetrahedralMesh::EdgeIterator::GetNodeB 3ms 0.037% 69.56% 82ms 1.02% Cell::GetCellId 82ms 1.02% 70.58% 82ms 1.02% __GI___fstatat64 2ms 0.025% 70.61% 81ms 1.01% std::filesystem::status 1ms 0.012% 70.62% 80ms 1% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 5ms 0.062% 70.68% 80ms 1% TetrahedralMesh::EdgeIterator::GetNodeA 2ms 0.025% 70.71% 79ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 64ms 0.8% 71.51% 79ms 0.98% AbstractElement::GetNodeGlobalIndex 1ms 0.012% 71.52% 79ms 0.98% std::filesystem::create_directory 67ms 0.83% 72.35% 78ms 0.97% vertexsort 4ms 0.05% 72.40% 77ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.40% 77ms 0.96% tcache_get (inline) 77ms 0.96% 73.36% 77ms 0.96% tcache_get_n (inline) 0 0% 73.36% 76ms 0.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.36% 76ms 0.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.93% 74.29% 75ms 0.93% std::vector::size (inline) 74ms 0.92% 75.21% 74ms 0.92% Node::GetIndex 11ms 0.14% 75.35% 70ms 0.87% CellPropertyCollection::AddProperty 49ms 0.61% 75.96% 66ms 0.82% malloc_consolidate 39ms 0.49% 76.45% 64ms 0.8% std::basic_streambuf::xsputn 3ms 0.037% 76.48% 60ms 0.75% Node::ConstructNodeAttributes (inline) 0 0% 76.48% 60ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.48% 60ms 0.75% std::__new_allocator::destroy (inline) 0 0% 76.48% 60ms 0.75% std::allocator_traits::destroy (inline) 49ms 0.61% 77.09% 59ms 0.73% std::num_put::do_put 30ms 0.37% 77.47% 58ms 0.72% hack_digit 0 0% 77.47% 57ms 0.71% Node::ClearAppliedForce 57ms 0.71% 78.18% 57ms 0.71% __memcpy_avx_unaligned_erms 57ms 0.71% 78.89% 57ms 0.71% counterclockwise 0 0% 78.89% 56ms 0.7% boost::numeric::ublas::norm_2 (inline) 14ms 0.17% 79.06% 56ms 0.7% boost::numeric::ublas::vector_norm_2::apply (inline) 53ms 0.66% 79.72% 54ms 0.67% boost::detail::shared_count::shared_count (inline) 53ms 0.66% 80.38% 53ms 0.66% [libstdc++.so.6.0.33] 1ms 0.012% 80.39% 53ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 52ms 0.65% 81.04% 52ms 0.65% [libchaste_mesh.so] 52ms 0.65% 81.69% 52ms 0.65% boost::shared_ptr::operator-> (inline) 18ms 0.22% 81.91% 51ms 0.63% AbstractTetrahedralMesh::GetElement 29ms 0.36% 82.27% 51ms 0.63% boost::numeric::ublas::c_matrix::operator() 0 0% 82.27% 50ms 0.62% std::vector::vector (inline) 48ms 0.6% 82.87% 48ms 0.6% boost::numeric::ublas::c_vector::operator() 0 0% 82.87% 47ms 0.59% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.87% 47ms 0.59% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.87% 46ms 0.57% AbstractCentreBasedCellPopulation::CreateCellPair 46ms 0.57% 83.44% 46ms 0.57% Node::rGetLocation 1ms 0.012% 83.46% 45ms 0.56% BoundaryNodeWriter::Visit 14ms 0.17% 83.63% 44ms 0.55% AbstractCellCycleModel::GetAge 0 0% 83.63% 44ms 0.55% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.63% 43ms 0.54% std::_Vector_base::_Vector_base (inline) 1ms 0.012% 83.64% 43ms 0.54% std::__new_allocator::construct (inline) 0 0% 83.64% 43ms 0.54% std::allocator_traits::construct (inline) 0 0% 83.64% 42ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.012% 83.65% 42ms 0.52% std::__basic_file::close 0 0% 83.65% 42ms 0.52% std::map::find (inline) 12ms 0.15% 83.80% 41ms 0.51% Determinant (inline) 0 0% 83.80% 41ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.80% 41ms 0.51% _IO_new_fclose 0 0% 83.80% 41ms 0.51% std::_Vector_base::_M_create_storage (inline)