File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6516ms, 82.82% of 7868ms total Dropped 561 nodes (cum <= 39.34ms) flat flat% sum% cum cum% 0 0% 0% 7827ms 99.48% __libc_start_call_main 0 0% 0% 7827ms 99.48% __libc_start_main_impl 0 0% 0% 7827ms 99.48% _start 0 0% 0% 7810ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7810ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7810ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7810ms 99.26% main 0 0% 0% 7773ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7773ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7773ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7770ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0% 3368ms 42.81% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.038% 2901ms 36.87% MeshBasedCellPopulation::Update 0 0% 0.038% 2890ms 36.73% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1507ms 19.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.051% 1444ms 18.35% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.064% 1394ms 17.72% MutableMesh::ReMesh 0 0% 0.064% 1347ms 17.12% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.17% 1291ms 16.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.41% 1237ms 15.72% MeshBasedCellPopulation::SpringIterator::operator++ 131ms 1.66% 2.07% 1016ms 12.91% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.038% 2.11% 981ms 12.47% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 430ms 5.47% 7.57% 932ms 11.85% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.59% 915ms 11.63% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.064% 7.65% 888ms 11.29% CellPopulationElementWriter::Visit 9ms 0.11% 7.77% 885ms 11.25% CellPropertyCollection::GetPropertiesType (inline) 258ms 3.28% 11.04% 857ms 10.89% __dynamic_cast 2ms 0.025% 11.07% 817ms 10.38% MeshBasedCellPopulation::AcceptCellWriter 48ms 0.61% 11.68% 814ms 10.35% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 26ms 0.33% 12.01% 775ms 9.85% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.064% 12.07% 694ms 8.82% TetrahedralMesh::ImportFromMesher 6ms 0.076% 12.15% 689ms 8.76% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.16% 624ms 7.93% std::ostream::operator<< (inline) 90ms 1.14% 13.31% 623ms 7.92% std::ostream::_M_insert 58ms 0.74% 14.04% 611ms 7.77% std::map::operator[] (partial-inline) 2ms 0.025% 14.07% 544ms 6.91% triangulate 36ms 0.46% 14.53% 534ms 6.79% operator new 5ms 0.064% 14.59% 526ms 6.69% Cell::GetCellProliferativeType 9ms 0.11% 14.71% 526ms 6.69% LegacyCellProliferativeTypesWriter::VisitCell 10ms 0.13% 14.83% 516ms 6.56% std::set::insert (inline) 512ms 6.51% 21.34% 512ms 6.51% __strcmp_avx2 24ms 0.31% 21.64% 507ms 6.44% std::_Rb_tree::_M_insert_unique 0 0% 21.64% 501ms 6.37% std::_Rb_tree::lower_bound (inline) 0 0% 21.64% 501ms 6.37% std::map::lower_bound (inline) 29ms 0.37% 22.01% 498ms 6.33% std::__new_allocator::allocate (inline) 179ms 2.28% 24.29% 493ms 6.27% __GI___libc_malloc 0 0% 24.29% 490ms 6.23% std::allocator_traits::allocate (inline) 25ms 0.32% 24.61% 488ms 6.20% std::_Rb_tree::find (inline) 1ms 0.013% 24.62% 469ms 5.96% delaunay 1ms 0.013% 24.63% 467ms 5.94% divconqdelaunay 50ms 0.64% 25.27% 466ms 5.92% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.013% 25.28% 460ms 5.85% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.28% 441ms 5.60% std::set::count (inline) 186ms 2.36% 27.64% 436ms 5.54% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.64% 428ms 5.44% std::set::~set (inline) 90ms 1.14% 28.79% 414ms 5.26% std::_Rb_tree::_M_erase 0 0% 28.79% 403ms 5.12% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 28.80% 393ms 4.99% NodeLocationWriter::Visit 0 0% 28.80% 378ms 4.80% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.025% 28.83% 370ms 4.70% Cell::GetMutationState 0 0% 28.83% 369ms 4.69% std::_Rb_tree::_M_get_node (inline) 17ms 0.22% 29.04% 365ms 4.64% std::_Rb_tree::_Rb_tree (partial-inline) 32ms 0.41% 29.45% 348ms 4.42% std::num_put::_M_insert_float 2ms 0.025% 29.47% 338ms 4.30% std::set::set (inline) 120ms 1.53% 31.00% 333ms 4.23% __GI___libc_free 10ms 0.13% 31.13% 326ms 4.14% std::less::operator() (inline) 321ms 4.08% 35.21% 321ms 4.08% std::_Rb_tree::_S_right (inline) 13ms 0.17% 35.37% 316ms 4.02% AbstractCellPopulation::IsCellAttachedToLocationIndex 316ms 4.02% 39.39% 316ms 4.02% std::operator< (inline) 0 0% 39.39% 307ms 3.90% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 39.40% 306ms 3.89% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.025% 39.43% 301ms 3.83% Cell::ReadyToDivide 39ms 0.5% 39.92% 301ms 3.83% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 39.95% 294ms 3.74% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 14ms 0.18% 40.12% 294ms 3.74% std::_Rb_tree::_M_insert_ (inline) 0 0% 40.12% 293ms 3.72% std::_Rb_tree::_M_drop_node (inline) 0 0% 40.12% 292ms 3.71% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.051% 40.18% 289ms 3.67% Element::Element 1ms 0.013% 40.19% 287ms 3.65% OutputFileHandler::OpenOutputFile 8ms 0.1% 40.29% 285ms 3.62% std::__new_allocator::deallocate (inline) 0 0% 40.29% 284ms 3.61% std::allocator_traits::deallocate (inline) 11ms 0.14% 40.43% 269ms 3.42% divconqrecurse 8ms 0.1% 40.53% 267ms 3.39% CellPropertyCollection::HasProperty 0 0% 40.53% 263ms 3.34% AbstractCellProperty::IsType (inline) 0 0% 40.53% 263ms 3.34% Cell::HasCellProperty (inline) 1ms 0.013% 40.54% 261ms 3.32% CellProliferativeTypesWriter::VisitCell 74ms 0.94% 41.48% 258ms 3.28% std::_Rb_tree::_M_clone_node (inline) 5ms 0.064% 41.55% 256ms 3.25% std::__cxx11::collate::do_transform 159ms 2.02% 43.57% 251ms 3.19% _int_malloc 76ms 0.97% 44.53% 249ms 3.16% mergehulls 4ms 0.051% 44.59% 238ms 3.02% ___vsnprintf 0 0% 44.59% 234ms 2.97% __vsnprintf_internal (inline) 33ms 0.42% 45.01% 230ms 2.92% __printf_buffer 0 0% 45.01% 227ms 2.89% std::_Rb_tree::_M_put_node (inline) 173ms 2.20% 47.20% 213ms 2.71% _int_free 49ms 0.62% 47.83% 207ms 2.63% AbstractCellProperty::IsSame 17ms 0.22% 48.04% 206ms 2.62% TetrahedralMesh::Clear 64ms 0.81% 48.86% 189ms 2.40% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.051% 48.91% 187ms 2.38% AbstractPhaseBasedCellCycleModel::ReadyToDivide 13ms 0.17% 49.07% 186ms 2.36% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.064% 49.14% 183ms 2.33% Element::RegisterWithNodes (inline) 6ms 0.076% 49.21% 179ms 2.28% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 49.25% 175ms 2.22% Node::AddElement 12ms 0.15% 49.40% 173ms 2.20% __printf_fp_l_buffer 0 0% 49.40% 173ms 2.20% __printf_fp_spec (inline) 37ms 0.47% 49.87% 158ms 2.01% std::type_info::operator== (inline) 41ms 0.52% 50.39% 152ms 1.93% TetrahedralMesh::EdgesEnd (partial-inline) 76ms 0.97% 51.36% 152ms 1.93% __printf_fp_buffer_1 5ms 0.064% 51.42% 150ms 1.91% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.42% 148ms 1.88% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 51.44% 146ms 1.86% std::basic_filebuf::open 0 0% 51.44% 146ms 1.86% std::basic_ofstream::open (inline) 0 0% 51.44% 135ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.44% 132ms 1.68% OutputFileHandler::OutputFileHandler 20ms 0.25% 51.69% 131ms 1.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 51.69% 131ms 1.66% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.69% 131ms 1.66% OutputFileHandler::CommonConstructor 9ms 0.11% 51.80% 131ms 1.66% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 51.82% 125ms 1.59% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.064% 51.88% 125ms 1.59% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 51.88% 125ms 1.59% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.88% 124ms 1.58% AbstractCellBasedWriter::CloseFile 1ms 0.013% 51.89% 124ms 1.58% std::basic_filebuf::close 0 0% 51.89% 124ms 1.58% std::basic_ofstream::close (inline) 1ms 0.013% 51.91% 123ms 1.56% alternateaxes 52ms 0.66% 52.57% 123ms 1.56% std::__ostream_insert 0 0% 52.57% 122ms 1.55% std::__basic_file::open 108ms 1.37% 53.94% 122ms 1.55% vertexmedian 1ms 0.013% 53.95% 121ms 1.54% _IO_new_fopen 1ms 0.013% 53.97% 121ms 1.54% boost::numeric::ublas::c_vector::c_vector (inline) 121ms 1.54% 55.50% 121ms 1.54% std::_Rb_tree_increment 0 0% 55.50% 121ms 1.54% std::_Vector_base::_M_allocate (inline) 0 0% 55.50% 120ms 1.53% __fopen_internal (inline) 6ms 0.076% 55.58% 120ms 1.53% std::_Rb_tree_const_iterator::operator++ (inline) 25ms 0.32% 55.90% 119ms 1.51% std::num_put::_M_insert_int 0 0% 55.90% 117ms 1.49% _IO_new_file_fopen 7ms 0.089% 55.99% 116ms 1.47% Node::~Node 11ms 0.14% 56.13% 116ms 1.47% boost::detail::shared_count::~shared_count (inline) 0 0% 56.13% 116ms 1.47% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 56.14% 115ms 1.46% __GI__IO_file_open 113ms 1.44% 57.57% 113ms 1.44% incircle 19ms 0.24% 57.82% 112ms 1.42% AbstractTetrahedralElement::RefreshJacobian 0 0% 57.82% 110ms 1.40% FilesystemPermissions::SetFilePermissions (inline) 110ms 1.40% 59.21% 110ms 1.40% __GI_fchmodat 0 0% 59.21% 110ms 1.40% std::filesystem::permissions 2ms 0.025% 59.24% 108ms 1.37% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 59.27% 107ms 1.36% std::vector::push_back (inline) 8ms 0.1% 59.37% 106ms 1.35% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.19% 59.56% 104ms 1.32% MeshBasedCellPopulation::SpringIterator::SpringIterator 69ms 0.88% 60.43% 104ms 1.32% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 104ms 1.32% 61.76% 104ms 1.32% boost::detail::sp_counted_base::release 103ms 1.31% 63.07% 103ms 1.31% __libc_open64 102ms 1.30% 64.36% 102ms 1.30% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 64.39% 102ms 1.30% std::basic_filebuf::overflow 0 0% 64.39% 101ms 1.28% std::basic_filebuf::_M_terminate_output 2ms 0.025% 64.41% 101ms 1.28% std::operator<< (inline) 2ms 0.025% 64.44% 100ms 1.27% std::basic_filebuf::_M_convert_to_external 10ms 0.13% 64.57% 100ms 1.27% std::vector::_M_realloc_insert 1ms 0.013% 64.58% 98ms 1.25% std::__basic_file::xsputn 5ms 0.064% 64.64% 97ms 1.23% AbstractCellPopulation::GetLocationIndexUsingCell 41ms 0.52% 65.16% 97ms 1.23% boost::shared_ptr::shared_ptr (inline) 96ms 1.22% 66.38% 96ms 1.22% __GI___libc_write 1ms 0.013% 66.40% 95ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 33ms 0.42% 66.81% 93ms 1.18% boost::numeric::ublas::indexing_vector_assign 36ms 0.46% 67.27% 91ms 1.16% AbstractElement::GetNodeLocation 87ms 1.11% 68.38% 87ms 1.11% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 5ms 0.064% 68.44% 85ms 1.08% TetrahedralMesh::EdgeIterator::GetNodeB 84ms 1.07% 69.51% 84ms 1.07% [libchaste_cell_based.so] 60ms 0.76% 70.27% 83ms 1.05% std::basic_streambuf::xsputn 57ms 0.72% 71.00% 80ms 1.02% malloc_consolidate 42ms 0.53% 71.53% 73ms 0.93% std::basic_filebuf::xsputn 57ms 0.72% 72.25% 72ms 0.92% AbstractElement::GetNodeGlobalIndex 3ms 0.038% 72.29% 70ms 0.89% Cell::GetCellId 70ms 0.89% 73.18% 70ms 0.89% __memcpy_avx_unaligned_erms 69ms 0.88% 74.06% 69ms 0.88% std::vector::size (inline) 0 0% 74.06% 66ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 0 0% 74.06% 66ms 0.84% std::__new_allocator::destroy (inline) 0 0% 74.06% 66ms 0.84% std::allocator_traits::destroy (inline) 65ms 0.83% 74.89% 65ms 0.83% Node::GetIndex 59ms 0.75% 75.64% 65ms 0.83% vertexsort 6ms 0.076% 75.71% 63ms 0.8% std::_Vector_base::_M_deallocate (inline) 0 0% 75.71% 61ms 0.78% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 61ms 0.78% 76.49% 61ms 0.78% counterclockwise 0 0% 76.49% 61ms 0.78% std::filesystem::create_directory 2ms 0.025% 76.51% 60ms 0.76% std::filesystem::status 0 0% 76.51% 59ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 59ms 0.75% 77.26% 59ms 0.75% __GI___fstatat64 9ms 0.11% 77.38% 58ms 0.74% CellPropertyCollection::AddProperty 50ms 0.64% 78.01% 58ms 0.74% std::num_put::do_put 0 0% 78.01% 58ms 0.74% std::vector::vector (inline) 5ms 0.064% 78.08% 57ms 0.72% TetrahedralMesh::EdgeIterator::GetNodeA 57ms 0.72% 78.80% 57ms 0.72% [libchaste_mesh.so] 0 0% 78.80% 56ms 0.71% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 55ms 0.7% 79.50% 56ms 0.71% boost::detail::shared_count::shared_count (inline) 0 0% 79.50% 55ms 0.7% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 79.50% 53ms 0.67% std::_Vector_base::_Vector_base (inline) 19ms 0.24% 79.74% 52ms 0.66% AbstractTetrahedralMesh::GetElement 3ms 0.038% 79.78% 52ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.025% 79.80% 52ms 0.66% std::_Vector_base::_M_create_storage (inline) 0 0% 79.80% 51ms 0.65% tcache_get (inline) 51ms 0.65% 80.45% 51ms 0.65% tcache_get_n (inline) 8ms 0.1% 80.55% 48ms 0.61% Element::~Element 0 0% 80.55% 45ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 14ms 0.18% 80.73% 44ms 0.56% AbstractCellCycleModel::GetAge 16ms 0.2% 80.94% 44ms 0.56% Determinant (inline) 44ms 0.56% 81.49% 44ms 0.56% boost::shared_ptr::operator-> (inline) 25ms 0.32% 81.81% 44ms 0.56% hack_digit 0 0% 81.81% 44ms 0.56% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 4ms 0.051% 81.86% 44ms 0.56% std::_Rb_tree_header::_Rb_tree_header (inline) 28ms 0.36% 82.22% 43ms 0.55% boost::numeric::ublas::c_matrix::operator() 0 0% 82.22% 41ms 0.52% AbstractCentreBasedCellPopulation::CreateCellPair 3ms 0.038% 82.26% 41ms 0.52% Node::ClearAppliedForce 0 0% 82.26% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 0 0% 82.26% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 40ms 0.51% 82.77% 40ms 0.51% std::_Rb_tree_header::_M_reset (inline) 4ms 0.051% 82.82% 40ms 0.51% std::__new_allocator::construct (inline) 0 0% 82.82% 40ms 0.51% std::allocator_traits::construct (inline) 0 0% 82.82% 40ms 0.51% std::map::find (inline)