File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5456ms, 84.96% of 6422ms total Dropped 512 nodes (cum <= 32.11ms) flat flat% sum% cum cum% 0 0% 0% 6392ms 99.53% __libc_start_call_main 0 0% 0% 6392ms 99.53% __libc_start_main_impl 0 0% 0% 6392ms 99.53% _start 0 0% 0% 6376ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6376ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6376ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6376ms 99.28% main 0 0% 0% 6348ms 98.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6348ms 98.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6348ms 98.85% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6346ms 98.82% AbstractCellBasedSimulation::Solve 1ms 0.016% 0.016% 3031ms 47.20% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.016% 2668ms 41.54% MeshBasedCellPopulation::Update 2ms 0.031% 0.047% 2097ms 32.65% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.047% 1368ms 21.30% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.062% 1250ms 19.46% MutableMesh::ReMesh 1ms 0.016% 0.078% 1215ms 18.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.22% 0.3% 1204ms 18.75% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.016% 0.31% 1087ms 16.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.016% 0.33% 1041ms 16.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 101ms 1.57% 1.90% 1006ms 15.66% TetrahedralMesh::EdgeIterator::operator++ 7ms 0.11% 2.01% 788ms 12.27% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.25% 2.26% 775ms 12.07% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 391ms 6.09% 8.35% 760ms 11.83% std::_Rb_tree::_M_lower_bound (inline) 41ms 0.64% 8.98% 723ms 11.26% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 14ms 0.22% 9.20% 717ms 11.16% CellPopulationElementWriter::Visit 7ms 0.11% 9.31% 691ms 10.76% AbstractCellPopulation::GetCellUsingLocationIndex 123ms 1.92% 11.23% 662ms 10.31% __dynamic_cast 3ms 0.047% 11.27% 634ms 9.87% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.17% 11.45% 632ms 9.84% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.078% 11.52% 617ms 9.61% TetrahedralMesh::ImportFromMesher 38ms 0.59% 12.11% 603ms 9.39% operator new 9ms 0.14% 12.25% 569ms 8.86% std::set::insert (inline) 208ms 3.24% 15.49% 565ms 8.80% __GI___libc_malloc 12ms 0.19% 15.68% 560ms 8.72% std::_Rb_tree::_M_insert_unique 16ms 0.25% 15.93% 531ms 8.27% std::__new_allocator::allocate (inline) 0 0% 15.93% 528ms 8.22% std::allocator_traits::allocate (inline) 7ms 0.11% 16.04% 524ms 8.16% AbstractCellProperty::IsSubType (inline) 9ms 0.14% 16.18% 495ms 7.71% std::_Rb_tree::find (inline) 0 0% 16.18% 483ms 7.52% triangulate 91ms 1.42% 17.60% 474ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 0 0% 17.60% 463ms 7.21% std::set::count (inline) 0 0% 17.60% 455ms 7.09% std::set::~set (inline) 0 0% 17.60% 434ms 6.76% delaunay 3ms 0.047% 17.64% 434ms 6.76% divconqdelaunay 0 0% 17.64% 432ms 6.73% std::ostream::operator<< (inline) 60ms 0.93% 18.58% 429ms 6.68% std::ostream::_M_insert 0 0% 18.58% 425ms 6.62% std::_Rb_tree::_M_create_node (inline) 0 0% 18.58% 419ms 6.52% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 18.58% 413ms 6.43% std::_Rb_tree::_M_get_node (inline) 60ms 0.93% 19.51% 408ms 6.35% std::map::operator[] (partial-inline) 406ms 6.32% 25.83% 406ms 6.32% __strcmp_evex 0 0% 25.83% 404ms 6.29% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.093% 25.93% 398ms 6.20% Cell::GetCellProliferativeType 42ms 0.65% 26.58% 382ms 5.95% std::_Rb_tree::_M_erase 197ms 3.07% 29.65% 366ms 5.70% __cxxabiv1::__si_class_type_info::__do_dyncast 29ms 0.45% 30.10% 362ms 5.64% std::_Rb_tree::_M_insert_ (inline) 1ms 0.016% 30.12% 353ms 5.50% AbstractCellBasedSimulation::DoCellBirth 18ms 0.28% 30.40% 353ms 5.50% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 30.40% 338ms 5.26% std::_Rb_tree::_M_drop_node (inline) 2ms 0.031% 30.43% 329ms 5.12% std::set::set (inline) 0 0% 30.43% 308ms 4.80% std::_Rb_tree::lower_bound (inline) 0 0% 30.43% 308ms 4.80% std::map::lower_bound (inline) 36ms 0.56% 30.99% 302ms 4.70% std::_Rb_tree::_M_copy (inline) 7ms 0.11% 31.10% 288ms 4.48% boost::detail::shared_count::~shared_count (inline) 0 0% 31.10% 288ms 4.48% boost::shared_ptr::~shared_ptr (inline) 3ms 0.047% 31.14% 287ms 4.47% Element::Element 2ms 0.031% 31.17% 279ms 4.34% Cell::GetMutationState 185ms 2.88% 34.05% 279ms 4.34% _int_malloc 272ms 4.24% 38.29% 274ms 4.27% boost::detail::sp_counted_base::release 1ms 0.016% 38.31% 273ms 4.25% NodeLocationWriter::Visit 65ms 1.01% 39.32% 265ms 4.13% __GI___libc_free 99ms 1.54% 40.86% 257ms 4.00% std::_Rb_tree::_M_clone_node (inline) 14ms 0.22% 41.08% 254ms 3.96% std::less::operator() (inline) 5ms 0.078% 41.16% 249ms 3.88% divconqrecurse 240ms 3.74% 44.89% 240ms 3.74% std::operator< (inline) 13ms 0.2% 45.09% 239ms 3.72% std::__new_allocator::deallocate (inline) 0 0% 45.09% 238ms 3.71% std::allocator_traits::deallocate (inline) 17ms 0.26% 45.36% 238ms 3.71% std::num_put::_M_insert_float 66ms 1.03% 46.39% 234ms 3.64% mergehulls 4ms 0.062% 46.45% 226ms 3.52% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.11% 46.56% 220ms 3.43% Cell::ReadyToDivide 1ms 0.016% 46.57% 217ms 3.38% Element::RegisterWithNodes (inline) 8ms 0.12% 46.70% 213ms 3.32% Node::AddElement 0 0% 46.70% 213ms 3.32% std::_Rb_tree::_M_put_node (inline) 210ms 3.27% 49.97% 210ms 3.27% std::_Rb_tree::_S_right (inline) 1ms 0.016% 49.98% 202ms 3.15% MeshBasedCellPopulation::GetDampingConstant 1ms 0.016% 50.00% 201ms 3.13% AbstractCentreBasedCellPopulation::GetDampingConstant 172ms 2.68% 52.68% 197ms 3.07% _int_free 4ms 0.062% 52.74% 191ms 2.97% std::__cxx11::collate::do_transform 74ms 1.15% 53.89% 186ms 2.90% std::_Rb_tree::_M_get_insert_unique_pos (inline) 183ms 2.85% 56.74% 183ms 2.85% [libchaste_cell_based.so] 0 0% 56.74% 180ms 2.80% ___vsnprintf 0 0% 56.74% 180ms 2.80% __vsnprintf_internal (inline) 13ms 0.2% 56.94% 178ms 2.77% __printf_buffer 1ms 0.016% 56.96% 168ms 2.62% CellProliferativeTypesWriter::VisitCell 6ms 0.093% 57.05% 164ms 2.55% AbstractCellProperty::IsType (inline) 7ms 0.11% 57.16% 164ms 2.55% CellPropertyCollection::HasProperty 0 0% 57.16% 162ms 2.52% Cell::HasCellProperty (inline) 1ms 0.016% 57.18% 161ms 2.51% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.062% 57.24% 156ms 2.43% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.078% 57.32% 156ms 2.43% __printf_fp_l_buffer 0 0% 57.32% 156ms 2.43% __printf_fp_spec (inline) 0 0% 57.32% 150ms 2.34% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 57.32% 148ms 2.30% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 57.32% 148ms 2.30% OutputFileHandler::OpenOutputFile 2ms 0.031% 57.35% 147ms 2.29% MeshBasedCellPopulation::SpringsEnd (inline) 63ms 0.98% 58.33% 143ms 2.23% __printf_fp_buffer_1 9ms 0.14% 58.47% 131ms 2.04% AbstractTetrahedralElement::CalculateJacobian 11ms 0.17% 58.64% 128ms 1.99% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 58.64% 128ms 1.99% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.031% 58.67% 125ms 1.95% alternateaxes 0 0% 58.67% 125ms 1.95% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.67% 125ms 1.95% std::__new_allocator::destroy (inline) 0 0% 58.67% 125ms 1.95% std::allocator_traits::destroy (inline) 2ms 0.031% 58.70% 124ms 1.93% TetrahedralMesh::Clear 111ms 1.73% 60.43% 123ms 1.92% vertexmedian 1ms 0.016% 60.45% 121ms 1.88% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 60.45% 115ms 1.79% std::_Vector_base::_M_allocate (inline) 18ms 0.28% 60.73% 113ms 1.76% AbstractCellProperty::IsSame 112ms 1.74% 62.47% 112ms 1.74% [libchaste_mesh.so] 18ms 0.28% 62.75% 105ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 104ms 1.62% 64.37% 104ms 1.62% incircle 67ms 1.04% 65.42% 99ms 1.54% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 24ms 0.37% 65.79% 99ms 1.54% std::num_put::_M_insert_int 3ms 0.047% 65.84% 98ms 1.53% std::vector::push_back (inline) 8ms 0.12% 65.96% 97ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.96% 97ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.078% 66.04% 95ms 1.48% std::type_info::operator== (inline) 11ms 0.17% 66.21% 93ms 1.45% AbstractTetrahedralElement::RefreshJacobian 3ms 0.047% 66.26% 92ms 1.43% boost::numeric::ublas::c_vector::c_vector (inline) 45ms 0.7% 66.96% 91ms 1.42% std::__ostream_insert 6ms 0.093% 67.05% 91ms 1.42% std::vector::_M_realloc_insert 89ms 1.39% 68.44% 89ms 1.39% std::_Rb_tree_insert_and_rebalance 2ms 0.031% 68.47% 88ms 1.37% boost::numeric::ublas::vector_assign (inline) 5ms 0.078% 68.55% 83ms 1.29% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 68.55% 83ms 1.29% std::basic_ofstream::basic_ofstream (inline) 55ms 0.86% 69.40% 76ms 1.18% malloc_consolidate 1ms 0.016% 69.42% 76ms 1.18% std::basic_filebuf::open 0 0% 69.42% 76ms 1.18% std::basic_ofstream::open (inline) 0 0% 69.42% 74ms 1.15% Node::~Node 31ms 0.48% 69.90% 73ms 1.14% AbstractElement::GetNodeLocation 1ms 0.016% 69.92% 73ms 1.14% std::operator<< (inline) 1ms 0.016% 69.93% 71ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.031% 69.96% 71ms 1.11% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.14% 70.10% 70ms 1.09% TetrahedralMesh::EdgeIterator::GetNodeB 8ms 0.12% 70.23% 69ms 1.07% CellPropertyCollection::AddProperty 0 0% 70.23% 69ms 1.07% OutputFileHandler::CommonConstructor 0 0% 70.23% 69ms 1.07% OutputFileHandler::OutputFileHandler 0 0% 70.23% 68ms 1.06% tcache_get (inline) 68ms 1.06% 71.29% 68ms 1.06% tcache_get_n (inline) 1ms 0.016% 71.30% 67ms 1.04% OutputFileHandler::MakeFoldersAndReturnFullPath 67ms 1.04% 72.35% 67ms 1.04% [libstdc++.so.6.0.33] 4ms 0.062% 72.41% 63ms 0.98% AbstractCellPopulation::GetLocationIndexUsingCell 61ms 0.95% 73.36% 61ms 0.95% counterclockwise 14ms 0.22% 73.58% 60ms 0.93% boost::numeric::ublas::indexing_vector_assign 0 0% 73.58% 59ms 0.92% Cell::GetCellId 30ms 0.47% 74.04% 58ms 0.9% std::basic_filebuf::xsputn 57ms 0.89% 74.93% 57ms 0.89% std::vector::size (inline) 25ms 0.39% 75.32% 55ms 0.86% AbstractElement::GetNodeGlobalIndex 28ms 0.44% 75.76% 55ms 0.86% AbstractTetrahedralMesh::GetElement 54ms 0.84% 76.60% 54ms 0.84% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 47ms 0.73% 77.33% 54ms 0.84% vertexsort 11ms 0.17% 77.50% 53ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.50% 51ms 0.79% CellPropertyCollection::~CellPropertyCollection (inline) 31ms 0.48% 77.98% 51ms 0.79% hack_digit 0 0% 77.98% 50ms 0.78% AbstractCellBasedWriter::CloseFile 0 0% 77.98% 50ms 0.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 77.98% 50ms 0.78% std::basic_filebuf::close 0 0% 77.98% 50ms 0.78% std::basic_ofstream::close (inline) 47ms 0.73% 78.71% 47ms 0.73% __memcpy_avx512_unaligned_erms 30ms 0.47% 79.18% 47ms 0.73% boost::shared_ptr::shared_ptr (inline) 0 0% 79.18% 46ms 0.72% std::__basic_file::open 0 0% 79.18% 45ms 0.7% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 79.18% 45ms 0.7% _IO_new_fopen 0 0% 79.18% 45ms 0.7% __fopen_internal (inline) 44ms 0.69% 79.87% 44ms 0.69% std::_Rb_tree::_S_left (inline) 31ms 0.48% 80.35% 43ms 0.67% CellPropertyCollection::GetProperty 26ms 0.4% 80.75% 43ms 0.67% std::basic_streambuf::xsputn 42ms 0.65% 81.41% 42ms 0.65% Node::GetIndex 0 0% 81.41% 42ms 0.65% _IO_new_file_fopen 0 0% 81.41% 42ms 0.65% __GI__IO_file_open 34ms 0.53% 81.94% 42ms 0.65% std::num_put::do_put 10ms 0.16% 82.09% 41ms 0.64% Determinant (inline) 3ms 0.047% 82.14% 41ms 0.64% Node::ConstructNodeAttributes (inline) 32ms 0.5% 82.64% 41ms 0.64% boost::numeric::ublas::c_matrix::operator() 0 0% 82.64% 41ms 0.64% std::vector::vector (inline) 4ms 0.062% 82.70% 40ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.70% 39ms 0.61% FilesystemPermissions::SetFilePermissions (inline) 39ms 0.61% 83.31% 39ms 0.61% __GI_fchmodat 0 0% 83.31% 39ms 0.61% std::filesystem::permissions 1ms 0.016% 83.32% 38ms 0.59% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.32% 38ms 0.59% Node::ClearAppliedForce 0 0% 83.32% 38ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 35ms 0.55% 83.87% 38ms 0.59% __GI___libc_write 2ms 0.031% 83.90% 38ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.016% 83.91% 38ms 0.59% std::basic_filebuf::overflow 0 0% 83.91% 37ms 0.58% BoundaryNodeWriter::Visit 0 0% 83.91% 37ms 0.58% std::_Vector_base::_Vector_base (inline) 0 0% 83.91% 37ms 0.58% std::__basic_file::xsputn 0 0% 83.91% 37ms 0.58% std::basic_filebuf::_M_convert_to_external 0 0% 83.91% 37ms 0.58% std::basic_filebuf::_M_terminate_output 0 0% 83.91% 35ms 0.55% std::_Vector_base::_M_create_storage (inline) 33ms 0.51% 84.43% 34ms 0.53% __libc_open64 0 0% 84.43% 34ms 0.53% std::map::map (inline) 0 0% 84.43% 33ms 0.51% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 84.43% 33ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 84.43% 33ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 33ms 0.51% 84.94% 33ms 0.51% Node::rGetLocation 0 0% 84.94% 33ms 0.51% std::filesystem::create_directory 1ms 0.016% 84.96% 33ms 0.51% std::filesystem::status