File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4085ms, 85.91% of 4755ms total Dropped 464 nodes (cum <= 23.77ms) flat flat% sum% cum cum% 0 0% 0% 4728ms 99.43% __libc_start_call_main 0 0% 0% 4728ms 99.43% __libc_start_main_impl 0 0% 0% 4728ms 99.43% _start 0 0% 0% 4715ms 99.16% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4715ms 99.16% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4715ms 99.16% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4715ms 99.16% main 0 0% 0% 4679ms 98.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4679ms 98.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4679ms 98.40% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4677ms 98.36% AbstractCellBasedSimulation::Solve 0 0% 0% 2020ms 42.48% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 1795ms 37.75% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 1772ms 37.27% MeshBasedCellPopulation::Update 0 0% 0% 929ms 19.54% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0% 859ms 18.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 819ms 17.22% MutableMesh::ReMesh 20ms 0.42% 0.42% 814ms 17.12% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.42% 763ms 16.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.42% 732ms 15.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 82ms 1.72% 2.15% 673ms 14.15% TetrahedralMesh::EdgeIterator::operator++ 7ms 0.15% 2.29% 571ms 12.01% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.042% 2.33% 553ms 11.63% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.19% 2.52% 534ms 11.23% CellPopulationElementWriter::Visit 274ms 5.76% 8.29% 510ms 10.73% std::_Rb_tree::_M_lower_bound (inline) 26ms 0.55% 8.83% 497ms 10.45% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.34% 9.17% 485ms 10.20% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.25% 9.42% 474ms 9.97% MeshBasedCellPopulation::AcceptCellWriter 104ms 2.19% 11.61% 428ms 9.00% __dynamic_cast 0 0% 11.61% 413ms 8.69% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.063% 11.67% 407ms 8.56% TetrahedralMesh::ImportFromMesher 73ms 1.54% 13.21% 382ms 8.03% std::_Rb_tree::~_Rb_tree (inline) 28ms 0.59% 13.80% 373ms 7.84% operator new 0 0% 13.80% 362ms 7.61% std::set::~set (inline) 147ms 3.09% 16.89% 346ms 7.28% __GI___libc_malloc 37ms 0.78% 17.67% 338ms 7.11% std::ostream::_M_insert 0 0% 17.67% 338ms 7.11% std::ostream::operator<< (inline) 1ms 0.021% 17.69% 336ms 7.07% AbstractCellProperty::IsSubType (inline) 4ms 0.084% 17.77% 334ms 7.02% std::set::insert (inline) 0 0% 17.77% 332ms 6.98% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.084% 17.85% 330ms 6.94% std::_Rb_tree::_M_insert_unique 12ms 0.25% 18.11% 325ms 6.83% std::_Rb_tree::find (inline) 6ms 0.13% 18.23% 316ms 6.65% std::__new_allocator::allocate (inline) 0 0% 18.23% 314ms 6.60% std::allocator_traits::allocate (inline) 1ms 0.021% 18.25% 311ms 6.54% triangulate 24ms 0.5% 18.76% 307ms 6.46% std::_Rb_tree::_M_erase 0 0% 18.76% 304ms 6.39% std::set::count (inline) 5ms 0.11% 18.86% 284ms 5.97% Cell::GetCellProliferativeType 0 0% 18.86% 278ms 5.85% delaunay 4ms 0.084% 18.95% 278ms 5.85% divconqdelaunay 0 0% 18.95% 278ms 5.85% std::_Rb_tree::_M_drop_node (inline) 15ms 0.32% 19.26% 273ms 5.74% boost::detail::shared_count::~shared_count (inline) 0 0% 19.26% 273ms 5.74% boost::shared_ptr::~shared_ptr (inline) 24ms 0.5% 19.77% 263ms 5.53% std::map::operator[] (partial-inline) 261ms 5.49% 25.26% 261ms 5.49% __strcmp_evex 253ms 5.32% 30.58% 254ms 5.34% boost::detail::sp_counted_base::release 0 0% 30.58% 250ms 5.26% std::_Rb_tree::_M_create_node (inline) 0 0% 30.58% 247ms 5.19% std::_Rb_tree::_M_get_node (inline) 15ms 0.32% 30.89% 247ms 5.19% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.021% 30.91% 243ms 5.11% AbstractCellBasedSimulation::DoCellBirth 0 0% 30.91% 240ms 5.05% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 30.91% 239ms 5.03% AbstractCellBasedWriter::OpenOutputFileForAppend 134ms 2.82% 33.73% 238ms 5.01% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 33.73% 237ms 4.98% OutputFileHandler::OpenOutputFile 0 0% 33.73% 237ms 4.98% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.021% 33.75% 232ms 4.88% std::set::set (inline) 1ms 0.021% 33.77% 224ms 4.71% NodeLocationWriter::Visit 46ms 0.97% 34.74% 213ms 4.48% __GI___libc_free 25ms 0.53% 35.27% 213ms 4.48% std::_Rb_tree::_M_copy (inline) 31ms 0.65% 35.92% 211ms 4.44% std::_Rb_tree::_M_insert_ (inline) 0 0% 35.92% 209ms 4.40% std::_Rb_tree::lower_bound (inline) 0 0% 35.92% 209ms 4.40% std::map::lower_bound (inline) 3ms 0.063% 35.98% 204ms 4.29% std::less::operator() (inline) 201ms 4.23% 40.21% 201ms 4.23% std::operator< (inline) 16ms 0.34% 40.55% 194ms 4.08% std::num_put::_M_insert_float 5ms 0.11% 40.65% 189ms 3.97% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.13% 40.78% 189ms 3.97% Element::Element 91ms 1.91% 42.69% 188ms 3.95% std::_Rb_tree::_M_clone_node (inline) 3ms 0.063% 42.75% 169ms 3.55% Cell::GetMutationState 151ms 3.18% 45.93% 166ms 3.49% _int_free 94ms 1.98% 47.91% 161ms 3.39% _int_malloc 6ms 0.13% 48.03% 161ms 3.39% std::__new_allocator::deallocate (inline) 4ms 0.084% 48.12% 159ms 3.34% Cell::ReadyToDivide 10ms 0.21% 48.33% 159ms 3.34% CellPropertyCollection::HasProperty 0 0% 48.33% 159ms 3.34% std::allocator_traits::deallocate (inline) 0 0% 48.33% 156ms 3.28% Cell::HasCellProperty (inline) 2ms 0.042% 48.37% 146ms 3.07% divconqrecurse 2ms 0.042% 48.41% 146ms 3.07% std::__cxx11::collate::do_transform 2ms 0.042% 48.45% 145ms 3.05% AbstractCellProperty::IsType (inline) 0 0% 48.45% 144ms 3.03% std::_Rb_tree::_M_put_node (inline) 1ms 0.021% 48.48% 140ms 2.94% ___vsnprintf 0 0% 48.48% 139ms 2.92% __vsnprintf_internal (inline) 35ms 0.74% 49.21% 139ms 2.92% mergehulls 21ms 0.44% 49.65% 138ms 2.90% __printf_buffer 1ms 0.021% 49.67% 137ms 2.88% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 49.67% 137ms 2.88% MeshBasedCellPopulation::GetDampingConstant 0 0% 49.67% 134ms 2.82% std::_Rb_tree::_M_destroy_node (inline) 0 0% 49.67% 134ms 2.82% std::__new_allocator::destroy (inline) 0 0% 49.67% 134ms 2.82% std::allocator_traits::destroy (inline) 0 0% 49.67% 131ms 2.75% std::basic_ofstream::basic_ofstream (inline) 1ms 0.021% 49.70% 129ms 2.71% std::basic_ofstream::open (inline) 0 0% 49.70% 128ms 2.69% std::basic_filebuf::open 2ms 0.042% 49.74% 117ms 2.46% Element::RegisterWithNodes (inline) 0 0% 49.74% 116ms 2.44% CellProliferativeTypesWriter::VisitCell 41ms 0.86% 50.60% 115ms 2.42% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.084% 50.68% 114ms 2.40% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.063% 50.75% 113ms 2.38% Node::AddElement 2ms 0.042% 50.79% 111ms 2.33% TetrahedralMesh::Clear 17ms 0.36% 51.15% 107ms 2.25% AbstractCellProperty::IsSame 5ms 0.11% 51.25% 105ms 2.21% __printf_fp_l_buffer 0 0% 51.25% 105ms 2.21% __printf_fp_spec (inline) 104ms 2.19% 53.44% 104ms 2.19% std::_Rb_tree::_S_right (inline) 9ms 0.19% 53.63% 102ms 2.15% AbstractTetrahedralElement::CalculateJacobian 0 0% 53.63% 100ms 2.10% OutputFileHandler::CommonConstructor 0 0% 53.63% 100ms 2.10% OutputFileHandler::OutputFileHandler 0 0% 53.63% 100ms 2.10% _IO_new_fopen 0 0% 53.63% 100ms 2.10% __fopen_internal (inline) 1ms 0.021% 53.65% 100ms 2.10% std::__basic_file::open 0 0% 53.65% 99ms 2.08% OutputFileHandler::MakeFoldersAndReturnFullPath 49ms 1.03% 54.68% 97ms 2.04% __printf_fp_buffer_1 1ms 0.021% 54.70% 96ms 2.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 54.70% 94ms 1.98% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.11% 54.81% 94ms 1.98% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 54.81% 94ms 1.98% FilesystemPermissions::SetFilePermissions (inline) 68ms 1.43% 56.24% 94ms 1.98% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.021% 56.26% 94ms 1.98% _IO_new_file_fopen 3ms 0.063% 56.32% 94ms 1.98% std::filesystem::permissions 1ms 0.021% 56.34% 92ms 1.93% __GI__IO_file_open 0 0% 56.34% 91ms 1.91% AbstractCellBasedWriter::CloseFile 91ms 1.91% 58.25% 91ms 1.91% __GI_fchmodat 2ms 0.042% 58.30% 91ms 1.91% std::basic_filebuf::close 0 0% 58.30% 91ms 1.91% std::basic_ofstream::close (inline) 11ms 0.23% 58.53% 90ms 1.89% TetrahedralMesh::EdgesEnd (partial-inline) 7ms 0.15% 58.68% 90ms 1.89% std::type_info::operator== (inline) 2ms 0.042% 58.72% 88ms 1.85% alternateaxes 17ms 0.36% 59.07% 87ms 1.83% std::num_put::_M_insert_int 79ms 1.66% 60.74% 86ms 1.81% vertexmedian 0 0% 60.74% 81ms 1.70% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.27% 61.01% 80ms 1.68% MeshBasedCellPopulation::SpringIterator::SpringIterator 77ms 1.62% 62.63% 77ms 1.62% __libc_open64 3ms 0.063% 62.69% 76ms 1.60% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.042% 62.73% 69ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.021% 62.75% 69ms 1.45% boost::numeric::ublas::vector_assign (inline) 14ms 0.29% 63.05% 67ms 1.41% AbstractTetrahedralElement::RefreshJacobian 0 0% 63.05% 67ms 1.41% std::_Vector_base::_M_allocate (inline) 6ms 0.13% 63.18% 65ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.021% 63.20% 65ms 1.37% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.021% 63.22% 65ms 1.37% boost::numeric::ublas::c_vector::c_vector (inline) 64ms 1.35% 64.56% 64ms 1.35% [libchaste_cell_based.so] 64ms 1.35% 65.91% 64ms 1.35% incircle 0 0% 65.91% 64ms 1.35% std::filesystem::create_directory 0 0% 65.91% 63ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 49ms 1.03% 66.94% 63ms 1.32% malloc_consolidate 0 0% 66.94% 62ms 1.30% std::basic_filebuf::_M_terminate_output 1ms 0.021% 66.96% 61ms 1.28% std::__basic_file::xsputn 0 0% 66.96% 61ms 1.28% std::basic_filebuf::_M_convert_to_external 0 0% 66.96% 61ms 1.28% std::basic_filebuf::overflow 3ms 0.063% 67.02% 61ms 1.28% std::filesystem::status 60ms 1.26% 68.29% 60ms 1.26% __GI___libc_write 58ms 1.22% 69.51% 58ms 1.22% __GI___fstatat64 4ms 0.084% 69.59% 58ms 1.22% std::vector::push_back (inline) 37ms 0.78% 70.37% 54ms 1.14% AbstractElement::GetNodeGlobalIndex 0 0% 70.37% 54ms 1.14% Node::~Node 2ms 0.042% 70.41% 53ms 1.11% std::vector::_M_realloc_insert 18ms 0.38% 70.79% 52ms 1.09% boost::numeric::ublas::indexing_vector_assign 8ms 0.17% 70.96% 51ms 1.07% std::__ostream_insert 39ms 0.82% 71.78% 51ms 1.07% std::basic_streambuf::xsputn 0 0% 71.78% 48ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 48ms 1.01% 72.79% 48ms 1.01% std::vector::size (inline) 4ms 0.084% 72.87% 47ms 0.99% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.063% 72.93% 46ms 0.97% CellPropertyCollection::AddProperty 46ms 0.97% 73.90% 46ms 0.97% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 29ms 0.61% 74.51% 45ms 0.95% AbstractElement::GetNodeLocation 45ms 0.95% 75.46% 45ms 0.95% std::_Rb_tree_insert_and_rebalance 16ms 0.34% 75.79% 44ms 0.93% AbstractTetrahedralMesh::GetElement 29ms 0.61% 76.40% 43ms 0.9% std::basic_filebuf::xsputn 2ms 0.042% 76.45% 42ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.021% 76.47% 42ms 0.88% std::operator<< (inline) 0 0% 76.47% 41ms 0.86% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.47% 40ms 0.84% Cell::GetCellId 36ms 0.76% 77.22% 39ms 0.82% vertexsort 0 0% 77.22% 38ms 0.8% CellPropertyCollection::~CellPropertyCollection (inline) 17ms 0.36% 77.58% 37ms 0.78% Determinant (inline) 0 0% 77.58% 37ms 0.78% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 37ms 0.78% 78.36% 37ms 0.78% counterclockwise 37ms 0.78% 79.14% 37ms 0.78% std::_Rb_tree_increment 1ms 0.021% 79.16% 36ms 0.76% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.53% 79.68% 36ms 0.76% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.042% 79.73% 35ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 35ms 0.74% 80.46% 35ms 0.74% [libchaste_mesh.so] 29ms 0.61% 81.07% 34ms 0.72% CellPropertyCollection::GetProperty 34ms 0.72% 81.79% 34ms 0.72% __memcpy_avx512_unaligned_erms 4ms 0.084% 81.87% 34ms 0.72% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 81.87% 33ms 0.69% CxxTest::RealWorldDescription::setUp 0 0% 81.87% 33ms 0.69% PetscSetup::setUpWorld 0 0% 81.87% 33ms 0.69% PetscSetupUtils::CommonSetup 33ms 0.69% 82.57% 33ms 0.69% [libstdc++.so.6.0.33] 0 0% 82.57% 32ms 0.67% Node::ClearAppliedForce 0 0% 82.57% 32ms 0.67% Node::ConstructNodeAttributes (inline) 0 0% 82.57% 32ms 0.67% PMPI_Init_thread 0 0% 82.57% 32ms 0.67% PetscInitialize 0 0% 82.57% 32ms 0.67% PetscSetupUtils::InitialisePetsc 0 0% 82.57% 32ms 0.67% ompi_mpi_init 0 0% 82.57% 31ms 0.65% _dl_init 0 0% 82.57% 31ms 0.65% call_init (inline) 1ms 0.021% 82.59% 30ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.59% 30ms 0.63% tcache_get (inline) 30ms 0.63% 83.22% 30ms 0.63% tcache_get_n (inline) 0 0% 83.22% 29ms 0.61% std::vector::vector (inline) 1ms 0.021% 83.24% 28ms 0.59% 14ms 0.29% 83.53% 28ms 0.59% TetrahedralMesh::SolveElementMapping 28ms 0.59% 84.12% 28ms 0.59% __GI___mkdir 20ms 0.42% 84.54% 28ms 0.59% boost::shared_ptr::shared_ptr (inline) 0 0% 84.54% 28ms 0.59% std::basic_filebuf::_M_allocate_internal_buffer 19ms 0.4% 84.94% 28ms 0.59% std::num_put::do_put 0 0% 84.94% 27ms 0.57% _IO_new_fclose 14ms 0.29% 85.24% 27ms 0.57% hack_digit 0 0% 85.24% 27ms 0.57% std::__basic_file::close 2ms 0.042% 85.28% 26ms 0.55% _IO_new_file_close_it 0 0% 85.28% 26ms 0.55% _dl_start_user 1ms 0.021% 85.30% 26ms 0.55% std::_Vector_base::_M_create_storage (inline) 0 0% 85.30% 26ms 0.55% std::_Vector_base::_Vector_base (inline) 4ms 0.084% 85.38% 25ms 0.53% Inverse 25ms 0.53% 85.91% 25ms 0.53% __GI___close_nocancel