File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 3951ms, 85.45% of 4624ms total Dropped 481 nodes (cum <= 23.12ms) flat flat% sum% cum cum% 0 0% 0% 4592ms 99.31% __libc_start_call_main 0 0% 0% 4592ms 99.31% __libc_start_main_impl 0 0% 0% 4592ms 99.31% _start 0 0% 0% 4573ms 98.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4573ms 98.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4573ms 98.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4573ms 98.90% main 0 0% 0% 4534ms 98.05% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4534ms 98.05% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4534ms 98.05% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4531ms 97.99% AbstractCellBasedSimulation::Solve 0 0% 0% 1943ms 42.02% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 1754ms 37.93% AbstractCellPopulation::WriteResultsToFiles 3ms 0.065% 0.065% 1693ms 36.61% MeshBasedCellPopulation::Update 2ms 0.043% 0.11% 899ms 19.44% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.11% 829ms 17.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.26% 0.37% 781ms 16.89% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.37% 766ms 16.57% MutableMesh::ReMesh 1ms 0.022% 0.39% 726ms 15.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.022% 0.41% 697ms 15.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 74ms 1.60% 2.01% 636ms 13.75% TetrahedralMesh::EdgeIterator::operator++ 8ms 0.17% 2.18% 551ms 11.92% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.17% 2.36% 550ms 11.89% CellPopulationElementWriter::Visit 2ms 0.043% 2.40% 522ms 11.29% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.35% 2.75% 487ms 10.53% AbstractCellPopulation::GetCellUsingLocationIndex 248ms 5.36% 8.11% 481ms 10.40% std::_Rb_tree::_M_lower_bound (inline) 25ms 0.54% 8.65% 468ms 10.12% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 10ms 0.22% 8.87% 441ms 9.54% MeshBasedCellPopulation::AcceptCellWriter 83ms 1.79% 10.66% 431ms 9.32% __dynamic_cast 2ms 0.043% 10.71% 410ms 8.87% CellPropertyCollection::GetPropertiesType (inline) 84ms 1.82% 12.52% 398ms 8.61% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.15% 12.67% 386ms 8.35% TetrahedralMesh::ImportFromMesher 0 0% 12.67% 375ms 8.11% std::set::~set (inline) 2ms 0.043% 12.72% 334ms 7.22% AbstractCellProperty::IsSubType (inline) 2ms 0.043% 12.76% 332ms 7.18% std::set::insert (inline) 8ms 0.17% 12.93% 330ms 7.14% std::_Rb_tree::_M_insert_unique 27ms 0.58% 13.52% 321ms 6.94% operator new 29ms 0.63% 14.14% 310ms 6.70% std::_Rb_tree::_M_erase 11ms 0.24% 14.38% 303ms 6.55% std::_Rb_tree::find (inline) 1ms 0.022% 14.40% 302ms 6.53% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.022% 14.42% 302ms 6.53% triangulate 127ms 2.75% 17.17% 298ms 6.44% __GI___libc_malloc 0 0% 17.17% 290ms 6.27% std::set::count (inline) 2ms 0.043% 17.21% 286ms 6.19% std::ostream::operator<< (inline) 36ms 0.78% 17.99% 284ms 6.14% std::ostream::_M_insert 7ms 0.15% 18.14% 278ms 6.01% std::__new_allocator::allocate (inline) 1ms 0.022% 18.17% 277ms 5.99% Cell::GetCellProliferativeType 149ms 3.22% 21.39% 275ms 5.95% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 21.39% 275ms 5.95% std::allocator_traits::allocate (inline) 0 0% 21.39% 271ms 5.86% std::_Rb_tree::_M_drop_node (inline) 7ms 0.15% 21.54% 263ms 5.69% boost::detail::shared_count::~shared_count (inline) 0 0% 21.54% 263ms 5.69% boost::shared_ptr::~shared_ptr (inline) 1ms 0.022% 21.56% 261ms 5.64% delaunay 260ms 5.62% 27.18% 260ms 5.62% __strcmp_evex 1ms 0.022% 27.21% 260ms 5.62% divconqdelaunay 250ms 5.41% 32.61% 251ms 5.43% boost::detail::sp_counted_base::release 0 0% 32.61% 247ms 5.34% AbstractCellBasedSimulation::DoCellBirth 17ms 0.37% 32.98% 247ms 5.34% std::_Rb_tree::_Rb_tree (partial-inline) 27ms 0.58% 33.56% 247ms 5.34% std::map::operator[] (partial-inline) 0 0% 33.56% 243ms 5.26% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.56% 242ms 5.23% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.56% 239ms 5.17% OutputFileHandler::OpenOutputFile 0 0% 33.56% 229ms 4.95% std::set::set (inline) 0 0% 33.56% 219ms 4.74% std::_Rb_tree::_M_create_node (inline) 0 0% 33.56% 213ms 4.61% std::_Rb_tree::_M_get_node (inline) 29ms 0.63% 34.19% 209ms 4.52% std::_Rb_tree::_M_copy (inline) 0 0% 34.19% 208ms 4.50% std::_Rb_tree::_Alloc_node::operator() (inline) 35ms 0.76% 34.95% 201ms 4.35% __GI___libc_free 0 0% 34.95% 196ms 4.24% std::_Rb_tree::lower_bound (inline) 4ms 0.087% 35.03% 196ms 4.24% std::less::operator() (inline) 0 0% 35.03% 196ms 4.24% std::map::lower_bound (inline) 35ms 0.76% 35.79% 194ms 4.20% std::_Rb_tree::_M_insert_ (inline) 0 0% 35.79% 193ms 4.17% NodeLocationWriter::Visit 192ms 4.15% 39.94% 192ms 4.15% std::operator< (inline) 9ms 0.19% 40.14% 188ms 4.07% AbstractCellPopulation::IsCellAttachedToLocationIndex 83ms 1.79% 41.93% 179ms 3.87% std::_Rb_tree::_M_clone_node (inline) 3ms 0.065% 42.00% 176ms 3.81% Element::Element 2ms 0.043% 42.04% 169ms 3.65% Cell::GetMutationState 157ms 3.40% 45.44% 166ms 3.59% _int_free 1ms 0.022% 45.46% 166ms 3.59% std::__new_allocator::deallocate (inline) 0 0% 45.46% 166ms 3.59% std::allocator_traits::deallocate (inline) 16ms 0.35% 45.80% 161ms 3.48% std::num_put::_M_insert_float 1ms 0.022% 45.83% 151ms 3.27% Cell::ReadyToDivide 0 0% 45.83% 150ms 3.24% std::_Rb_tree::_M_put_node (inline) 89ms 1.92% 47.75% 138ms 2.98% _int_malloc 0 0% 47.75% 136ms 2.94% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.065% 47.82% 136ms 2.94% CellPropertyCollection::HasProperty 0 0% 47.82% 136ms 2.94% MeshBasedCellPopulation::GetDampingConstant 0 0% 47.82% 135ms 2.92% Cell::HasCellProperty (inline) 2ms 0.043% 47.86% 134ms 2.90% divconqrecurse 2ms 0.043% 47.90% 132ms 2.85% std::__cxx11::collate::do_transform 4ms 0.087% 47.99% 128ms 2.77% AbstractCellProperty::IsType (inline) 39ms 0.84% 48.83% 128ms 2.77% mergehulls 52ms 1.12% 49.96% 128ms 2.77% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.022% 49.98% 127ms 2.75% ___vsnprintf 0 0% 49.98% 126ms 2.72% __vsnprintf_internal (inline) 18ms 0.39% 50.37% 125ms 2.70% __printf_buffer 0 0% 50.37% 121ms 2.62% std::_Rb_tree::_M_destroy_node (inline) 0 0% 50.37% 121ms 2.62% std::__new_allocator::destroy (inline) 0 0% 50.37% 121ms 2.62% std::allocator_traits::destroy (inline) 4ms 0.087% 50.45% 119ms 2.57% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.022% 50.48% 116ms 2.51% Element::RegisterWithNodes (inline) 4ms 0.087% 50.56% 115ms 2.49% Node::AddElement 112ms 2.42% 52.98% 112ms 2.42% std::_Rb_tree::_S_right (inline) 0 0% 52.98% 109ms 2.36% CellProliferativeTypesWriter::VisitCell 0 0% 52.98% 109ms 2.36% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.022% 53.01% 109ms 2.36% std::filesystem::permissions 108ms 2.34% 55.34% 108ms 2.34% __GI_fchmodat 0 0% 55.34% 107ms 2.31% std::basic_ofstream::basic_ofstream (inline) 2ms 0.043% 55.38% 104ms 2.25% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.043% 55.43% 104ms 2.25% std::basic_filebuf::open 0 0% 55.43% 104ms 2.25% std::basic_ofstream::open (inline) 0 0% 55.43% 103ms 2.23% TetrahedralMesh::Clear 1ms 0.022% 55.45% 101ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.13% 55.58% 97ms 2.10% __printf_fp_l_buffer 0 0% 55.58% 97ms 2.10% __printf_fp_spec (inline) 14ms 0.3% 55.88% 95ms 2.05% AbstractCellProperty::IsSame 0 0% 55.88% 94ms 2.03% AbstractCellBasedWriter::CloseFile 0 0% 55.88% 94ms 2.03% AbstractCellPopulation::CloseRoundRobinWritersFiles 4ms 0.087% 55.97% 94ms 2.03% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.022% 55.99% 94ms 2.03% std::basic_ofstream::close (inline) 0 0% 55.99% 93ms 2.01% std::basic_filebuf::close 40ms 0.87% 56.86% 90ms 1.95% __printf_fp_buffer_1 0 0% 56.86% 87ms 1.88% OutputFileHandler::CommonConstructor 0 0% 56.86% 87ms 1.88% OutputFileHandler::OutputFileHandler 56ms 1.21% 58.07% 87ms 1.88% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 9ms 0.19% 58.26% 86ms 1.86% AbstractTetrahedralElement::CalculateJacobian 0 0% 58.26% 86ms 1.86% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.022% 58.28% 86ms 1.86% _IO_new_fopen 0 0% 58.28% 86ms 1.86% std::__basic_file::open 0 0% 58.28% 85ms 1.84% __fopen_internal (inline) 0 0% 58.28% 83ms 1.79% _IO_new_file_fopen 0 0% 58.28% 83ms 1.79% __GI__IO_file_open 10ms 0.22% 58.50% 81ms 1.75% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.15% 58.65% 81ms 1.75% std::type_info::operator== (inline) 1ms 0.022% 58.67% 80ms 1.73% alternateaxes 67ms 1.45% 60.12% 78ms 1.69% vertexmedian 74ms 1.60% 61.72% 74ms 1.60% __libc_open64 15ms 0.32% 62.05% 69ms 1.49% std::__ostream_insert 16ms 0.35% 62.39% 69ms 1.49% std::num_put::_M_insert_int 3ms 0.065% 62.46% 68ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 62.46% 68ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 62.46% 67ms 1.45% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.043% 62.50% 65ms 1.41% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.043% 62.54% 65ms 1.41% std::operator<< (inline) 4ms 0.087% 62.63% 63ms 1.36% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.022% 62.65% 63ms 1.36% boost::numeric::ublas::vector_assign (inline) 0 0% 62.65% 62ms 1.34% std::_Vector_base::_M_allocate (inline) 1ms 0.022% 62.67% 62ms 1.34% std::basic_filebuf::_M_terminate_output 1ms 0.022% 62.69% 62ms 1.34% std::basic_filebuf::overflow 2ms 0.043% 62.74% 61ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.022% 62.76% 61ms 1.32% std::__basic_file::xsputn 0 0% 62.76% 61ms 1.32% std::basic_filebuf::_M_convert_to_external 10ms 0.22% 62.98% 60ms 1.30% AbstractTetrahedralElement::RefreshJacobian 60ms 1.30% 64.27% 60ms 1.30% __GI___libc_write 60ms 1.30% 65.57% 60ms 1.30% incircle 0 0% 65.57% 58ms 1.25% Node::~Node 58ms 1.25% 66.83% 58ms 1.25% std::vector::size (inline) 1ms 0.022% 66.85% 56ms 1.21% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 55ms 1.19% 68.04% 55ms 1.19% [libchaste_cell_based.so] 0 0% 68.04% 55ms 1.19% std::filesystem::create_directory 41ms 0.89% 68.92% 54ms 1.17% AbstractElement::GetNodeGlobalIndex 54ms 1.17% 70.09% 54ms 1.17% std::_Rb_tree_insert_and_rebalance 1ms 0.022% 70.11% 53ms 1.15% std::vector::push_back (inline) 52ms 1.12% 71.24% 52ms 1.12% __GI___fstatat64 0 0% 71.24% 52ms 1.12% std::filesystem::status 5ms 0.11% 71.35% 52ms 1.12% std::vector::_M_realloc_insert 51ms 1.10% 72.45% 51ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.022% 72.47% 50ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 12ms 0.26% 72.73% 49ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.043% 72.77% 49ms 1.06% CellPropertyCollection::AddProperty 4ms 0.087% 72.86% 46ms 0.99% TetrahedralMesh::EdgeIterator::GetNodeA 11ms 0.24% 73.10% 44ms 0.95% AbstractTetrahedralMesh::GetElement 24ms 0.52% 73.62% 44ms 0.95% std::basic_filebuf::xsputn 16ms 0.35% 73.96% 42ms 0.91% boost::numeric::ublas::indexing_vector_assign 1ms 0.022% 73.98% 41ms 0.89% Cell::GetCellId 38ms 0.82% 74.81% 41ms 0.89% vertexsort 0 0% 74.81% 40ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 31ms 0.67% 75.48% 40ms 0.87% malloc_consolidate 35ms 0.76% 76.23% 40ms 0.87% std::basic_streambuf::xsputn 32ms 0.69% 76.92% 39ms 0.84% AbstractElement::GetNodeLocation 3ms 0.065% 76.99% 39ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 76.99% 37ms 0.8% _dl_init 1ms 0.022% 77.01% 37ms 0.8% call_init (inline) 0 0% 77.01% 36ms 0.78% CxxTest::RealWorldDescription::setUp 0 0% 77.01% 36ms 0.78% PMPI_Init_thread 0 0% 77.01% 36ms 0.78% PetscInitialize 0 0% 77.01% 36ms 0.78% PetscSetup::setUpWorld 0 0% 77.01% 36ms 0.78% PetscSetupUtils::CommonSetup 0 0% 77.01% 36ms 0.78% PetscSetupUtils::InitialisePetsc 0 0% 77.01% 36ms 0.78% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 77.01% 36ms 0.78% ompi_mpi_init 35ms 0.76% 77.77% 35ms 0.76% [libstdc++.so.6.0.33] 34ms 0.74% 78.50% 34ms 0.74% [libchaste_mesh.so] 1ms 0.022% 78.53% 33ms 0.71% Node::ClearAppliedForce 1ms 0.022% 78.55% 33ms 0.71% Node::ConstructNodeAttributes (inline) 15ms 0.32% 78.87% 33ms 0.71% TetrahedralMesh::SolveElementMapping 21ms 0.45% 79.33% 33ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.33% 32ms 0.69% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.022% 79.35% 31ms 0.67% 18ms 0.39% 79.74% 31ms 0.67% AbstractTetrahedralMesh::GetNumAllElements 29ms 0.63% 80.36% 31ms 0.67% CellPropertyCollection::GetProperty 1ms 0.022% 80.38% 30ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 30ms 0.65% 81.03% 30ms 0.65% __memcpy_avx512_unaligned_erms 0 0% 81.03% 30ms 0.65% _dl_start_user 6ms 0.13% 81.16% 30ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 18ms 0.39% 81.55% 29ms 0.63% hack_digit 29ms 0.63% 82.18% 29ms 0.63% std::_Rb_tree_increment 0 0% 82.18% 29ms 0.63% std::_Vector_base::_Vector_base (inline) 0 0% 82.18% 29ms 0.63% std::vector::vector (inline) 0 0% 82.18% 28ms 0.61% _IO_new_fclose 0 0% 82.18% 28ms 0.61% _IO_new_file_close_it 0 0% 82.18% 28ms 0.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.18% 28ms 0.61% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 28ms 0.61% 82.79% 28ms 0.61% counterclockwise 0 0% 82.79% 28ms 0.61% std::_Vector_base::_M_create_storage (inline) 1ms 0.022% 82.81% 28ms 0.61% std::__basic_file::close 19ms 0.41% 83.22% 28ms 0.61% std::num_put::do_put 0 0% 83.22% 27ms 0.58% tcache_get (inline) 27ms 0.58% 83.80% 27ms 0.58% tcache_get_n (inline) 2ms 0.043% 83.85% 26ms 0.56% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 83.85% 26ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 8ms 0.17% 84.02% 26ms 0.56% Determinant (inline) 26ms 0.56% 84.58% 26ms 0.56% __GI___close_nocancel 0 0% 84.58% 25ms 0.54% BoundaryNodeWriter::Visit 25ms 0.54% 85.12% 25ms 0.54% __GI___mkdir 12ms 0.26% 85.38% 24ms 0.52% boost::shared_ptr::shared_ptr (inline) 3ms 0.065% 85.45% 24ms 0.52% std::_Rb_tree::_M_emplace_hint_unique 0 0% 85.45% 24ms 0.52% std::map::map (inline) 0 0% 85.45% 24ms 0.52% std::map::~map (inline)