File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5240ms, 85.18% of 6152ms total Dropped 523 nodes (cum <= 30.76ms) flat flat% sum% cum cum% 0 0% 0% 6122ms 99.51% __libc_start_call_main 0 0% 0% 6122ms 99.51% __libc_start_main_impl 0 0% 0% 6122ms 99.51% _start 0 0% 0% 6108ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6108ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6108ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6108ms 99.28% main 0 0% 0% 6070ms 98.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6070ms 98.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6070ms 98.67% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.016% 0.016% 6068ms 98.63% AbstractCellBasedSimulation::Solve 0 0% 0.016% 2695ms 43.81% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.033% 0.049% 2353ms 38.25% MeshBasedCellPopulation::Update 0 0% 0.049% 2201ms 35.78% AbstractCellPopulation::WriteResultsToFiles 2ms 0.033% 0.081% 1210ms 19.67% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.098% 1162ms 18.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.098% 1099ms 17.86% MutableMesh::ReMesh 0 0% 0.098% 1046ms 17.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.24% 0.34% 1046ms 17.00% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.11% 0.46% 996ms 16.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 88ms 1.43% 1.89% 833ms 13.54% TetrahedralMesh::EdgeIterator::operator++ 359ms 5.84% 7.72% 775ms 12.60% std::_Rb_tree::_M_lower_bound (inline) 194ms 3.15% 10.87% 721ms 11.72% __dynamic_cast 5ms 0.081% 10.96% 711ms 11.56% CellPopulationElementWriter::Visit 2ms 0.033% 10.99% 704ms 11.44% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.016% 11.00% 683ms 11.10% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.065% 11.07% 642ms 10.44% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.31% 11.38% 640ms 10.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.081% 11.46% 577ms 9.38% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.081% 11.54% 573ms 9.31% TetrahedralMesh::ImportFromMesher 20ms 0.33% 11.87% 561ms 9.12% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.049% 11.91% 525ms 8.53% AbstractCellProperty::IsSubType (inline) 0 0% 11.91% 489ms 7.95% std::ostream::operator<< (inline) 59ms 0.96% 12.87% 488ms 7.93% std::ostream::_M_insert 19ms 0.31% 13.18% 454ms 7.38% std::_Rb_tree::find (inline) 44ms 0.72% 13.90% 453ms 7.36% std::map::operator[] (partial-inline) 29ms 0.47% 14.37% 435ms 7.07% operator new 0 0% 14.37% 417ms 6.78% std::set::count (inline) 137ms 2.23% 16.60% 405ms 6.58% __GI___libc_malloc 405ms 6.58% 23.18% 405ms 6.58% __strcmp_evex 0 0% 23.18% 395ms 6.42% triangulate 6ms 0.098% 23.28% 394ms 6.40% std::set::insert (inline) 2ms 0.033% 23.31% 393ms 6.39% Cell::GetCellProliferativeType 5ms 0.081% 23.39% 388ms 6.31% std::_Rb_tree::_M_insert_unique 24ms 0.39% 23.78% 388ms 6.31% std::__new_allocator::allocate (inline) 186ms 3.02% 26.80% 384ms 6.24% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.80% 383ms 6.23% std::allocator_traits::allocate (inline) 4ms 0.065% 26.87% 363ms 5.90% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.87% 363ms 5.90% std::_Rb_tree::lower_bound (inline) 0 0% 26.87% 363ms 5.90% std::map::lower_bound (inline) 0 0% 26.87% 352ms 5.72% delaunay 3ms 0.049% 26.92% 352ms 5.72% divconqdelaunay 31ms 0.5% 27.42% 336ms 5.46% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.049% 27.47% 334ms 5.43% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.47% 319ms 5.19% std::_Rb_tree::_M_create_node (inline) 0 0% 27.47% 312ms 5.07% std::set::~set (inline) 66ms 1.07% 28.54% 304ms 4.94% std::_Rb_tree::_M_erase 0 0% 28.54% 296ms 4.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.54% 295ms 4.80% std::_Rb_tree::_M_get_node (inline) 1ms 0.016% 28.56% 287ms 4.67% NodeLocationWriter::Visit 8ms 0.13% 28.69% 286ms 4.65% std::less::operator() (inline) 278ms 4.52% 33.21% 278ms 4.52% std::operator< (inline) 15ms 0.24% 33.45% 263ms 4.28% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.33% 33.78% 262ms 4.26% std::num_put::_M_insert_float 252ms 4.10% 37.87% 252ms 4.10% std::_Rb_tree::_S_right (inline) 10ms 0.16% 38.04% 250ms 4.06% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 38.04% 248ms 4.03% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.04% 248ms 4.03% Cell::GetMutationState 0 0% 38.04% 246ms 4.00% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.081% 38.12% 246ms 4.00% std::set::set (inline) 0 0% 38.12% 243ms 3.95% OutputFileHandler::OpenOutputFile 62ms 1.01% 39.13% 241ms 3.92% __GI___libc_free 2ms 0.033% 39.16% 234ms 3.80% Element::Element 3ms 0.049% 39.21% 227ms 3.69% Cell::ReadyToDivide 11ms 0.18% 39.39% 224ms 3.64% std::_Rb_tree::_M_insert_ (inline) 19ms 0.31% 39.69% 222ms 3.61% std::_Rb_tree::_M_copy (inline) 5ms 0.081% 39.78% 221ms 3.59% std::__cxx11::collate::do_transform 0 0% 39.78% 220ms 3.58% std::_Rb_tree::_M_drop_node (inline) 10ms 0.16% 39.94% 214ms 3.48% divconqrecurse 136ms 2.21% 42.15% 211ms 3.43% _int_malloc 2ms 0.033% 42.18% 209ms 3.40% MeshBasedCellPopulation::GetDampingConstant 3ms 0.049% 42.23% 208ms 3.38% std::__new_allocator::deallocate (inline) 4ms 0.065% 42.30% 206ms 3.35% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.016% 42.31% 206ms 3.35% ___vsnprintf 0 0% 42.31% 205ms 3.33% __vsnprintf_internal (inline) 0 0% 42.31% 204ms 3.32% std::allocator_traits::deallocate (inline) 33ms 0.54% 42.85% 203ms 3.30% __printf_buffer 55ms 0.89% 43.74% 200ms 3.25% std::_Rb_tree::_M_clone_node (inline) 5ms 0.081% 43.82% 196ms 3.19% MeshBasedCellPopulation::SpringsEnd (inline) 53ms 0.86% 44.68% 193ms 3.14% mergehulls 0 0% 44.68% 180ms 2.93% std::_Rb_tree::_M_put_node (inline) 145ms 2.36% 47.04% 178ms 2.89% _int_free 2ms 0.033% 47.07% 177ms 2.88% CellProliferativeTypesWriter::VisitCell 8ms 0.13% 47.20% 176ms 2.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.033% 47.24% 174ms 2.83% AbstractCellProperty::IsType (inline) 3ms 0.049% 47.29% 166ms 2.70% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.13% 47.42% 160ms 2.60% __printf_fp_l_buffer 0 0% 47.42% 160ms 2.60% __printf_fp_spec (inline) 33ms 0.54% 47.95% 159ms 2.58% TetrahedralMesh::EdgesEnd (partial-inline) 45ms 0.73% 48.68% 159ms 2.58% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.081% 48.76% 156ms 2.54% CellPropertyCollection::HasProperty 0 0% 48.76% 155ms 2.52% Cell::HasCellProperty (inline) 11ms 0.18% 48.94% 153ms 2.49% TetrahedralMesh::Clear 5ms 0.081% 49.02% 148ms 2.41% Element::RegisterWithNodes (inline) 17ms 0.28% 49.30% 147ms 2.39% MeshBasedCellPopulation::SpringIterator::SpringIterator 87ms 1.41% 50.72% 144ms 2.34% __printf_fp_buffer_1 13ms 0.21% 50.93% 142ms 2.31% AbstractTetrahedralElement::CalculateJacobian 7ms 0.11% 51.04% 140ms 2.28% Node::AddElement 24ms 0.39% 51.43% 127ms 2.06% AbstractCellProperty::IsSame 29ms 0.47% 51.90% 122ms 1.98% std::num_put::_M_insert_int 1ms 0.016% 51.92% 118ms 1.92% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.92% 112ms 1.82% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.92% 111ms 1.80% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.081% 52.00% 111ms 1.80% AbstractTetrahedralElement::CalculateInverseJacobian 65ms 1.06% 53.06% 110ms 1.79% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 53.06% 109ms 1.77% AbstractCellBasedWriter::CloseFile 0 0% 53.06% 109ms 1.77% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.016% 53.07% 109ms 1.77% std::basic_ofstream::close (inline) 0 0% 53.07% 108ms 1.76% std::basic_filebuf::close 1ms 0.016% 53.09% 108ms 1.76% std::basic_filebuf::open 0 0% 53.09% 108ms 1.76% std::basic_ofstream::open (inline) 3ms 0.049% 53.14% 104ms 1.69% boost::numeric::ublas::vector_assign (inline) 27ms 0.44% 53.58% 103ms 1.67% std::type_info::operator== (inline) 0 0% 53.58% 102ms 1.66% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.016% 53.59% 102ms 1.66% std::filesystem::permissions 101ms 1.64% 55.23% 101ms 1.64% __GI_fchmodat 13ms 0.21% 55.45% 100ms 1.63% AbstractTetrahedralElement::RefreshJacobian 0 0% 55.45% 100ms 1.63% OutputFileHandler::CommonConstructor 0 0% 55.45% 100ms 1.63% OutputFileHandler::OutputFileHandler 40ms 0.65% 56.10% 97ms 1.58% std::__ostream_insert 0 0% 56.10% 95ms 1.54% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.016% 56.11% 93ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 8ms 0.13% 56.24% 92ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.016% 56.26% 92ms 1.50% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.065% 56.32% 91ms 1.48% Node::~Node 91ms 1.48% 57.80% 91ms 1.48% incircle 7ms 0.11% 57.92% 91ms 1.48% std::vector::push_back (inline) 10ms 0.16% 58.08% 89ms 1.45% boost::detail::shared_count::~shared_count (inline) 0 0% 58.08% 89ms 1.45% boost::shared_ptr::~shared_ptr (inline) 0 0% 58.08% 88ms 1.43% std::_Vector_base::_M_allocate (inline) 37ms 0.6% 58.68% 85ms 1.38% boost::shared_ptr::shared_ptr (inline) 2ms 0.033% 58.71% 85ms 1.38% std::__basic_file::open 0 0% 58.71% 84ms 1.37% _IO_new_fopen 0 0% 58.71% 84ms 1.37% __fopen_internal (inline) 5ms 0.081% 58.79% 82ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.016% 58.81% 82ms 1.33% _IO_new_file_fopen 2ms 0.033% 58.84% 82ms 1.33% alternateaxes 12ms 0.2% 59.04% 81ms 1.32% std::vector::_M_realloc_insert 80ms 1.30% 60.34% 80ms 1.30% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 72ms 1.17% 61.51% 80ms 1.30% vertexmedian 0 0% 61.51% 79ms 1.28% __GI__IO_file_open 1ms 0.016% 61.52% 78ms 1.27% std::basic_filebuf::_M_terminate_output 2ms 0.033% 61.56% 77ms 1.25% std::basic_filebuf::_M_convert_to_external 0 0% 61.56% 77ms 1.25% std::basic_filebuf::overflow 74ms 1.20% 62.76% 75ms 1.22% __GI___libc_write 0 0% 62.76% 75ms 1.22% std::__basic_file::xsputn 0 0% 62.76% 74ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 68ms 1.11% 63.87% 73ms 1.19% boost::detail::sp_counted_base::release 72ms 1.17% 65.04% 72ms 1.17% __libc_open64 0 0% 65.04% 72ms 1.17% std::operator<< (inline) 70ms 1.14% 66.17% 70ms 1.14% std::_Rb_tree_insert_and_rebalance 4ms 0.065% 66.24% 69ms 1.12% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.42% 66.66% 69ms 1.12% AbstractElement::GetNodeLocation 69ms 1.12% 67.78% 69ms 1.12% [libchaste_cell_based.so] 1ms 0.016% 67.80% 66ms 1.07% Cell::GetCellId 37ms 0.6% 68.40% 65ms 1.06% std::basic_filebuf::xsputn 10ms 0.16% 68.56% 62ms 1.01% TetrahedralMesh::EdgeIterator::GetNodeB 15ms 0.24% 68.81% 62ms 1.01% boost::numeric::ublas::indexing_vector_assign 46ms 0.75% 69.55% 60ms 0.98% std::num_put::do_put 41ms 0.67% 70.22% 57ms 0.93% AbstractTetrahedralMesh::GetNumAllElements 35ms 0.57% 70.79% 57ms 0.93% malloc_consolidate 57ms 0.93% 71.72% 57ms 0.93% std::vector::size (inline) 42ms 0.68% 72.40% 55ms 0.89% AbstractElement::GetNodeGlobalIndex 0 0% 72.40% 55ms 0.89% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.40% 55ms 0.89% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.40% 54ms 0.88% Node::ClearAppliedForce 0 0% 72.40% 54ms 0.88% Node::ConstructNodeAttributes (inline) 2ms 0.033% 72.43% 52ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeA 46ms 0.75% 73.18% 52ms 0.85% vertexsort 51ms 0.83% 74.01% 51ms 0.83% Node::GetIndex 4ms 0.065% 74.07% 50ms 0.81% CellPropertyCollection::AddProperty 0 0% 74.07% 50ms 0.81% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 50ms 0.81% 74.89% 50ms 0.81% std::_Rb_tree_increment 1ms 0.016% 74.90% 50ms 0.81% std::filesystem::create_directory 49ms 0.8% 75.70% 49ms 0.8% __memcpy_avx512_unaligned_erms 49ms 0.8% 76.50% 49ms 0.8% counterclockwise 48ms 0.78% 77.28% 48ms 0.78% boost::detail::shared_count::shared_count (inline) 4ms 0.065% 77.34% 48ms 0.78% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.016% 77.36% 48ms 0.78% std::filesystem::status 0 0% 77.36% 48ms 0.78% tcache_get (inline) 48ms 0.78% 78.14% 48ms 0.78% tcache_get_n (inline) 46ms 0.75% 78.88% 46ms 0.75% __GI___fstatat64 4ms 0.065% 78.95% 46ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.95% 45ms 0.73% NodeAttributes::NodeAttributes 31ms 0.5% 79.45% 45ms 0.73% std::basic_streambuf::xsputn 44ms 0.72% 80.17% 44ms 0.72% [libchaste_mesh.so] 23ms 0.37% 80.54% 44ms 0.72% boost::numeric::ublas::c_matrix::operator() (partial-inline) 23ms 0.37% 80.92% 42ms 0.68% AbstractTetrahedralMesh::GetElement 0 0% 80.92% 41ms 0.67% BoundaryNodeWriter::Visit 0 0% 80.92% 40ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 80.92% 40ms 0.65% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.92% 40ms 0.65% std::__new_allocator::destroy (inline) 0 0% 80.92% 40ms 0.65% std::allocator_traits::destroy (inline) 16ms 0.26% 81.18% 38ms 0.62% Determinant (inline) 0 0% 81.18% 37ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.18% 37ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 37ms 0.6% 81.78% 37ms 0.6% boost::numeric::ublas::c_vector::operator() (partial-inline) 26ms 0.42% 82.20% 37ms 0.6% hack_digit 0 0% 82.20% 36ms 0.59% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.20% 35ms 0.57% CxxTest::RealWorldDescription::setUp 0 0% 82.20% 35ms 0.57% PMPI_Init_thread 0 0% 82.20% 35ms 0.57% PetscInitialize 0 0% 82.20% 35ms 0.57% PetscSetup::setUpWorld 0 0% 82.20% 35ms 0.57% PetscSetupUtils::CommonSetup 0 0% 82.20% 35ms 0.57% PetscSetupUtils::InitialisePetsc 35ms 0.57% 82.77% 35ms 0.57% boost::numeric::ublas::same_impl_ex 35ms 0.57% 83.34% 35ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 83.34% 35ms 0.57% ompi_mpi_init 35ms 0.57% 83.91% 35ms 0.57% unlink_chunk 0 0% 83.91% 34ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.91% 34ms 0.55% std::map::find (inline) 0 0% 83.91% 33ms 0.54% _dl_init 0 0% 83.91% 33ms 0.54% boost::numeric::ublas::norm_2 (inline) 11ms 0.18% 84.09% 33ms 0.54% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.09% 33ms 0.54% call_init (inline) 4ms 0.065% 84.15% 33ms 0.54% std::__copy_move::__copy_m (inline) 0 0% 84.15% 33ms 0.54% std::__copy_move_a (inline) 0 0% 84.15% 33ms 0.54% std::__copy_move_a1 (inline) 0 0% 84.15% 33ms 0.54% std::__copy_move_a2 (inline) 0 0% 84.15% 33ms 0.54% std::copy (inline) 0 0% 84.15% 32ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 32ms 0.52% 84.67% 32ms 0.52% Node::IsDeleted 0 0% 84.67% 32ms 0.52% std::vector::vector (inline) 31ms 0.5% 85.18% 31ms 0.5% [libstdc++.so.6.0.33]