File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5165ms, 83.90% of 6156ms total Dropped 514 nodes (cum <= 30.78ms) flat flat% sum% cum cum% 0 0% 0% 6124ms 99.48% __libc_start_call_main 0 0% 0% 6124ms 99.48% __libc_start_main_impl 0 0% 0% 6124ms 99.48% _start 0 0% 0% 6111ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6111ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6111ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6111ms 99.27% main 0 0% 0% 6066ms 98.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6066ms 98.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6066ms 98.54% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6064ms 98.51% AbstractCellBasedSimulation::Solve 0 0% 0% 2545ms 41.34% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2262ms 36.74% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 2259ms 36.70% MeshBasedCellPopulation::Update 0 0% 0% 1247ms 20.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 1125ms 18.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.016% 0.016% 1124ms 18.26% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.032% 1101ms 17.88% MutableMesh::ReMesh 3ms 0.049% 0.081% 1081ms 17.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.26% 0.34% 987ms 16.03% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.032% 0.37% 783ms 12.72% AbstractTwoBodyInteractionForce::AddForceContribution 336ms 5.46% 5.83% 748ms 12.15% std::_Rb_tree::_M_lower_bound (inline) 84ms 1.36% 7.20% 746ms 12.12% TetrahedralMesh::EdgeIterator::operator++ 47ms 0.76% 7.96% 720ms 11.70% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.097% 8.06% 707ms 11.48% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 230ms 3.74% 11.79% 705ms 11.45% __dynamic_cast 7ms 0.11% 11.91% 690ms 11.21% CellPopulationElementWriter::Visit 10ms 0.16% 12.07% 630ms 10.23% CellPropertyCollection::GetPropertiesType (inline) 29ms 0.47% 12.54% 580ms 9.42% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.097% 12.64% 578ms 9.39% MeshBasedCellPopulation::AcceptCellWriter 13ms 0.21% 12.85% 553ms 8.98% TetrahedralMesh::ImportFromMesher 2ms 0.032% 12.88% 515ms 8.37% AbstractCellProperty::IsSubType (inline) 35ms 0.57% 13.45% 478ms 7.76% std::map::operator[] (partial-inline) 0 0% 13.45% 477ms 7.75% std::ostream::operator<< (inline) 72ms 1.17% 14.62% 475ms 7.72% std::ostream::_M_insert 2ms 0.032% 14.65% 424ms 6.89% triangulate 25ms 0.41% 15.06% 417ms 6.77% operator new 0 0% 15.06% 400ms 6.50% std::_Rb_tree::lower_bound (inline) 0 0% 15.06% 400ms 6.50% std::map::lower_bound (inline) 136ms 2.21% 17.27% 392ms 6.37% __GI___libc_malloc 16ms 0.26% 17.53% 386ms 6.27% std::_Rb_tree::find (inline) 1ms 0.016% 17.54% 381ms 6.19% std::set::insert (inline) 8ms 0.13% 17.67% 380ms 6.17% std::_Rb_tree::_M_insert_unique 5ms 0.081% 17.76% 377ms 6.12% Cell::GetCellProliferativeType 31ms 0.5% 18.26% 371ms 6.03% std::__new_allocator::allocate (inline) 0 0% 18.26% 367ms 5.96% std::allocator_traits::allocate (inline) 0 0% 18.26% 366ms 5.95% delaunay 1ms 0.016% 18.27% 366ms 5.95% divconqdelaunay 359ms 5.83% 24.11% 359ms 5.83% __strcmp_evex 0 0% 24.11% 353ms 5.73% std::set::count (inline) 1ms 0.016% 24.12% 346ms 5.62% LegacyCellProliferativeTypesWriter::VisitCell 174ms 2.83% 26.95% 313ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.032% 26.98% 310ms 5.04% NodeLocationWriter::Visit 28ms 0.45% 27.44% 308ms 5.00% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.44% 306ms 4.97% std::_Rb_tree::_M_create_node (inline) 0 0% 27.44% 292ms 4.74% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.44% 290ms 4.71% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 33ms 0.54% 27.97% 289ms 4.69% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.97% 288ms 4.68% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 27.97% 288ms 4.68% OutputFileHandler::OpenOutputFile 0 0% 27.97% 284ms 4.61% std::set::~set (inline) 0 0% 27.97% 282ms 4.58% std::_Rb_tree::_M_get_node (inline) 3ms 0.049% 28.02% 280ms 4.55% AbstractCellBasedSimulation::DoCellBirth 55ms 0.89% 28.91% 277ms 4.50% std::_Rb_tree::_M_erase 25ms 0.41% 29.32% 276ms 4.48% std::num_put::_M_insert_float 6ms 0.097% 29.42% 271ms 4.40% std::less::operator() (inline) 265ms 4.30% 33.72% 265ms 4.30% std::operator< (inline) 5ms 0.081% 33.80% 262ms 4.26% Cell::GetMutationState 2ms 0.032% 33.84% 261ms 4.24% std::set::set (inline) 246ms 4.00% 37.83% 246ms 4.00% std::_Rb_tree::_S_right (inline) 7ms 0.11% 37.95% 244ms 3.96% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.049% 38.00% 236ms 3.83% Element::Element 16ms 0.26% 38.26% 232ms 3.77% std::_Rb_tree::_M_insert_ (inline) 65ms 1.06% 39.31% 229ms 3.72% __GI___libc_free 26ms 0.42% 39.73% 225ms 3.65% std::_Rb_tree::_M_copy (inline) 8ms 0.13% 39.86% 220ms 3.57% std::__cxx11::collate::do_transform 1ms 0.016% 39.88% 218ms 3.54% MeshBasedCellPopulation::GetDampingConstant 1ms 0.016% 39.90% 217ms 3.53% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.13% 40.03% 213ms 3.46% std::__new_allocator::deallocate (inline) 0 0% 40.03% 212ms 3.44% std::_Rb_tree::_M_drop_node (inline) 7ms 0.11% 40.14% 209ms 3.40% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 40.14% 208ms 3.38% std::allocator_traits::deallocate (inline) 126ms 2.05% 42.19% 206ms 3.35% _int_malloc 3ms 0.049% 42.24% 204ms 3.31% ___vsnprintf 1ms 0.016% 42.25% 201ms 3.27% __vsnprintf_internal (inline) 23ms 0.37% 42.63% 200ms 3.25% __printf_buffer 10ms 0.16% 42.79% 199ms 3.23% divconqrecurse 50ms 0.81% 43.60% 196ms 3.18% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.60% 195ms 3.17% CellProliferativeTypesWriter::VisitCell 46ms 0.75% 44.35% 185ms 3.01% mergehulls 2ms 0.032% 44.38% 177ms 2.88% Cell::ReadyToDivide 10ms 0.16% 44.54% 175ms 2.84% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 44.54% 173ms 2.81% std::_Rb_tree::_M_put_node (inline) 135ms 2.19% 46.73% 163ms 2.65% _int_free 2ms 0.032% 46.77% 161ms 2.62% AbstractCellProperty::IsType (inline) 5ms 0.081% 46.85% 161ms 2.62% __printf_fp_l_buffer 0 0% 46.85% 161ms 2.62% __printf_fp_spec (inline) 3ms 0.049% 46.90% 155ms 2.52% boost::numeric::ublas::vector_assign (inline) 1ms 0.016% 46.91% 154ms 2.50% CellPropertyCollection::HasProperty 5ms 0.081% 46.99% 154ms 2.50% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 46.99% 153ms 2.49% Cell::HasCellProperty (inline) 4ms 0.065% 47.06% 152ms 2.47% Element::RegisterWithNodes (inline) 73ms 1.19% 48.25% 150ms 2.44% __printf_fp_buffer_1 6ms 0.097% 48.34% 145ms 2.36% Node::AddElement 4ms 0.065% 48.41% 142ms 2.31% TetrahedralMesh::Clear 51ms 0.83% 49.24% 141ms 2.29% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 49.24% 133ms 2.16% std::basic_ofstream::basic_ofstream (inline) 16ms 0.26% 49.50% 132ms 2.14% AbstractTetrahedralElement::CalculateJacobian 0 0% 49.50% 132ms 2.14% FilesystemPermissions::SetFilePermissions (inline) 132ms 2.14% 51.64% 132ms 2.14% __GI_fchmodat 0 0% 51.64% 132ms 2.14% std::filesystem::permissions 0 0% 51.64% 131ms 2.13% std::basic_filebuf::open 0 0% 51.64% 131ms 2.13% std::basic_ofstream::open (inline) 104ms 1.69% 53.33% 128ms 2.08% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.049% 53.38% 125ms 2.03% AbstractPhaseBasedCellCycleModel::ReadyToDivide 124ms 2.01% 55.39% 124ms 2.01% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.016% 55.41% 121ms 1.97% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 46ms 0.75% 56.16% 121ms 1.97% std::__ostream_insert 31ms 0.5% 56.66% 118ms 1.92% AbstractCellProperty::IsSame 0 0% 56.66% 113ms 1.84% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.24% 56.90% 110ms 1.79% TetrahedralMesh::EdgesEnd (partial-inline) 19ms 0.31% 57.21% 109ms 1.77% boost::numeric::ublas::indexing_vector_assign 0 0% 57.21% 107ms 1.74% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 57.21% 106ms 1.72% AbstractCellBasedWriter::CloseFile 3ms 0.049% 57.26% 106ms 1.72% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 57.26% 106ms 1.72% std::basic_filebuf::close 0 0% 57.26% 106ms 1.72% std::basic_ofstream::close (inline) 0 0% 57.26% 101ms 1.64% _IO_new_fopen 0 0% 57.26% 101ms 1.64% __fopen_internal (inline) 1ms 0.016% 57.28% 101ms 1.64% alternateaxes 0 0% 57.28% 101ms 1.64% std::__basic_file::open 1ms 0.016% 57.29% 100ms 1.62% _IO_new_file_fopen 1ms 0.016% 57.31% 100ms 1.62% std::operator<< (inline) 90ms 1.46% 58.77% 100ms 1.62% vertexmedian 5ms 0.081% 58.85% 98ms 1.59% Node::~Node 98ms 1.59% 60.45% 98ms 1.59% incircle 1ms 0.016% 60.46% 97ms 1.58% OutputFileHandler::CommonConstructor 0 0% 60.46% 97ms 1.58% OutputFileHandler::OutputFileHandler 1ms 0.016% 60.48% 96ms 1.56% __GI__IO_file_open 0 0% 60.48% 93ms 1.51% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.049% 60.53% 90ms 1.46% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.53% 87ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.28% 60.80% 87ms 1.41% AbstractTetrahedralElement::RefreshJacobian 16ms 0.26% 61.06% 87ms 1.41% std::type_info::operator== (inline) 12ms 0.19% 61.26% 86ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 30ms 0.49% 61.74% 86ms 1.40% std::num_put::_M_insert_int 84ms 1.36% 63.11% 84ms 1.36% std::_Rb_tree_insert_and_rebalance 0 0% 63.11% 84ms 1.36% std::_Vector_base::_M_allocate (inline) 82ms 1.33% 64.44% 83ms 1.35% __libc_open64 7ms 0.11% 64.55% 83ms 1.35% boost::detail::shared_count::~shared_count (inline) 0 0% 64.55% 83ms 1.35% boost::shared_ptr::~shared_ptr (inline) 4ms 0.065% 64.62% 82ms 1.33% std::vector::push_back (inline) 80ms 1.30% 65.92% 80ms 1.30% [libchaste_cell_based.so] 1ms 0.016% 65.94% 79ms 1.28% std::basic_filebuf::_M_terminate_output 1ms 0.016% 65.95% 77ms 1.25% std::basic_filebuf::overflow 76ms 1.23% 67.19% 76ms 1.23% __GI___libc_write 0 0% 67.19% 76ms 1.23% std::__basic_file::xsputn 0 0% 67.19% 76ms 1.23% std::basic_filebuf::_M_convert_to_external 6ms 0.097% 67.28% 72ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 67.28% 72ms 1.17% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 67.28% 72ms 1.17% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.097% 67.38% 71ms 1.15% std::vector::_M_realloc_insert 68ms 1.10% 68.49% 70ms 1.14% boost::detail::sp_counted_base::release 42ms 0.68% 69.17% 67ms 1.09% malloc_consolidate 37ms 0.6% 69.77% 67ms 1.09% std::basic_filebuf::xsputn 65ms 1.06% 70.83% 65ms 1.06% boost::numeric::ublas::c_vector::operator() 37ms 0.6% 71.43% 65ms 1.06% boost::shared_ptr::shared_ptr (inline) 7ms 0.11% 71.54% 64ms 1.04% std::_Rb_tree_const_iterator::operator++ (inline) 64ms 1.04% 72.58% 64ms 1.04% std::_Rb_tree_increment 1ms 0.016% 72.60% 62ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 23ms 0.37% 72.97% 60ms 0.97% AbstractElement::GetNodeLocation 56ms 0.91% 73.88% 59ms 0.96% vertexsort 2ms 0.032% 73.91% 57ms 0.93% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.91% 57ms 0.93% Cell::GetCellId 4ms 0.065% 73.98% 57ms 0.93% boost::numeric::ublas::vector_reference::operator() (inline) 48ms 0.78% 74.76% 56ms 0.91% AbstractElement::GetNodeGlobalIndex 2ms 0.032% 74.79% 53ms 0.86% Node::ClearAppliedForce 2ms 0.032% 74.82% 52ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeB 52ms 0.84% 75.67% 52ms 0.84% __memcpy_avx512_unaligned_erms 1ms 0.016% 75.68% 51ms 0.83% Node::ConstructNodeAttributes (inline) 0 0% 75.68% 49ms 0.8% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.016% 75.70% 49ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.016% 75.71% 49ms 0.8% std::filesystem::create_directory 1ms 0.016% 75.73% 49ms 0.8% std::filesystem::status 48ms 0.78% 76.51% 48ms 0.78% __GI___fstatat64 0 0% 76.51% 47ms 0.76% boost::numeric::ublas::norm_2 (inline) 9ms 0.15% 76.66% 47ms 0.76% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.66% 46ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.66% 46ms 0.75% boost::numeric::ublas::vector_binary_scalar1::operator() (inline) 0 0% 76.66% 45ms 0.73% boost::numeric::ublas::vector_binary_scalar2::operator() (inline) 28ms 0.45% 77.11% 45ms 0.73% std::basic_streambuf::xsputn 0 0% 77.11% 45ms 0.73% tcache_get (inline) 45ms 0.73% 77.84% 45ms 0.73% tcache_get_n (inline) 0 0% 77.84% 44ms 0.71% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 3ms 0.049% 77.89% 43ms 0.7% NodeAttributes::NodeAttributes 26ms 0.42% 78.31% 43ms 0.7% boost::numeric::ublas::c_matrix::operator() (partial-inline) 25ms 0.41% 78.72% 43ms 0.7% hack_digit 2ms 0.032% 78.75% 43ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 42ms 0.68% 79.43% 42ms 0.68% Node::GetIndex 42ms 0.68% 80.12% 42ms 0.68% counterclockwise 0 0% 80.12% 41ms 0.67% CxxTest::RealWorldDescription::setUp 11ms 0.18% 80.30% 41ms 0.67% Determinant (inline) 0 0% 80.30% 41ms 0.67% PetscInitialize 0 0% 80.30% 41ms 0.67% PetscSetup::setUpWorld 0 0% 80.30% 41ms 0.67% PetscSetupUtils::CommonSetup 0 0% 80.30% 41ms 0.67% PetscSetupUtils::InitialisePetsc 17ms 0.28% 80.57% 40ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 80.57% 40ms 0.65% PMPI_Init_thread 0 0% 80.57% 40ms 0.65% ompi_mpi_init 5ms 0.081% 80.65% 40ms 0.65% std::_Vector_base::_M_deallocate (inline) 1ms 0.016% 80.67% 39ms 0.63% 0 0% 80.67% 39ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.67% 39ms 0.63% std::__new_allocator::destroy (inline) 0 0% 80.67% 39ms 0.63% std::allocator_traits::destroy (inline) 0 0% 80.67% 38ms 0.62% _dl_init 38ms 0.62% 81.29% 38ms 0.62% boost::numeric::ublas::same_impl_ex 0 0% 81.29% 38ms 0.62% call_init (inline) 5ms 0.081% 81.37% 37ms 0.6% std::__copy_move::__copy_m (inline) 0 0% 81.37% 37ms 0.6% std::__copy_move_a (inline) 0 0% 81.37% 37ms 0.6% std::__copy_move_a1 (inline) 0 0% 81.37% 37ms 0.6% std::__copy_move_a2 (inline) 0 0% 81.37% 37ms 0.6% std::copy (inline) 37ms 0.6% 81.97% 37ms 0.6% unlink_chunk 0 0% 81.97% 36ms 0.58% CellPropertyCollection::~CellPropertyCollection (inline) 27ms 0.44% 82.41% 36ms 0.58% std::num_put::do_put 8ms 0.13% 82.54% 34ms 0.55% CellPropertyCollection::AddProperty 34ms 0.55% 83.09% 34ms 0.55% [libstdc++.so.6.0.33] 0 0% 83.09% 33ms 0.54% std::map::map (inline) 17ms 0.28% 83.37% 32ms 0.52% AbstractCellCycleModel::GetAge 1ms 0.016% 83.38% 32ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.016% 83.40% 32ms 0.52% BoundaryNodeWriter::Visit 0 0% 83.40% 31ms 0.5% _dl_start_user 31ms 0.5% 83.90% 31ms 0.5% std::codecvt::do_always_noconv 0 0% 83.90% 31ms 0.5% std::vector::vector (inline)