File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6797ms, 85.19% of 7979ms total Dropped 604 nodes (cum <= 39.90ms) flat flat% sum% cum cum% 0 0% 0% 7940ms 99.51% __libc_start_call_main 0 0% 0% 7940ms 99.51% __libc_start_main_impl 0 0% 0% 7940ms 99.51% _start 0 0% 0% 7924ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7924ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7924ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7924ms 99.31% main 0 0% 0% 7881ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7881ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7881ms 98.77% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7877ms 98.72% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3478ms 43.59% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.038% 3008ms 37.70% MeshBasedCellPopulation::Update 0 0% 0.038% 2860ms 35.84% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.05% 1531ms 19.19% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.05% 1482ms 18.57% MutableMesh::ReMesh 1ms 0.013% 0.063% 1476ms 18.50% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.063% 1383ms 17.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.16% 1315ms 16.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 26ms 0.33% 0.49% 1281ms 16.05% MeshBasedCellPopulation::SpringIterator::operator++ 124ms 1.55% 2.04% 1037ms 13.00% TetrahedralMesh::EdgeIterator::operator++ 411ms 5.15% 7.19% 934ms 11.71% std::_Rb_tree::_M_lower_bound (inline) 275ms 3.45% 10.64% 926ms 11.61% __dynamic_cast 3ms 0.038% 10.68% 925ms 11.59% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.025% 10.70% 913ms 11.44% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.063% 10.77% 875ms 10.97% CellPropertyCollection::GetPropertiesType (inline) 12ms 0.15% 10.92% 871ms 10.92% CellPopulationElementWriter::Visit 30ms 0.38% 11.29% 834ms 10.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.15% 11.44% 761ms 9.54% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.48% 753ms 9.44% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.44% 11.92% 743ms 9.31% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.025% 11.94% 702ms 8.80% AbstractCellProperty::IsSubType (inline) 29ms 0.36% 12.31% 593ms 7.43% operator new 50ms 0.63% 12.93% 585ms 7.33% std::map::operator[] (partial-inline) 2ms 0.025% 12.96% 557ms 6.98% triangulate 188ms 2.36% 15.32% 554ms 6.94% __GI___libc_malloc 0 0% 15.32% 553ms 6.93% std::ostream::operator<< (inline) 89ms 1.12% 16.43% 551ms 6.91% std::ostream::_M_insert 6ms 0.075% 16.51% 538ms 6.74% std::set::insert (inline) 5ms 0.063% 16.57% 532ms 6.67% std::_Rb_tree::_M_insert_unique 29ms 0.36% 16.93% 531ms 6.65% std::__new_allocator::allocate (inline) 6ms 0.075% 17.01% 529ms 6.63% Cell::GetCellProliferativeType 0 0% 17.01% 525ms 6.58% std::allocator_traits::allocate (inline) 524ms 6.57% 23.57% 524ms 6.57% __strcmp_avx2 29ms 0.36% 23.94% 510ms 6.39% std::_Rb_tree::find (inline) 0 0% 23.94% 487ms 6.10% delaunay 223ms 2.79% 26.73% 485ms 6.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.73% 484ms 6.07% std::_Rb_tree::lower_bound (inline) 0 0% 26.73% 484ms 6.07% std::map::lower_bound (inline) 3ms 0.038% 26.77% 483ms 6.05% divconqdelaunay 3ms 0.038% 26.81% 471ms 5.90% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.81% 466ms 5.84% std::set::count (inline) 3ms 0.038% 26.85% 462ms 5.79% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.85% 427ms 5.35% std::_Rb_tree::_M_create_node (inline) 39ms 0.49% 27.33% 418ms 5.24% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.33% 407ms 5.10% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.33% 395ms 4.95% std::_Rb_tree::_M_get_node (inline) 0 0% 27.33% 395ms 4.95% std::set::~set (inline) 86ms 1.08% 28.41% 371ms 4.65% std::_Rb_tree::_M_erase 2ms 0.025% 28.44% 367ms 4.60% NodeLocationWriter::Visit 20ms 0.25% 28.69% 360ms 4.51% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.14% 28.83% 357ms 4.47% std::less::operator() (inline) 346ms 4.34% 33.16% 346ms 4.34% std::operator< (inline) 2ms 0.025% 33.19% 342ms 4.29% Cell::GetMutationState 17ms 0.21% 33.40% 337ms 4.22% std::_Rb_tree::_M_insert_ (inline) 8ms 0.1% 33.50% 331ms 4.15% std::set::set (inline) 0 0% 33.50% 329ms 4.12% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.50% 327ms 4.10% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.50% 326ms 4.09% OutputFileHandler::OpenOutputFile 4ms 0.05% 33.55% 322ms 4.04% Element::Element 3ms 0.038% 33.59% 316ms 3.96% Cell::ReadyToDivide 308ms 3.86% 37.45% 308ms 3.86% std::_Rb_tree::_S_right (inline) 24ms 0.3% 37.75% 302ms 3.78% std::num_put::_M_insert_float 7ms 0.088% 37.84% 301ms 3.77% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 37.85% 298ms 3.73% MeshBasedCellPopulation::GetDampingConstant 6ms 0.075% 37.92% 297ms 3.72% AbstractCentreBasedCellPopulation::GetDampingConstant 35ms 0.44% 38.36% 296ms 3.71% std::_Rb_tree::_M_copy (inline) 95ms 1.19% 39.55% 295ms 3.70% __GI___libc_free 8ms 0.1% 39.65% 287ms 3.60% divconqrecurse 192ms 2.41% 42.06% 273ms 3.42% _int_malloc 72ms 0.9% 42.96% 268ms 3.36% mergehulls 0 0% 42.96% 267ms 3.35% std::_Rb_tree::_M_drop_node (inline) 64ms 0.8% 43.76% 250ms 3.13% std::_Rb_tree::_M_clone_node (inline) 4ms 0.05% 43.82% 249ms 3.12% std::__cxx11::collate::do_transform 12ms 0.15% 43.97% 246ms 3.08% std::__new_allocator::deallocate (inline) 2ms 0.025% 43.99% 245ms 3.07% CellProliferativeTypesWriter::VisitCell 0 0% 43.99% 242ms 3.03% std::allocator_traits::deallocate (inline) 5ms 0.063% 44.05% 237ms 2.97% AbstractCellProperty::IsType (inline) 0 0% 44.05% 237ms 2.97% ___vsnprintf 0 0% 44.05% 237ms 2.97% __vsnprintf_internal (inline) 31ms 0.39% 44.44% 231ms 2.90% __printf_buffer 3ms 0.038% 44.48% 229ms 2.87% CellPropertyCollection::HasProperty 0 0% 44.48% 228ms 2.86% Cell::HasCellProperty (inline) 10ms 0.13% 44.60% 214ms 2.68% TetrahedralMesh::Clear 5ms 0.063% 44.67% 212ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 44.67% 210ms 2.63% std::_Rb_tree::_M_put_node (inline) 4ms 0.05% 44.72% 206ms 2.58% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 167ms 2.09% 46.81% 199ms 2.49% _int_free 3ms 0.038% 46.85% 197ms 2.47% Element::RegisterWithNodes (inline) 6ms 0.075% 46.92% 191ms 2.39% Node::AddElement 65ms 0.81% 47.74% 190ms 2.38% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.063% 47.80% 188ms 2.36% __printf_fp_l_buffer 0 0% 47.80% 188ms 2.36% __printf_fp_spec (inline) 11ms 0.14% 47.94% 186ms 2.33% MeshBasedCellPopulation::SpringsEnd (inline) 93ms 1.17% 49.10% 177ms 2.22% __printf_fp_buffer_1 14ms 0.18% 49.28% 173ms 2.17% AbstractTetrahedralElement::CalculateJacobian 51ms 0.64% 49.92% 172ms 2.16% AbstractCellProperty::IsSame 30ms 0.38% 50.29% 172ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 50.31% 171ms 2.14% OutputFileHandler::OutputFileHandler 0 0% 50.31% 170ms 2.13% OutputFileHandler::CommonConstructor 0 0% 50.31% 167ms 2.09% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 50.31% 163ms 2.04% std::basic_ofstream::basic_ofstream (inline) 2ms 0.025% 50.33% 160ms 2.01% std::basic_filebuf::open 0 0% 50.33% 160ms 2.01% std::basic_ofstream::open (inline) 91ms 1.14% 51.47% 144ms 1.80% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 50ms 0.63% 52.10% 142ms 1.78% std::__ostream_insert 0 0% 52.10% 137ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 0 0% 52.10% 135ms 1.69% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 52.12% 135ms 1.69% std::filesystem::permissions 1ms 0.013% 52.14% 133ms 1.67% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.14% 132ms 1.65% AbstractCellBasedWriter::CloseFile 132ms 1.65% 53.79% 132ms 1.65% __GI_fchmodat 2ms 0.025% 53.82% 132ms 1.65% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 53.83% 132ms 1.65% std::basic_ofstream::close (inline) 1ms 0.013% 53.84% 131ms 1.64% _IO_new_fopen 0 0% 53.84% 131ms 1.64% std::__basic_file::open 0 0% 53.84% 131ms 1.64% std::basic_filebuf::close 0 0% 53.84% 130ms 1.63% __fopen_internal (inline) 0 0% 53.84% 129ms 1.62% _IO_new_file_fopen 17ms 0.21% 54.05% 129ms 1.62% boost::detail::shared_count::~shared_count (inline) 0 0% 54.05% 129ms 1.62% boost::shared_ptr::~shared_ptr (inline) 7ms 0.088% 54.14% 128ms 1.60% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.11% 54.25% 127ms 1.59% Node::~Node 1ms 0.013% 54.27% 126ms 1.58% __GI__IO_file_open 1ms 0.013% 54.28% 126ms 1.58% boost::numeric::ublas::vector_assign (inline) 124ms 1.55% 55.83% 124ms 1.55% incircle 3ms 0.038% 55.87% 123ms 1.54% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.063% 55.93% 122ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 15ms 0.19% 56.12% 121ms 1.52% std::type_info::operator== (inline) 1ms 0.013% 56.13% 120ms 1.50% alternateaxes 2ms 0.025% 56.16% 120ms 1.50% std::vector::push_back (inline) 23ms 0.29% 56.45% 119ms 1.49% AbstractTetrahedralElement::RefreshJacobian 1ms 0.013% 56.46% 119ms 1.49% std::operator<< (inline) 106ms 1.33% 57.79% 119ms 1.49% vertexmedian 19ms 0.24% 58.03% 117ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 58.03% 115ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.14% 58.17% 114ms 1.43% std::vector::_M_realloc_insert 108ms 1.35% 59.52% 109ms 1.37% __libc_open64 109ms 1.37% 60.88% 109ms 1.37% std::_Rb_tree_insert_and_rebalance 14ms 0.18% 61.06% 108ms 1.35% MeshBasedCellPopulation::SpringIterator::SpringIterator 30ms 0.38% 61.44% 107ms 1.34% std::num_put::_M_insert_int 104ms 1.30% 62.74% 104ms 1.30% [libchaste_cell_based.so] 97ms 1.22% 63.96% 103ms 1.29% boost::detail::sp_counted_base::release 41ms 0.51% 64.47% 102ms 1.28% boost::shared_ptr::shared_ptr (inline) 0 0% 64.47% 92ms 1.15% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 64.47% 92ms 1.15% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 64.47% 92ms 1.15% std::filesystem::status 90ms 1.13% 65.60% 90ms 1.13% __GI___fstatat64 1ms 0.013% 65.61% 88ms 1.10% std::basic_filebuf::_M_convert_to_external 0 0% 65.61% 88ms 1.10% std::basic_filebuf::_M_terminate_output 0 0% 65.61% 88ms 1.10% std::basic_filebuf::overflow 1ms 0.013% 65.62% 87ms 1.09% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 7ms 0.088% 65.71% 87ms 1.09% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 65.72% 87ms 1.09% std::__basic_file::xsputn 56ms 0.7% 66.42% 87ms 1.09% std::basic_filebuf::xsputn 37ms 0.46% 66.89% 86ms 1.08% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 66.91% 86ms 1.08% std::filesystem::create_directory 85ms 1.07% 67.98% 85ms 1.07% __GI___libc_write 1ms 0.013% 67.99% 84ms 1.05% tcache_get (inline) 2ms 0.025% 68.02% 83ms 1.04% Cell::GetCellId 83ms 1.04% 69.06% 83ms 1.04% std::_Rb_tree_increment 83ms 1.04% 70.10% 83ms 1.04% tcache_get_n (inline) 63ms 0.79% 70.89% 82ms 1.03% AbstractElement::GetNodeGlobalIndex 82ms 1.03% 71.91% 82ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 27ms 0.34% 72.25% 81ms 1.02% AbstractElement::GetNodeLocation 2ms 0.025% 72.28% 79ms 0.99% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 72.28% 78ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 72.29% 78ms 0.98% TetrahedralMesh::EdgeIterator::GetNodeB 75ms 0.94% 73.23% 75ms 0.94% __memcpy_avx_unaligned_erms 75ms 0.94% 74.17% 75ms 0.94% counterclockwise 75ms 0.94% 75.11% 75ms 0.94% std::vector::size (inline) 3ms 0.038% 75.15% 72ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 75.15% 70ms 0.88% boost::numeric::ublas::norm_2 (inline) 19ms 0.24% 75.39% 70ms 0.88% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 75.39% 69ms 0.86% AbstractCellPopulation::GetLocationIndexUsingCell 69ms 0.86% 76.25% 69ms 0.86% Node::GetIndex 39ms 0.49% 76.74% 69ms 0.86% malloc_consolidate 64ms 0.8% 77.54% 68ms 0.85% vertexsort 5ms 0.063% 77.60% 62ms 0.78% CellPropertyCollection::AddProperty 39ms 0.49% 78.09% 62ms 0.78% boost::numeric::ublas::c_matrix::operator() (partial-inline) 60ms 0.75% 78.84% 61ms 0.76% boost::detail::shared_count::shared_count (inline) 0 0% 78.84% 57ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.84% 57ms 0.71% std::__new_allocator::destroy (inline) 0 0% 78.84% 57ms 0.71% std::allocator_traits::destroy (inline) 32ms 0.4% 79.25% 57ms 0.71% std::basic_streambuf::xsputn 26ms 0.33% 79.57% 56ms 0.7% AbstractTetrahedralMesh::GetElement 3ms 0.038% 79.61% 56ms 0.7% Node::ConstructNodeAttributes (inline) 55ms 0.69% 80.30% 55ms 0.69% [libchaste_mesh.so] 17ms 0.21% 80.51% 54ms 0.68% Determinant (inline) 0 0% 80.51% 54ms 0.68% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 54ms 0.68% 81.19% 54ms 0.68% [libstdc++.so.6.0.33] 0 0% 81.19% 53ms 0.66% Node::ClearAppliedForce 35ms 0.44% 81.63% 52ms 0.65% hack_digit 39ms 0.49% 82.12% 52ms 0.65% std::num_put::do_put 0 0% 82.12% 51ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 3ms 0.038% 82.15% 51ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.15% 50ms 0.63% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 50ms 0.63% 82.78% 50ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 82.78% 49ms 0.61% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.78% 48ms 0.6% BoundaryNodeWriter::Visit 48ms 0.6% 83.38% 48ms 0.6% Node::rGetLocation 0 0% 83.38% 47ms 0.59% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 46ms 0.58% 83.96% 46ms 0.58% __GI___mkdir 46ms 0.58% 84.53% 46ms 0.58% boost::numeric::ublas::c_vector::operator() 0 0% 84.53% 46ms 0.58% std::vector::vector (inline) 0 0% 84.53% 44ms 0.55% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 84.55% 43ms 0.54% std::_Vector_base::_M_create_storage (inline) 6ms 0.075% 84.62% 42ms 0.53% Inverse 0 0% 84.62% 42ms 0.53% _dl_init 0 0% 84.62% 42ms 0.53% call_init (inline) 42ms 0.53% 85.15% 42ms 0.53% unlink_chunk 2ms 0.025% 85.17% 41ms 0.51% _IO_new_fclose 1ms 0.013% 85.19% 41ms 0.51% std::__basic_file::close 0 0% 85.19% 40ms 0.5% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.19% 40ms 0.5% FileFinder::GetAbsolutePath[abi:cxx11] 0 0% 85.19% 40ms 0.5% FileFinder::IsDir 0 0% 85.19% 40ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)