File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6725ms, 84.32% of 7976ms total Dropped 598 nodes (cum <= 39.88ms) flat flat% sum% cum cum% 0 0% 0% 7938ms 99.52% __libc_start_call_main 0 0% 0% 7938ms 99.52% __libc_start_main_impl 0 0% 0% 7938ms 99.52% _start 0 0% 0% 7921ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7921ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7921ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7921ms 99.31% main 0 0% 0% 7881ms 98.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7881ms 98.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7881ms 98.81% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7877ms 98.76% AbstractCellBasedSimulation::Solve 0 0% 0% 3321ms 41.64% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2972ms 37.26% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.013% 2838ms 35.58% MeshBasedCellPopulation::Update 3ms 0.038% 0.05% 1573ms 19.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.05% 1423ms 17.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.05% 1403ms 17.59% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.038% 0.088% 1378ms 17.28% MutableMesh::ReMesh 2ms 0.025% 0.11% 1373ms 17.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.31% 1231ms 15.43% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.038% 0.35% 1020ms 12.79% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 105ms 1.32% 1.67% 1008ms 12.64% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.05% 1.72% 970ms 12.16% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.15% 1.87% 961ms 12.05% CellPropertyCollection::GetPropertiesType (inline) 422ms 5.29% 7.16% 942ms 11.81% std::_Rb_tree::_M_lower_bound (inline) 266ms 3.34% 10.49% 906ms 11.36% __dynamic_cast 12ms 0.15% 10.64% 896ms 11.23% CellPopulationElementWriter::Visit 47ms 0.59% 11.23% 873ms 10.95% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 4ms 0.05% 11.28% 860ms 10.78% MeshBasedCellPopulation::AcceptCellWriter 38ms 0.48% 11.76% 815ms 10.22% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.1% 11.86% 741ms 9.29% TetrahedralMesh::ImportFromMesher 6ms 0.075% 11.94% 732ms 9.18% AbstractCellProperty::IsSubType (inline) 52ms 0.65% 12.59% 635ms 7.96% operator new 2ms 0.025% 12.61% 632ms 7.92% std::ostream::operator<< (inline) 81ms 1.02% 13.63% 629ms 7.89% std::ostream::_M_insert 2ms 0.025% 13.65% 597ms 7.48% Cell::GetCellProliferativeType 52ms 0.65% 14.31% 587ms 7.36% std::map::operator[] (partial-inline) 7ms 0.088% 14.39% 575ms 7.21% std::set::insert (inline) 172ms 2.16% 16.55% 572ms 7.17% __GI___libc_malloc 11ms 0.14% 16.69% 569ms 7.13% std::_Rb_tree::_M_insert_unique 28ms 0.35% 17.04% 567ms 7.11% std::__new_allocator::allocate (inline) 0 0% 17.04% 564ms 7.07% std::allocator_traits::allocate (inline) 10ms 0.13% 17.16% 534ms 6.70% LegacyCellProliferativeTypesWriter::VisitCell 519ms 6.51% 23.67% 519ms 6.51% __strcmp_avx2 26ms 0.33% 24.00% 514ms 6.44% std::_Rb_tree::find (inline) 0 0% 24.00% 483ms 6.06% std::_Rb_tree::lower_bound (inline) 0 0% 24.00% 483ms 6.06% std::map::lower_bound (inline) 0 0% 24.00% 479ms 6.01% std::_Rb_tree::_M_create_node (inline) 0 0% 24.00% 478ms 5.99% std::set::count (inline) 2ms 0.025% 24.02% 478ms 5.99% triangulate 3ms 0.038% 24.06% 474ms 5.94% AbstractCellBasedSimulation::DoCellBirth 216ms 2.71% 26.77% 473ms 5.93% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.77% 452ms 5.67% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.77% 438ms 5.49% std::_Rb_tree::_M_get_node (inline) 50ms 0.63% 27.39% 436ms 5.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.39% 420ms 5.27% delaunay 2ms 0.025% 27.42% 420ms 5.27% divconqdelaunay 0 0% 27.42% 408ms 5.12% std::set::~set (inline) 33ms 0.41% 27.83% 390ms 4.89% std::_Rb_tree::_Rb_tree (partial-inline) 26ms 0.33% 28.16% 386ms 4.84% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 28.17% 385ms 4.83% NodeLocationWriter::Visit 84ms 1.05% 29.23% 385ms 4.83% std::_Rb_tree::_M_erase 12ms 0.15% 29.38% 365ms 4.58% std::less::operator() (inline) 5ms 0.063% 29.44% 363ms 4.55% std::set::set (inline) 3ms 0.038% 29.48% 360ms 4.51% Cell::GetMutationState 353ms 4.43% 33.90% 353ms 4.43% std::operator< (inline) 39ms 0.49% 34.39% 347ms 4.35% std::num_put::_M_insert_float 3ms 0.038% 34.43% 338ms 4.24% Cell::ReadyToDivide 0 0% 34.43% 337ms 4.23% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.43% 336ms 4.21% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.43% 330ms 4.14% OutputFileHandler::OpenOutputFile 43ms 0.54% 34.97% 327ms 4.10% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 34.99% 324ms 4.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 34.99% 324ms 4.06% MeshBasedCellPopulation::GetDampingConstant 5ms 0.063% 35.06% 322ms 4.04% Element::Element 299ms 3.75% 38.80% 299ms 3.75% std::_Rb_tree::_S_right (inline) 192ms 2.41% 41.21% 298ms 3.74% _int_malloc 6ms 0.075% 41.29% 292ms 3.66% CellProliferativeTypesWriter::VisitCell 9ms 0.11% 41.40% 289ms 3.62% AbstractCellPopulation::IsCellAttachedToLocationIndex 108ms 1.35% 42.75% 289ms 3.62% __GI___libc_free 87ms 1.09% 43.84% 281ms 3.52% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.84% 278ms 3.49% std::_Rb_tree::_M_drop_node (inline) 9ms 0.11% 43.96% 269ms 3.37% CellPropertyCollection::HasProperty 6ms 0.075% 44.03% 267ms 3.35% AbstractCellProperty::IsType (inline) 0 0% 44.03% 264ms 3.31% Cell::HasCellProperty (inline) 4ms 0.05% 44.08% 260ms 3.26% std::__cxx11::collate::do_transform 13ms 0.16% 44.25% 260ms 3.26% std::__new_allocator::deallocate (inline) 0 0% 44.25% 258ms 3.23% std::allocator_traits::deallocate (inline) 6ms 0.075% 44.32% 245ms 3.07% ___vsnprintf 0 0% 44.32% 239ms 3.00% __vsnprintf_internal (inline) 9ms 0.11% 44.43% 239ms 3.00% divconqrecurse 24ms 0.3% 44.73% 237ms 2.97% __printf_buffer 6ms 0.075% 44.81% 224ms 2.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 70ms 0.88% 45.69% 220ms 2.76% mergehulls 0 0% 45.69% 218ms 2.73% std::_Rb_tree::_M_put_node (inline) 13ms 0.16% 45.85% 215ms 2.70% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.075% 45.93% 210ms 2.63% Element::RegisterWithNodes (inline) 19ms 0.24% 46.16% 209ms 2.62% TetrahedralMesh::Clear 51ms 0.64% 46.80% 206ms 2.58% AbstractCellProperty::IsSame 3ms 0.038% 46.84% 204ms 2.56% Node::AddElement 1ms 0.013% 46.85% 199ms 2.49% __printf_fp_spec (inline) 16ms 0.2% 47.05% 198ms 2.48% __printf_fp_l_buffer 166ms 2.08% 49.13% 181ms 2.27% _int_free 9ms 0.11% 49.25% 173ms 2.17% MeshBasedCellPopulation::SpringsEnd (inline) 83ms 1.04% 50.29% 172ms 2.16% __printf_fp_buffer_1 57ms 0.71% 51.00% 172ms 2.16% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 51.00% 170ms 2.13% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 51.02% 169ms 2.12% std::basic_filebuf::open 0 0% 51.02% 169ms 2.12% std::basic_ofstream::open (inline) 10ms 0.13% 51.14% 157ms 1.97% AbstractTetrahedralElement::CalculateJacobian 38ms 0.48% 51.62% 155ms 1.94% std::type_info::operator== (inline) 140ms 1.76% 53.37% 140ms 1.76% std::_Rb_tree_increment 11ms 0.14% 53.51% 138ms 1.73% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 53.52% 137ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 31ms 0.39% 53.91% 134ms 1.68% std::num_put::_M_insert_int 40ms 0.5% 54.41% 133ms 1.67% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.14% 54.55% 130ms 1.63% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.55% 130ms 1.63% OutputFileHandler::CommonConstructor 0 0% 54.55% 130ms 1.63% OutputFileHandler::OutputFileHandler 10ms 0.13% 54.68% 127ms 1.59% Node::~Node 0 0% 54.68% 126ms 1.58% std::_Vector_base::_M_allocate (inline) 0 0% 54.68% 125ms 1.57% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 54.69% 125ms 1.57% std::filesystem::permissions 1ms 0.013% 54.70% 124ms 1.55% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 54.70% 124ms 1.55% OutputFileHandler::MakeFoldersAndReturnFullPath 124ms 1.55% 56.26% 124ms 1.55% __GI_fchmodat 0 0% 56.26% 124ms 1.55% std::__basic_file::open 22ms 0.28% 56.53% 123ms 1.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 56.54% 123ms 1.54% _IO_new_fopen 1ms 0.013% 56.56% 122ms 1.53% AbstractCellBasedWriter::CloseFile 0 0% 56.56% 122ms 1.53% __fopen_internal (inline) 33ms 0.41% 56.97% 121ms 1.52% std::__ostream_insert 1ms 0.013% 56.98% 121ms 1.52% std::basic_filebuf::close 0 0% 56.98% 121ms 1.52% std::basic_ofstream::close (inline) 0 0% 56.98% 120ms 1.50% _IO_new_file_fopen 11ms 0.14% 57.12% 119ms 1.49% boost::detail::shared_count::~shared_count (inline) 0 0% 57.12% 119ms 1.49% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 57.13% 117ms 1.47% __GI__IO_file_open 4ms 0.05% 57.18% 116ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 17ms 0.21% 57.40% 114ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (partial-inline) 110ms 1.38% 58.78% 110ms 1.38% std::_Rb_tree_insert_and_rebalance 16ms 0.2% 58.98% 107ms 1.34% AbstractTetrahedralElement::RefreshJacobian 46ms 0.58% 59.55% 107ms 1.34% boost::shared_ptr::shared_ptr (inline) 0 0% 59.55% 106ms 1.33% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.038% 59.59% 106ms 1.33% alternateaxes 80ms 1.00% 60.59% 106ms 1.33% std::basic_filebuf::xsputn 4ms 0.05% 60.64% 106ms 1.33% std::vector::push_back (inline) 3ms 0.038% 60.68% 105ms 1.32% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.063% 60.74% 105ms 1.32% boost::numeric::ublas::vector_assign (inline) 103ms 1.29% 62.04% 104ms 1.30% boost::detail::sp_counted_base::release 99ms 1.24% 63.28% 103ms 1.29% vertexmedian 98ms 1.23% 64.51% 98ms 1.23% __libc_open64 5ms 0.063% 64.57% 98ms 1.23% std::operator<< (inline) 0 0% 64.57% 97ms 1.22% tcache_get (inline) 97ms 1.22% 65.78% 97ms 1.22% tcache_get_n (inline) 11ms 0.14% 65.92% 96ms 1.20% std::vector::_M_realloc_insert 94ms 1.18% 67.10% 94ms 1.18% incircle 62ms 0.78% 67.88% 90ms 1.13% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.063% 67.94% 88ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 88ms 1.10% 69.04% 88ms 1.10% [libchaste_cell_based.so] 3ms 0.038% 69.08% 87ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 87ms 1.09% 70.17% 87ms 1.09% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 7ms 0.088% 70.26% 86ms 1.08% CellPropertyCollection::AddProperty 4ms 0.05% 70.31% 86ms 1.08% std::basic_filebuf::_M_terminate_output 65ms 0.81% 71.13% 85ms 1.07% malloc_consolidate 1ms 0.013% 71.14% 84ms 1.05% std::basic_filebuf::overflow 82ms 1.03% 72.17% 83ms 1.04% __GI___libc_write 0 0% 72.17% 83ms 1.04% std::__basic_file::xsputn 0 0% 72.17% 83ms 1.04% std::basic_filebuf::_M_convert_to_external 0 0% 72.17% 81ms 1.02% Cell::GetCellId 35ms 0.44% 72.61% 78ms 0.98% AbstractElement::GetNodeLocation 77ms 0.97% 73.57% 77ms 0.97% Node::GetIndex 24ms 0.3% 73.87% 77ms 0.97% boost::numeric::ublas::indexing_vector_assign 4ms 0.05% 73.92% 69ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeA 69ms 0.87% 74.79% 69ms 0.87% __GI___fstatat64 0 0% 74.79% 69ms 0.87% std::filesystem::status 2ms 0.025% 74.81% 68ms 0.85% AbstractCellPopulation::GetLocationIndexUsingCell 44ms 0.55% 75.36% 68ms 0.85% std::basic_streambuf::xsputn 0 0% 75.36% 66ms 0.83% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 75.38% 66ms 0.83% std::filesystem::create_directory 61ms 0.76% 76.14% 65ms 0.81% vertexsort 56ms 0.7% 76.84% 63ms 0.79% AbstractElement::GetNodeGlobalIndex 60ms 0.75% 77.60% 61ms 0.76% boost::detail::shared_count::shared_count (inline) 0 0% 77.60% 60ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.60% 60ms 0.75% std::__new_allocator::destroy (inline) 0 0% 77.60% 60ms 0.75% std::allocator_traits::destroy (inline) 2ms 0.025% 77.62% 59ms 0.74% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.05% 77.67% 57ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeB 56ms 0.7% 78.37% 56ms 0.7% __memcpy_avx_unaligned_erms 50ms 0.63% 79.00% 56ms 0.7% std::num_put::do_put 21ms 0.26% 79.26% 55ms 0.69% Determinant (inline) 39ms 0.49% 79.75% 55ms 0.69% boost::numeric::ublas::c_matrix::operator() (partial-inline) 52ms 0.65% 80.40% 52ms 0.65% counterclockwise 1ms 0.013% 80.42% 52ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.42% 52ms 0.65% std::vector::vector (inline) 6ms 0.075% 80.49% 48ms 0.6% Node::ConstructNodeAttributes (inline) 48ms 0.6% 81.09% 48ms 0.6% [libchaste_mesh.so] 31ms 0.39% 81.48% 48ms 0.6% hack_digit 25ms 0.31% 81.80% 47ms 0.59% AbstractTetrahedralMesh::GetElement 0 0% 81.80% 47ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 47ms 0.59% 82.38% 47ms 0.59% [libstdc++.so.6.0.33] 1ms 0.013% 82.40% 46ms 0.58% std::__new_allocator::construct (inline) 0 0% 82.40% 46ms 0.58% std::allocator_traits::construct (inline) 0 0% 82.40% 45ms 0.56% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 82.41% 45ms 0.56% std::_Vector_base::_M_create_storage (inline) 0 0% 82.41% 45ms 0.56% std::_Vector_base::_Vector_base (inline) 22ms 0.28% 82.69% 44ms 0.55% AbstractCellCycleModel::GetAge 1ms 0.013% 82.70% 44ms 0.55% Node::ClearAppliedForce 0 0% 82.70% 44ms 0.55% std::basic_filebuf::_M_allocate_internal_buffer 4ms 0.05% 82.75% 43ms 0.54% std::_Vector_base::_M_deallocate (inline) 43ms 0.54% 83.29% 43ms 0.54% std::ostream::sentry::sentry 0 0% 83.29% 42ms 0.53% CellPropertyCollection::~CellPropertyCollection (inline) 42ms 0.53% 83.81% 42ms 0.53% std::vector::size (inline) 0 0% 83.81% 41ms 0.51% std::_Rb_tree::_M_construct_node (inline) 40ms 0.5% 84.32% 40ms 0.5% boost::shared_ptr::operator-> (inline)