File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6620ms, 83.80% of 7900ms total Dropped 566 nodes (cum <= 39.50ms) flat flat% sum% cum cum% 0 0% 0% 7861ms 99.51% __libc_start_call_main 0 0% 0% 7861ms 99.51% __libc_start_main_impl 0 0% 0% 7861ms 99.51% _start 0 0% 0% 7844ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7844ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7844ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7844ms 99.29% main 0 0% 0% 7804ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7804ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7804ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7801ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3397ms 43.00% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2925ms 37.03% MeshBasedCellPopulation::Update 1ms 0.013% 0.025% 2885ms 36.52% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.038% 1507ms 19.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1440ms 18.23% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.038% 1433ms 18.14% MutableMesh::ReMesh 1ms 0.013% 0.051% 1355ms 17.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.089% 0.14% 1275ms 16.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.34% 1268ms 16.05% MeshBasedCellPopulation::SpringIterator::operator++ 136ms 1.72% 2.06% 1052ms 13.32% TetrahedralMesh::EdgeIterator::operator++ 452ms 5.72% 7.78% 973ms 12.32% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.1% 7.89% 929ms 11.76% CellPopulationElementWriter::Visit 2ms 0.025% 7.91% 922ms 11.67% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 269ms 3.41% 11.32% 887ms 11.23% __dynamic_cast 12ms 0.15% 11.47% 876ms 11.09% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.025% 11.49% 871ms 11.03% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.013% 11.51% 762ms 9.65% MeshBasedCellPopulation::AcceptCellWriter 46ms 0.58% 12.09% 755ms 9.56% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 10ms 0.13% 12.22% 740ms 9.37% TetrahedralMesh::ImportFromMesher 31ms 0.39% 12.61% 737ms 9.33% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 12.70% 704ms 8.91% AbstractCellProperty::IsSubType (inline) 4ms 0.051% 12.75% 611ms 7.73% std::ostream::operator<< (inline) 45ms 0.57% 13.32% 606ms 7.67% std::map::operator[] (partial-inline) 99ms 1.25% 14.57% 603ms 7.63% std::ostream::_M_insert 34ms 0.43% 15.00% 587ms 7.43% operator new 189ms 2.39% 17.39% 550ms 6.96% __GI___libc_malloc 1ms 0.013% 17.41% 537ms 6.80% triangulate 7ms 0.089% 17.49% 535ms 6.77% std::set::insert (inline) 14ms 0.18% 17.67% 528ms 6.68% std::_Rb_tree::_M_insert_unique 34ms 0.43% 18.10% 519ms 6.57% std::__new_allocator::allocate (inline) 6ms 0.076% 18.18% 517ms 6.54% Cell::GetCellProliferativeType 0 0% 18.18% 515ms 6.52% std::allocator_traits::allocate (inline) 511ms 6.47% 24.65% 511ms 6.47% __strcmp_avx2 18ms 0.23% 24.87% 510ms 6.46% std::_Rb_tree::find (inline) 0 0% 24.87% 508ms 6.43% std::_Rb_tree::lower_bound (inline) 0 0% 24.87% 508ms 6.43% std::map::lower_bound (inline) 8ms 0.1% 24.97% 488ms 6.18% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.97% 479ms 6.06% std::set::count (inline) 0 0% 24.97% 473ms 5.99% delaunay 3ms 0.038% 25.01% 471ms 5.96% divconqdelaunay 5ms 0.063% 25.08% 463ms 5.86% AbstractCellBasedSimulation::DoCellBirth 189ms 2.39% 27.47% 437ms 5.53% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.47% 425ms 5.38% std::_Rb_tree::_M_create_node (inline) 44ms 0.56% 28.03% 416ms 5.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.03% 395ms 5.00% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.03% 394ms 4.99% std::_Rb_tree::_M_get_node (inline) 0 0% 28.03% 389ms 4.92% std::set::~set (inline) 57ms 0.72% 28.75% 368ms 4.66% std::_Rb_tree::_M_erase 9ms 0.11% 28.86% 359ms 4.54% std::less::operator() (inline) 2ms 0.025% 28.89% 358ms 4.53% Cell::GetMutationState 1ms 0.013% 28.90% 352ms 4.46% NodeLocationWriter::Visit 350ms 4.43% 33.33% 350ms 4.43% std::operator< (inline) 19ms 0.24% 33.57% 346ms 4.38% std::_Rb_tree::_Rb_tree (partial-inline) 22ms 0.28% 33.85% 334ms 4.23% std::_Rb_tree::_M_insert_ (inline) 4ms 0.051% 33.90% 332ms 4.20% Cell::ReadyToDivide 8ms 0.1% 34.00% 324ms 4.10% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 34.03% 316ms 4.00% MeshBasedCellPopulation::GetDampingConstant 108ms 1.37% 35.39% 316ms 4.00% __GI___libc_free 3ms 0.038% 35.43% 316ms 4.00% std::set::set (inline) 2ms 0.025% 35.46% 314ms 3.97% AbstractCentreBasedCellPopulation::GetDampingConstant 314ms 3.97% 39.43% 314ms 3.97% std::_Rb_tree::_S_right (inline) 1ms 0.013% 39.44% 313ms 3.96% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.44% 312ms 3.95% AbstractCellBasedWriter::OpenOutputFileForAppend 18ms 0.23% 39.67% 309ms 3.91% std::num_put::_M_insert_float 0 0% 39.67% 307ms 3.89% OutputFileHandler::OpenOutputFile 35ms 0.44% 40.11% 299ms 3.78% std::_Rb_tree::_M_copy (inline) 11ms 0.14% 40.25% 295ms 3.73% std::__new_allocator::deallocate (inline) 2ms 0.025% 40.28% 292ms 3.70% Element::Element 0 0% 40.28% 290ms 3.67% std::allocator_traits::deallocate (inline) 0 0% 40.28% 289ms 3.66% std::_Rb_tree::_M_drop_node (inline) 183ms 2.32% 42.59% 288ms 3.65% _int_malloc 74ms 0.94% 43.53% 257ms 3.25% std::_Rb_tree::_M_clone_node (inline) 9ms 0.11% 43.65% 254ms 3.22% divconqrecurse 6ms 0.076% 43.72% 241ms 3.05% CellPropertyCollection::HasProperty 3ms 0.038% 43.76% 240ms 3.04% AbstractCellProperty::IsType (inline) 0 0% 43.76% 239ms 3.03% Cell::HasCellProperty (inline) 2ms 0.025% 43.78% 237ms 3.00% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 43.92% 236ms 2.99% std::__cxx11::collate::do_transform 0 0% 43.92% 235ms 2.97% std::_Rb_tree::_M_put_node (inline) 66ms 0.84% 44.76% 233ms 2.95% mergehulls 2ms 0.025% 44.78% 218ms 2.76% ___vsnprintf 5ms 0.063% 44.85% 216ms 2.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 44.85% 216ms 2.73% __vsnprintf_internal (inline) 21ms 0.27% 45.11% 212ms 2.68% __printf_buffer 6ms 0.076% 45.19% 207ms 2.62% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 179ms 2.27% 47.46% 207ms 2.62% _int_free 19ms 0.24% 47.70% 203ms 2.57% TetrahedralMesh::Clear 3ms 0.038% 47.73% 200ms 2.53% Element::RegisterWithNodes (inline) 6ms 0.076% 47.81% 195ms 2.47% Node::AddElement 52ms 0.66% 48.47% 189ms 2.39% AbstractCellProperty::IsSame 14ms 0.18% 48.65% 186ms 2.35% MeshBasedCellPopulation::SpringsEnd (inline) 54ms 0.68% 49.33% 180ms 2.28% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 49.33% 173ms 2.19% std::basic_ofstream::basic_ofstream (inline) 7ms 0.089% 49.42% 167ms 2.11% __printf_fp_l_buffer 0 0% 49.42% 167ms 2.11% __printf_fp_spec (inline) 2ms 0.025% 49.44% 167ms 2.11% std::basic_filebuf::open 0 0% 49.44% 167ms 2.11% std::basic_ofstream::open (inline) 14ms 0.18% 49.62% 152ms 1.92% AbstractTetrahedralElement::CalculateJacobian 70ms 0.89% 50.51% 149ms 1.89% __printf_fp_buffer_1 35ms 0.44% 50.95% 148ms 1.87% std::num_put::_M_insert_int 0 0% 50.95% 144ms 1.82% alternateaxes 1ms 0.013% 50.96% 143ms 1.81% AbstractCellPopulation::CloseRoundRobinWritersFiles 37ms 0.47% 51.43% 143ms 1.81% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.43% 142ms 1.80% AbstractCellBasedWriter::CloseFile 0 0% 51.43% 142ms 1.80% std::basic_filebuf::close 0 0% 51.43% 142ms 1.80% std::basic_ofstream::close (inline) 128ms 1.62% 53.05% 142ms 1.80% vertexmedian 58ms 0.73% 53.78% 137ms 1.73% std::__ostream_insert 33ms 0.42% 54.20% 137ms 1.73% std::type_info::operator== (inline) 3ms 0.038% 54.24% 136ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.025% 54.27% 136ms 1.72% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 54.28% 131ms 1.66% OutputFileHandler::CommonConstructor 0 0% 54.28% 131ms 1.66% OutputFileHandler::OutputFileHandler 7ms 0.089% 54.37% 128ms 1.62% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.37% 128ms 1.62% _IO_new_fopen 0 0% 54.37% 128ms 1.62% __fopen_internal (inline) 0 0% 54.37% 128ms 1.62% std::__basic_file::open 1ms 0.013% 54.38% 125ms 1.58% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 54.38% 125ms 1.58% _IO_new_file_fopen 2ms 0.025% 54.41% 124ms 1.57% __GI__IO_file_open 3ms 0.038% 54.44% 124ms 1.57% std::_Vector_base::_M_allocate (inline) 4ms 0.051% 54.49% 122ms 1.54% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.16% 54.66% 117ms 1.48% boost::detail::shared_count::~shared_count (inline) 0 0% 54.66% 117ms 1.48% boost::shared_ptr::~shared_ptr (inline) 6ms 0.076% 54.73% 116ms 1.47% Node::~Node 6ms 0.076% 54.81% 115ms 1.46% std::vector::push_back (inline) 17ms 0.22% 55.03% 113ms 1.43% AbstractTetrahedralElement::RefreshJacobian 15ms 0.19% 55.22% 111ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 111ms 1.41% 56.62% 111ms 1.41% incircle 18ms 0.23% 56.85% 111ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 17ms 0.22% 57.06% 110ms 1.39% MeshBasedCellPopulation::SpringIterator::SpringIterator 110ms 1.39% 58.46% 110ms 1.39% __libc_open64 4ms 0.051% 58.51% 110ms 1.39% std::operator<< (inline) 0 0% 58.51% 108ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 108ms 1.37% 59.87% 108ms 1.37% std::_Rb_tree_insert_and_rebalance 64ms 0.81% 60.68% 107ms 1.35% boost::shared_ptr::shared_ptr (inline) 4ms 0.051% 60.73% 107ms 1.35% std::vector::_M_realloc_insert 2ms 0.025% 60.76% 104ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.76% 104ms 1.32% FilesystemPermissions::SetFilePermissions (inline) 104ms 1.32% 62.08% 104ms 1.32% std::_Rb_tree_increment 1ms 0.013% 62.09% 104ms 1.32% std::filesystem::permissions 103ms 1.30% 63.39% 103ms 1.30% __GI_fchmodat 101ms 1.28% 64.67% 102ms 1.29% boost::detail::sp_counted_base::release 2ms 0.025% 64.70% 97ms 1.23% std::basic_filebuf::_M_terminate_output 1ms 0.013% 64.71% 96ms 1.22% std::__basic_file::xsputn 0 0% 64.71% 96ms 1.22% std::basic_filebuf::_M_convert_to_external 0 0% 64.71% 96ms 1.22% std::basic_filebuf::overflow 95ms 1.20% 65.91% 95ms 1.20% __GI___libc_write 27ms 0.34% 66.25% 94ms 1.19% boost::numeric::ublas::indexing_vector_assign 56ms 0.71% 66.96% 91ms 1.15% std::basic_streambuf::xsputn 58ms 0.73% 67.70% 88ms 1.11% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 88ms 1.11% 68.81% 88ms 1.11% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 68.82% 85ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 85ms 1.08% 69.90% 85ms 1.08% Node::GetIndex 53ms 0.67% 70.57% 84ms 1.06% malloc_consolidate 1ms 0.013% 70.58% 83ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 83ms 1.05% 71.63% 83ms 1.05% [libchaste_cell_based.so] 45ms 0.57% 72.20% 83ms 1.05% std::basic_filebuf::xsputn 36ms 0.46% 72.66% 81ms 1.03% AbstractElement::GetNodeLocation 2ms 0.025% 72.68% 76ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.68% 76ms 0.96% Cell::GetCellId 69ms 0.87% 73.56% 69ms 0.87% std::vector::size (inline) 0 0% 73.56% 67ms 0.85% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 73.58% 67ms 0.85% std::filesystem::create_directory 1ms 0.013% 73.59% 66ms 0.84% std::filesystem::status 65ms 0.82% 74.42% 65ms 0.82% __GI___fstatat64 48ms 0.61% 75.03% 65ms 0.82% std::num_put::do_put 64ms 0.81% 75.84% 64ms 0.81% [libchaste_mesh.so] 8ms 0.1% 75.94% 63ms 0.8% CellPropertyCollection::AddProperty 62ms 0.78% 76.72% 62ms 0.78% __memcpy_avx_unaligned_erms 56ms 0.71% 77.43% 62ms 0.78% vertexsort 7ms 0.089% 77.52% 60ms 0.76% std::_Vector_base::_M_deallocate (inline) 2ms 0.025% 77.54% 59ms 0.75% Node::ConstructNodeAttributes (inline) 0 0% 77.54% 59ms 0.75% tcache_get (inline) 59ms 0.75% 78.29% 59ms 0.75% tcache_get_n (inline) 0 0% 78.29% 58ms 0.73% Node::ClearAppliedForce 57ms 0.72% 79.01% 57ms 0.72% counterclockwise 1ms 0.013% 79.03% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 79.03% 54ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.03% 54ms 0.68% std::__new_allocator::destroy (inline) 0 0% 79.03% 54ms 0.68% std::allocator_traits::destroy (inline) 1ms 0.013% 79.04% 53ms 0.67% std::_Rb_tree::_M_emplace_hint_unique 36ms 0.46% 79.49% 51ms 0.65% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 79.51% 51ms 0.65% BoundaryNodeWriter::Visit 34ms 0.43% 79.94% 50ms 0.63% boost::numeric::ublas::c_matrix::operator() 0 0% 79.94% 49ms 0.62% std::vector::vector (inline) 48ms 0.61% 80.54% 48ms 0.61% Node::IsDeleted 48ms 0.61% 81.15% 48ms 0.61% unlink_chunk 20ms 0.25% 81.41% 47ms 0.59% AbstractTetrahedralMesh::GetNumAllElements 0 0% 81.41% 47ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 25ms 0.32% 81.72% 46ms 0.58% AbstractTetrahedralMesh::GetElement 3ms 0.038% 81.76% 46ms 0.58% NodeAttributes::NodeAttributes 0 0% 81.76% 46ms 0.58% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 81.77% 45ms 0.57% TetrahedralMesh::EdgeIterator::GetNodeA 29ms 0.37% 82.14% 45ms 0.57% hack_digit 0 0% 82.14% 44ms 0.56% std::_Vector_base::_M_create_storage (inline) 0 0% 82.14% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 42ms 0.53% 82.67% 43ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 82.67% 42ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.53% 83.20% 42ms 0.53% boost::numeric::ublas::c_vector::operator() (inline) 2ms 0.025% 83.23% 41ms 0.52% _IO_new_fclose 0 0% 83.23% 41ms 0.52% std::__basic_file::close 5ms 0.063% 83.29% 40ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 40ms 0.51% 83.80% 40ms 0.51% [libstdc++.so.6.0.33]