File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6803ms, 85.01% of 8003ms total Dropped 584 nodes (cum <= 40.02ms) flat flat% sum% cum cum% 0 0% 0% 7967ms 99.55% __libc_start_call_main 0 0% 0% 7967ms 99.55% __libc_start_main_impl 0 0% 0% 7967ms 99.55% _start 0 0% 0% 7949ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7949ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7949ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7949ms 99.33% main 0 0% 0% 7907ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7907ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7907ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7903ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0% 3469ms 43.35% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.012% 3028ms 37.84% MeshBasedCellPopulation::Update 0 0% 0.012% 2867ms 35.82% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.012% 1558ms 19.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 1490ms 18.62% MutableMesh::ReMesh 1ms 0.012% 0.025% 1476ms 18.44% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.037% 1415ms 17.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.062% 0.1% 1364ms 17.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.34% 1285ms 16.06% MeshBasedCellPopulation::SpringIterator::operator++ 120ms 1.50% 1.84% 1049ms 13.11% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.075% 1.91% 979ms 12.23% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 1.94% 958ms 11.97% AbstractTwoBodyInteractionForce::AddForceContribution 263ms 3.29% 5.22% 958ms 11.97% __dynamic_cast 469ms 5.86% 11.08% 954ms 11.92% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.12% 11.21% 914ms 11.42% CellPropertyCollection::GetPropertiesType (inline) 35ms 0.44% 11.65% 854ms 10.67% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.075% 11.72% 842ms 10.52% CellPopulationElementWriter::Visit 9ms 0.11% 11.83% 826ms 10.32% MeshBasedCellPopulation::AcceptCellWriter 34ms 0.42% 12.26% 761ms 9.51% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.037% 12.30% 742ms 9.27% AbstractCellProperty::IsSubType (inline) 14ms 0.17% 12.47% 708ms 8.85% TetrahedralMesh::ImportFromMesher 3ms 0.037% 12.51% 639ms 7.98% triangulate 34ms 0.42% 12.93% 624ms 7.80% operator new 0 0% 12.93% 595ms 7.43% std::ostream::operator<< (inline) 104ms 1.30% 14.23% 592ms 7.40% std::ostream::_M_insert 209ms 2.61% 16.84% 585ms 7.31% __GI___libc_malloc 64ms 0.8% 17.64% 582ms 7.27% std::map::operator[] (partial-inline) 21ms 0.26% 17.91% 564ms 7.05% std::__new_allocator::allocate (inline) 7ms 0.087% 17.99% 561ms 7.01% std::set::insert (inline) 0 0% 17.99% 558ms 6.97% std::allocator_traits::allocate (inline) 0 0% 17.99% 556ms 6.95% delaunay 1ms 0.012% 18.01% 556ms 6.95% divconqdelaunay 8ms 0.1% 18.11% 555ms 6.93% std::_Rb_tree::_M_insert_unique 9ms 0.11% 18.22% 544ms 6.80% Cell::GetCellProliferativeType 541ms 6.76% 24.98% 541ms 6.76% __strcmp_avx2 21ms 0.26% 25.24% 530ms 6.62% std::_Rb_tree::find (inline) 3ms 0.037% 25.28% 521ms 6.51% LegacyCellProliferativeTypesWriter::VisitCell 251ms 3.14% 28.41% 501ms 6.26% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.41% 486ms 6.07% std::set::count (inline) 0 0% 28.41% 472ms 5.90% std::_Rb_tree::lower_bound (inline) 0 0% 28.41% 472ms 5.90% std::map::lower_bound (inline) 0 0% 28.41% 461ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 28.41% 433ms 5.41% std::_Rb_tree::_M_get_node (inline) 6ms 0.075% 28.49% 432ms 5.40% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.49% 432ms 5.40% std::_Rb_tree::_Alloc_node::operator() (inline) 34ms 0.42% 28.91% 421ms 5.26% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.91% 394ms 4.92% std::set::~set (inline) 2ms 0.025% 28.94% 390ms 4.87% Cell::GetMutationState 77ms 0.96% 29.90% 383ms 4.79% std::_Rb_tree::_M_erase 27ms 0.34% 30.24% 355ms 4.44% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.012% 30.25% 353ms 4.41% NodeLocationWriter::Visit 30ms 0.37% 30.63% 351ms 4.39% std::_Rb_tree::_M_insert_ (inline) 6ms 0.075% 30.70% 332ms 4.15% std::less::operator() (inline) 0 0% 30.70% 328ms 4.10% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 30.70% 326ms 4.07% AbstractCellBasedWriter::OpenOutputFileForAppend 326ms 4.07% 34.77% 326ms 4.07% std::operator< (inline) 0 0% 34.77% 323ms 4.04% OutputFileHandler::OpenOutputFile 5ms 0.062% 34.84% 323ms 4.04% std::set::set (inline) 5ms 0.062% 34.90% 320ms 4.00% MeshBasedCellPopulation::GetDampingConstant 3ms 0.037% 34.94% 315ms 3.94% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.11% 35.05% 313ms 3.91% divconqrecurse 25ms 0.31% 35.36% 306ms 3.82% std::num_put::_M_insert_float 34ms 0.42% 35.79% 298ms 3.72% std::_Rb_tree::_M_copy (inline) 6ms 0.075% 35.86% 297ms 3.71% Element::Element 97ms 1.21% 37.07% 297ms 3.71% __GI___libc_free 296ms 3.70% 40.77% 296ms 3.70% std::_Rb_tree::_S_right (inline) 87ms 1.09% 41.86% 292ms 3.65% mergehulls 0 0% 41.86% 289ms 3.61% std::_Rb_tree::_M_drop_node (inline) 6ms 0.075% 41.93% 287ms 3.59% Cell::ReadyToDivide 171ms 2.14% 44.07% 286ms 3.57% _int_malloc 10ms 0.12% 44.20% 280ms 3.50% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.062% 44.26% 269ms 3.36% std::__new_allocator::deallocate (inline) 0 0% 44.26% 268ms 3.35% std::allocator_traits::deallocate (inline) 1ms 0.012% 44.27% 266ms 3.32% CellProliferativeTypesWriter::VisitCell 65ms 0.81% 45.08% 259ms 3.24% std::_Rb_tree::_M_clone_node (inline) 10ms 0.12% 45.21% 254ms 3.17% std::__cxx11::collate::do_transform 7ms 0.087% 45.30% 242ms 3.02% AbstractCellProperty::IsType (inline) 5ms 0.062% 45.36% 242ms 3.02% CellPropertyCollection::HasProperty 0 0% 45.36% 239ms 2.99% Cell::HasCellProperty (inline) 0 0% 45.36% 233ms 2.91% ___vsnprintf 0 0% 45.36% 233ms 2.91% __vsnprintf_internal (inline) 0 0% 45.36% 230ms 2.87% std::_Rb_tree::_M_put_node (inline) 28ms 0.35% 45.71% 228ms 2.85% __printf_buffer 165ms 2.06% 47.77% 200ms 2.50% _int_free 68ms 0.85% 48.62% 196ms 2.45% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.05% 48.67% 191ms 2.39% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.05% 48.72% 191ms 2.39% Element::RegisterWithNodes (inline) 3ms 0.037% 48.76% 191ms 2.39% MeshBasedCellPopulation::SpringsEnd (inline) 11ms 0.14% 48.89% 189ms 2.36% TetrahedralMesh::Clear 2ms 0.025% 48.92% 187ms 2.34% Node::AddElement 7ms 0.087% 49.01% 186ms 2.32% __printf_fp_l_buffer 0 0% 49.01% 186ms 2.32% __printf_fp_spec (inline) 4ms 0.05% 49.06% 183ms 2.29% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 32ms 0.4% 49.46% 178ms 2.22% TetrahedralMesh::EdgesEnd (partial-inline) 35ms 0.44% 49.89% 177ms 2.21% AbstractCellProperty::IsSame 89ms 1.11% 51.01% 173ms 2.16% __printf_fp_buffer_1 0 0% 51.01% 166ms 2.07% std::basic_ofstream::basic_ofstream (inline) 4ms 0.05% 51.06% 160ms 2.00% std::basic_filebuf::open 0 0% 51.06% 160ms 2.00% std::basic_ofstream::open (inline) 102ms 1.27% 52.33% 156ms 1.95% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 52.36% 154ms 1.92% alternateaxes 137ms 1.71% 54.07% 152ms 1.90% vertexmedian 1ms 0.012% 54.08% 149ms 1.86% OutputFileHandler::OutputFileHandler 0 0% 54.08% 148ms 1.85% OutputFileHandler::CommonConstructor 8ms 0.1% 54.18% 145ms 1.81% AbstractTetrahedralElement::CalculateJacobian 0 0% 54.18% 145ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 26ms 0.32% 54.50% 142ms 1.77% std::type_info::operator== (inline) 46ms 0.57% 55.08% 139ms 1.74% std::__ostream_insert 134ms 1.67% 56.75% 134ms 1.67% incircle 11ms 0.14% 56.89% 132ms 1.65% boost::detail::shared_count::~shared_count (inline) 0 0% 56.89% 132ms 1.65% boost::shared_ptr::~shared_ptr (inline) 0 0% 56.89% 128ms 1.60% AbstractCellBasedWriter::CloseFile 0 0% 56.89% 128ms 1.60% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 56.89% 128ms 1.60% std::basic_filebuf::close 0 0% 56.89% 128ms 1.60% std::basic_ofstream::close (inline) 2ms 0.025% 56.92% 127ms 1.59% std::_Vector_base::_M_allocate (inline) 29ms 0.36% 57.28% 127ms 1.59% std::num_put::_M_insert_int 8ms 0.1% 57.38% 125ms 1.56% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.012% 57.39% 123ms 1.54% std::__basic_file::open 16ms 0.2% 57.59% 122ms 1.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.012% 57.60% 122ms 1.52% _IO_new_fopen 5ms 0.062% 57.67% 121ms 1.51% Node::~Node 1ms 0.012% 57.68% 121ms 1.51% __fopen_internal (inline) 2ms 0.025% 57.70% 121ms 1.51% boost::numeric::ublas::vector_assign (inline) 0 0% 57.70% 120ms 1.50% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.037% 57.74% 120ms 1.50% std::filesystem::permissions 15ms 0.19% 57.93% 118ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.012% 57.94% 118ms 1.47% _IO_new_file_fopen 8ms 0.1% 58.04% 118ms 1.47% std::vector::push_back (inline) 2ms 0.025% 58.07% 117ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 117ms 1.46% 59.53% 117ms 1.46% __GI_fchmodat 0 0% 59.53% 116ms 1.45% __GI__IO_file_open 23ms 0.29% 59.82% 115ms 1.44% AbstractTetrahedralElement::RefreshJacobian 0 0% 59.82% 114ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.012% 59.83% 114ms 1.42% std::operator<< (inline) 111ms 1.39% 61.21% 113ms 1.41% boost::detail::sp_counted_base::release 4ms 0.05% 61.26% 108ms 1.35% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.087% 61.35% 107ms 1.34% AbstractTetrahedralElement::CalculateInverseJacobian 49ms 0.61% 61.96% 107ms 1.34% boost::shared_ptr::shared_ptr (inline) 6ms 0.075% 62.04% 107ms 1.34% std::vector::_M_realloc_insert 102ms 1.27% 63.31% 102ms 1.27% __libc_open64 5ms 0.062% 63.38% 94ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 91ms 1.14% 64.51% 91ms 1.14% [libchaste_cell_based.so] 91ms 1.14% 65.65% 91ms 1.14% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 65.66% 90ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.71% 66.38% 89ms 1.11% std::basic_filebuf::xsputn 52ms 0.65% 67.02% 86ms 1.07% malloc_consolidate 3ms 0.037% 67.06% 86ms 1.07% std::basic_filebuf::overflow 0 0% 67.06% 85ms 1.06% tcache_get (inline) 85ms 1.06% 68.12% 85ms 1.06% tcache_get_n (inline) 79ms 0.99% 69.11% 85ms 1.06% vertexsort 6ms 0.075% 69.19% 84ms 1.05% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.19% 84ms 1.05% std::basic_filebuf::_M_terminate_output 1ms 0.012% 69.20% 83ms 1.04% std::basic_filebuf::_M_convert_to_external 82ms 1.02% 70.22% 82ms 1.02% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 70.22% 82ms 1.02% std::__basic_file::xsputn 81ms 1.01% 71.24% 81ms 1.01% __GI___libc_write 27ms 0.34% 71.57% 81ms 1.01% boost::numeric::ublas::indexing_vector_assign 81ms 1.01% 72.59% 81ms 1.01% std::_Rb_tree_increment 0 0% 72.59% 80ms 1% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 72.61% 80ms 1% std::filesystem::create_directory 1ms 0.012% 72.62% 75ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 6ms 0.075% 72.70% 75ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeA 30ms 0.37% 73.07% 74ms 0.92% AbstractElement::GetNodeLocation 74ms 0.92% 74.00% 74ms 0.92% counterclockwise 5ms 0.062% 74.06% 73ms 0.91% CellPropertyCollection::AddProperty 0 0% 74.06% 73ms 0.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.06% 73ms 0.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.85% 74.91% 68ms 0.85% __GI___fstatat64 0 0% 74.91% 68ms 0.85% std::filesystem::status 42ms 0.52% 75.43% 65ms 0.81% std::basic_streambuf::xsputn 1ms 0.012% 75.45% 63ms 0.79% Cell::GetCellId 62ms 0.77% 76.22% 62ms 0.77% Node::GetIndex 62ms 0.77% 77.00% 62ms 0.77% [libstdc++.so.6.0.33] 62ms 0.77% 77.77% 62ms 0.77% boost::numeric::ublas::c_vector::operator() 4ms 0.05% 77.82% 60ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 77.82% 59ms 0.74% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.82% 59ms 0.74% std::__new_allocator::destroy (inline) 0 0% 77.82% 59ms 0.74% std::allocator_traits::destroy (inline) 56ms 0.7% 78.52% 58ms 0.72% boost::detail::shared_count::shared_count (inline) 3ms 0.037% 78.56% 57ms 0.71% Node::ConstructNodeAttributes (inline) 56ms 0.7% 79.26% 56ms 0.7% std::vector::size (inline) 1ms 0.012% 79.27% 55ms 0.69% Node::ClearAppliedForce 26ms 0.32% 79.60% 54ms 0.67% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.60% 54ms 0.67% std::vector::vector (inline) 0 0% 79.60% 53ms 0.66% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 53ms 0.66% 80.26% 53ms 0.66% [libchaste_mesh.so] 0 0% 80.26% 53ms 0.66% boost::numeric::ublas::norm_2 (inline) 22ms 0.27% 80.53% 53ms 0.66% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.53% 52ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.012% 80.54% 51ms 0.64% BoundaryNodeWriter::Visit 0 0% 80.54% 51ms 0.64% std::_Vector_base::_Vector_base (inline) 1ms 0.012% 80.56% 50ms 0.62% std::_Vector_base::_M_create_storage (inline) 36ms 0.45% 81.01% 50ms 0.62% std::num_put::do_put 50ms 0.62% 81.63% 50ms 0.62% unlink_chunk 28ms 0.35% 81.98% 48ms 0.6% hack_digit 31ms 0.39% 82.37% 47ms 0.59% AbstractElement::GetNodeGlobalIndex 0 0% 82.37% 46ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 82.37% 46ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 43ms 0.54% 82.91% 43ms 0.54% __memcpy_avx_unaligned_erms 43ms 0.54% 83.44% 43ms 0.54% boost::shared_ptr::operator-> (inline) 22ms 0.27% 83.72% 42ms 0.52% AbstractCellCycleModel::GetAge 18ms 0.22% 83.94% 42ms 0.52% AbstractTetrahedralMesh::GetElement 42ms 0.52% 84.47% 42ms 0.52% __GI___mkdir 42ms 0.52% 84.99% 42ms 0.52% std::ostream::sentry::sentry 1ms 0.012% 85.01% 41ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.01% 41ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline)