File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6675ms, 83.96% of 7950ms total Dropped 567 nodes (cum <= 39.75ms) flat flat% sum% cum cum% 0 0% 0% 7915ms 99.56% __libc_start_call_main 0 0% 0% 7915ms 99.56% __libc_start_main_impl 0 0% 0% 7915ms 99.56% _start 0 0% 0% 7899ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7899ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7899ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7899ms 99.36% main 0 0% 0% 7861ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7861ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7861ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7860ms 98.87% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3305ms 41.57% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2909ms 36.59% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 2824ms 35.52% MeshBasedCellPopulation::Update 0 0% 0.038% 1635ms 20.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1488ms 18.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.11% 0.15% 1436ms 18.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.15% 1383ms 17.40% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.15% 1382ms 17.38% MutableMesh::ReMesh 18ms 0.23% 0.38% 1206ms 15.17% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.14% 0.52% 1017ms 12.79% AbstractTwoBodyInteractionForce::AddForceContribution 243ms 3.06% 3.57% 1008ms 12.68% __dynamic_cast 437ms 5.50% 9.07% 994ms 12.50% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 9.11% 987ms 12.42% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 9.23% 986ms 12.40% CellPropertyCollection::GetPropertiesType (inline) 99ms 1.25% 10.48% 970ms 12.20% TetrahedralMesh::EdgeIterator::operator++ 39ms 0.49% 10.97% 903ms 11.36% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 9ms 0.11% 11.08% 887ms 11.16% CellPopulationElementWriter::Visit 5ms 0.063% 11.14% 819ms 10.30% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.038% 11.18% 803ms 10.10% AbstractCellProperty::IsSubType (inline) 25ms 0.31% 11.50% 799ms 10.05% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 11.64% 710ms 8.93% TetrahedralMesh::ImportFromMesher 664ms 8.35% 19.99% 664ms 8.35% __strcmp_avx2 67ms 0.84% 20.83% 642ms 8.08% std::map::operator[] (partial-inline) 1ms 0.013% 20.84% 583ms 7.33% std::ostream::operator<< (inline) 70ms 0.88% 21.72% 581ms 7.31% std::ostream::_M_insert 6ms 0.075% 21.80% 578ms 7.27% Cell::GetCellProliferativeType 192ms 2.42% 24.21% 565ms 7.11% __cxxabiv1::__si_class_type_info::__do_dyncast 38ms 0.48% 24.69% 560ms 7.04% operator new 0 0% 24.69% 535ms 6.73% triangulate 0 0% 24.69% 529ms 6.65% std::_Rb_tree::lower_bound (inline) 0 0% 24.69% 529ms 6.65% std::map::lower_bound (inline) 5ms 0.063% 24.75% 526ms 6.62% std::set::insert (inline) 14ms 0.18% 24.93% 521ms 6.55% std::_Rb_tree::_M_insert_unique 5ms 0.063% 24.99% 519ms 6.53% LegacyCellProliferativeTypesWriter::VisitCell 196ms 2.47% 27.46% 517ms 6.50% __GI___libc_malloc 18ms 0.23% 27.69% 511ms 6.43% std::_Rb_tree::find (inline) 34ms 0.43% 28.11% 506ms 6.36% std::__new_allocator::allocate (inline) 0 0% 28.11% 503ms 6.33% std::allocator_traits::allocate (inline) 0 0% 28.11% 478ms 6.01% delaunay 1ms 0.013% 28.13% 477ms 6.00% divconqdelaunay 0 0% 28.13% 476ms 5.99% std::set::count (inline) 6ms 0.075% 28.20% 473ms 5.95% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.20% 440ms 5.53% std::_Rb_tree::_M_create_node (inline) 0 0% 28.20% 420ms 5.28% std::_Rb_tree::_Alloc_node::operator() (inline) 32ms 0.4% 28.60% 406ms 5.11% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.60% 398ms 5.01% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 28.63% 389ms 4.89% Cell::GetMutationState 32ms 0.4% 29.03% 381ms 4.79% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.03% 377ms 4.74% std::set::~set (inline) 83ms 1.04% 30.08% 373ms 4.69% std::_Rb_tree::_M_erase 0 0% 30.08% 356ms 4.48% NodeLocationWriter::Visit 4ms 0.05% 30.13% 348ms 4.38% std::set::set (inline) 21ms 0.26% 30.39% 347ms 4.36% std::_Rb_tree::_M_insert_ (inline) 341ms 4.29% 34.68% 341ms 4.29% std::_Rb_tree::_S_right (inline) 15ms 0.19% 34.87% 338ms 4.25% std::less::operator() (inline) 2ms 0.025% 34.89% 326ms 4.10% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 34.93% 324ms 4.08% AbstractCentreBasedCellPopulation::GetDampingConstant 323ms 4.06% 38.99% 323ms 4.06% std::operator< (inline) 1ms 0.013% 39.01% 322ms 4.05% Cell::ReadyToDivide 29ms 0.36% 39.37% 321ms 4.04% std::_Rb_tree::_M_copy (inline) 26ms 0.33% 39.70% 320ms 4.03% std::num_put::_M_insert_float 101ms 1.27% 40.97% 304ms 3.82% __GI___libc_free 8ms 0.1% 41.07% 299ms 3.76% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.038% 41.11% 292ms 3.67% Element::Element 0 0% 41.11% 289ms 3.64% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 41.11% 289ms 3.64% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 90ms 1.13% 42.24% 289ms 3.64% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.24% 283ms 3.56% OutputFileHandler::OpenOutputFile 12ms 0.15% 42.39% 275ms 3.46% divconqrecurse 2ms 0.025% 42.42% 271ms 3.41% CellProliferativeTypesWriter::VisitCell 0 0% 42.42% 269ms 3.38% std::_Rb_tree::_M_drop_node (inline) 8ms 0.1% 42.52% 260ms 3.27% std::__new_allocator::deallocate (inline) 0 0% 42.52% 256ms 3.22% std::allocator_traits::deallocate (inline) 170ms 2.14% 44.65% 249ms 3.13% _int_malloc 90ms 1.13% 45.79% 249ms 3.13% mergehulls 5ms 0.063% 45.85% 242ms 3.04% std::__cxx11::collate::do_transform 2ms 0.025% 45.87% 240ms 3.02% AbstractCellProperty::IsType (inline) 7ms 0.088% 45.96% 233ms 2.93% CellPropertyCollection::HasProperty 0 0% 45.96% 231ms 2.91% Cell::HasCellProperty (inline) 2ms 0.025% 45.99% 223ms 2.81% ___vsnprintf 0 0% 45.99% 221ms 2.78% __vsnprintf_internal (inline) 33ms 0.42% 46.40% 217ms 2.73% __printf_buffer 2ms 0.025% 46.43% 216ms 2.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 46.43% 216ms 2.72% std::_Rb_tree::_M_put_node (inline) 10ms 0.13% 46.55% 212ms 2.67% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 46.65% 204ms 2.57% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.088% 46.74% 202ms 2.54% Element::RegisterWithNodes (inline) 179ms 2.25% 48.99% 202ms 2.54% _int_free 23ms 0.29% 49.28% 197ms 2.48% TetrahedralMesh::Clear 53ms 0.67% 49.95% 193ms 2.43% AbstractCellProperty::IsSame 3ms 0.038% 49.99% 192ms 2.42% Node::AddElement 1ms 0.013% 50.00% 169ms 2.13% __printf_fp_spec (inline) 6ms 0.075% 50.08% 168ms 2.11% __printf_fp_l_buffer 40ms 0.5% 50.58% 167ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 50.59% 162ms 2.04% OutputFileHandler::OutputFileHandler 1ms 0.013% 50.60% 161ms 2.03% OutputFileHandler::CommonConstructor 56ms 0.7% 51.31% 160ms 2.01% std::_Rb_tree::_M_get_insert_unique_pos (inline) 89ms 1.12% 52.43% 154ms 1.94% __printf_fp_buffer_1 4ms 0.05% 52.48% 147ms 1.85% boost::numeric::ublas::vector_assign (inline) 0 0% 52.48% 146ms 1.84% OutputFileHandler::MakeFoldersAndReturnFullPath 9ms 0.11% 52.59% 146ms 1.84% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 52.62% 142ms 1.79% AbstractCellBasedWriter::CloseFile 0 0% 52.62% 142ms 1.79% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 52.64% 141ms 1.77% std::basic_filebuf::close 0 0% 52.64% 140ms 1.76% std::basic_ofstream::close (inline) 23ms 0.29% 52.93% 140ms 1.76% std::type_info::operator== (inline) 65ms 0.82% 53.75% 138ms 1.74% std::__ostream_insert 3ms 0.038% 53.79% 137ms 1.72% alternateaxes 14ms 0.18% 53.96% 133ms 1.67% AbstractTetrahedralElement::CalculateJacobian 121ms 1.52% 55.48% 133ms 1.67% vertexmedian 23ms 0.29% 55.77% 129ms 1.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 55.77% 128ms 1.61% std::basic_ofstream::basic_ofstream (inline) 2ms 0.025% 55.80% 126ms 1.58% std::basic_filebuf::open 0 0% 55.80% 126ms 1.58% std::basic_ofstream::open (inline) 0 0% 55.80% 122ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 0 0% 55.80% 122ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 122ms 1.53% 57.33% 122ms 1.53% __GI_fchmodat 0 0% 57.33% 122ms 1.53% std::filesystem::permissions 30ms 0.38% 57.71% 121ms 1.52% std::num_put::_M_insert_int 6ms 0.075% 57.79% 120ms 1.51% Node::~Node 1ms 0.013% 57.80% 116ms 1.46% std::operator<< (inline) 65ms 0.82% 58.62% 115ms 1.45% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 6ms 0.075% 58.69% 114ms 1.43% std::vector::push_back (inline) 113ms 1.42% 60.11% 113ms 1.42% std::_Rb_tree_insert_and_rebalance 0 0% 60.11% 112ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.2% 60.31% 111ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 14ms 0.18% 60.49% 110ms 1.38% boost::detail::shared_count::~shared_count (inline) 0 0% 60.49% 110ms 1.38% boost::shared_ptr::~shared_ptr (inline) 7ms 0.088% 60.58% 109ms 1.37% AbstractTetrahedralElement::CalculateInverseJacobian 32ms 0.4% 60.98% 107ms 1.35% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 61.01% 107ms 1.35% std::_Vector_base::_M_allocate (inline) 15ms 0.19% 61.19% 104ms 1.31% AbstractTetrahedralElement::RefreshJacobian 16ms 0.2% 61.40% 103ms 1.30% std::vector::_M_realloc_insert 2ms 0.025% 61.42% 102ms 1.28% std::basic_filebuf::_M_terminate_output 1ms 0.013% 61.43% 101ms 1.27% std::basic_filebuf::overflow 1ms 0.013% 61.45% 100ms 1.26% std::basic_filebuf::_M_convert_to_external 99ms 1.25% 62.69% 99ms 1.25% __GI___libc_write 0 0% 62.69% 99ms 1.25% std::__basic_file::xsputn 2ms 0.025% 62.72% 97ms 1.22% std::__basic_file::open 2ms 0.025% 62.74% 96ms 1.21% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 62.75% 94ms 1.18% _IO_new_fopen 0 0% 62.75% 93ms 1.17% __fopen_internal (inline) 91ms 1.14% 63.90% 92ms 1.16% boost::detail::sp_counted_base::release 92ms 1.16% 65.06% 92ms 1.16% incircle 1ms 0.013% 65.07% 90ms 1.13% _IO_new_file_fopen 89ms 1.12% 66.19% 89ms 1.12% [libchaste_cell_based.so] 38ms 0.48% 66.67% 89ms 1.12% boost::shared_ptr::shared_ptr (inline) 12ms 0.15% 66.82% 89ms 1.12% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 66.83% 88ms 1.11% __GI__IO_file_open 6ms 0.075% 66.91% 86ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.038% 66.94% 85ms 1.07% std::filesystem::status 84ms 1.06% 68.00% 84ms 1.06% std::_Rb_tree_increment 0 0% 68.00% 82ms 1.03% Cell::GetCellId 82ms 1.03% 69.03% 82ms 1.03% __GI___fstatat64 81ms 1.02% 70.05% 81ms 1.02% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 70.06% 80ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 12ms 0.15% 70.21% 80ms 1.01% CellPropertyCollection::AddProperty 0 0% 70.21% 78ms 0.98% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 57ms 0.72% 70.93% 78ms 0.98% std::basic_filebuf::xsputn 0 0% 70.93% 78ms 0.98% std::filesystem::create_directory 76ms 0.96% 71.89% 76ms 0.96% __libc_open64 34ms 0.43% 72.31% 73ms 0.92% AbstractElement::GetNodeLocation 5ms 0.063% 72.38% 73ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeB 56ms 0.7% 73.08% 73ms 0.92% std::basic_streambuf::xsputn 0 0% 73.08% 70ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.08% 70ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.86% 73.94% 68ms 0.86% Node::GetIndex 68ms 0.86% 74.79% 68ms 0.86% counterclockwise 1ms 0.013% 74.81% 67ms 0.84% AbstractCellPopulation::GetLocationIndexUsingCell 59ms 0.74% 75.55% 67ms 0.84% AbstractElement::GetNodeGlobalIndex 67ms 0.84% 76.39% 67ms 0.84% __memcpy_avx_unaligned_erms 64ms 0.81% 77.19% 64ms 0.81% [libchaste_mesh.so] 0 0% 77.19% 63ms 0.79% tcache_get (inline) 63ms 0.79% 77.99% 63ms 0.79% tcache_get_n (inline) 43ms 0.54% 78.53% 60ms 0.75% malloc_consolidate 0 0% 78.53% 56ms 0.7% AbstractCentreBasedCellPopulation::CreateCellPair 46ms 0.58% 79.11% 55ms 0.69% std::num_put::do_put 46ms 0.58% 79.69% 55ms 0.69% vertexsort 0 0% 79.69% 53ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.69% 53ms 0.67% std::__new_allocator::destroy (inline) 0 0% 79.69% 53ms 0.67% std::allocator_traits::destroy (inline) 0 0% 79.69% 52ms 0.65% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 79.94% 52ms 0.65% boost::numeric::ublas::vector_norm_2::apply (inline) 52ms 0.65% 80.59% 52ms 0.65% std::ostream::sentry::sentry 3ms 0.038% 80.63% 51ms 0.64% Node::ConstructNodeAttributes (inline) 51ms 0.64% 81.27% 51ms 0.64% boost::detail::shared_count::shared_count (inline) 16ms 0.2% 81.47% 49ms 0.62% AbstractCellCycleModel::GetAge 28ms 0.35% 81.82% 48ms 0.6% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 81.84% 48ms 0.6% BoundaryNodeWriter::Visit 0 0% 81.84% 48ms 0.6% Node::ClearAppliedForce 5ms 0.063% 81.90% 48ms 0.6% TetrahedralMesh::EdgeIterator::GetNodeA 5ms 0.063% 81.96% 46ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 45ms 0.57% 82.53% 45ms 0.57% std::vector::size (inline) 0 0% 82.53% 45ms 0.57% std::vector::vector (inline) 44ms 0.55% 83.08% 44ms 0.55% [libstdc++.so.6.0.33] 44ms 0.55% 83.64% 44ms 0.55% boost::numeric::ublas::c_vector::operator() 1ms 0.013% 83.65% 44ms 0.55% std::__new_allocator::construct (inline) 0 0% 83.65% 44ms 0.55% std::allocator_traits::construct (inline) 21ms 0.26% 83.91% 42ms 0.53% hack_digit 0 0% 83.91% 42ms 0.53% std::_Rb_tree::_M_construct_node (inline) 4ms 0.05% 83.96% 42ms 0.53% std::_Vector_base::_M_deallocate (inline) 0 0% 83.96% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline)