File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6346ms, 84.10% of 7546ms total Dropped 565 nodes (cum <= 37.73ms) flat flat% sum% cum cum% 0 0% 0% 7512ms 99.55% __libc_start_call_main 0 0% 0% 7512ms 99.55% __libc_start_main_impl 0 0% 0% 7512ms 99.55% _start 0 0% 0% 7497ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7497ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7497ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7497ms 99.35% main 0 0% 0% 7461ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7461ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7461ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7459ms 98.85% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3214ms 42.59% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.027% 2765ms 36.64% MeshBasedCellPopulation::Update 0 0% 0.027% 2677ms 35.48% AbstractCellPopulation::WriteResultsToFiles 2ms 0.027% 0.053% 1558ms 20.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.066% 1379ms 18.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.066% 1355ms 17.96% MutableMesh::ReMesh 1ms 0.013% 0.08% 1349ms 17.88% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.08% 0.16% 1327ms 17.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 28ms 0.37% 0.53% 1176ms 15.58% MeshBasedCellPopulation::SpringIterator::operator++ 15ms 0.2% 0.73% 955ms 12.66% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.013% 0.74% 950ms 12.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 415ms 5.50% 6.24% 945ms 12.52% std::_Rb_tree::_M_lower_bound (inline) 97ms 1.29% 7.53% 929ms 12.31% TetrahedralMesh::EdgeIterator::operator++ 249ms 3.30% 10.83% 918ms 12.17% __dynamic_cast 2ms 0.027% 10.85% 909ms 12.05% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.08% 10.93% 883ms 11.70% CellPopulationElementWriter::Visit 35ms 0.46% 11.40% 799ms 10.59% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.04% 11.44% 776ms 10.28% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.11% 11.54% 746ms 9.89% AbstractCellProperty::IsSubType (inline) 30ms 0.4% 11.94% 727ms 9.63% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.16% 12.10% 699ms 9.26% TetrahedralMesh::ImportFromMesher 39ms 0.52% 12.62% 618ms 8.19% std::map::operator[] (partial-inline) 2ms 0.027% 12.64% 579ms 7.67% std::ostream::operator<< (inline) 98ms 1.30% 13.94% 577ms 7.65% std::ostream::_M_insert 33ms 0.44% 14.38% 547ms 7.25% operator new 3ms 0.04% 14.42% 523ms 6.93% triangulate 8ms 0.11% 14.52% 521ms 6.90% Cell::GetCellProliferativeType 3ms 0.04% 14.56% 516ms 6.84% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 14.56% 515ms 6.82% std::_Rb_tree::lower_bound (inline) 0 0% 14.56% 515ms 6.82% std::map::lower_bound (inline) 6ms 0.08% 14.64% 512ms 6.79% std::set::insert (inline) 186ms 2.46% 17.11% 510ms 6.76% __GI___libc_malloc 506ms 6.71% 23.81% 506ms 6.71% __strcmp_avx2 7ms 0.093% 23.91% 506ms 6.71% std::_Rb_tree::_M_insert_unique 29ms 0.38% 24.29% 496ms 6.57% std::__new_allocator::allocate (inline) 0 0% 24.29% 491ms 6.51% std::allocator_traits::allocate (inline) 233ms 3.09% 27.38% 463ms 6.14% __cxxabiv1::__si_class_type_info::__do_dyncast 14ms 0.19% 27.56% 461ms 6.11% std::_Rb_tree::find (inline) 0 0% 27.56% 460ms 6.10% delaunay 3ms 0.04% 27.60% 459ms 6.08% divconqdelaunay 3ms 0.04% 27.64% 439ms 5.82% AbstractCellBasedSimulation::DoCellBirth 2ms 0.027% 27.67% 427ms 5.66% Cell::GetMutationState 0 0% 27.67% 426ms 5.65% std::_Rb_tree::_M_create_node (inline) 0 0% 27.67% 415ms 5.50% std::set::count (inline) 0 0% 27.67% 400ms 5.30% std::_Rb_tree::_Alloc_node::operator() (inline) 31ms 0.41% 28.08% 395ms 5.23% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.08% 389ms 5.16% std::_Rb_tree::_M_get_node (inline) 0 0% 28.08% 362ms 4.80% std::set::~set (inline) 76ms 1.01% 29.09% 355ms 4.70% std::_Rb_tree::_M_erase 2ms 0.027% 29.11% 347ms 4.60% NodeLocationWriter::Visit 15ms 0.2% 29.31% 346ms 4.59% std::_Rb_tree::_Rb_tree (partial-inline) 338ms 4.48% 33.79% 338ms 4.48% std::_Rb_tree::_S_right (inline) 1ms 0.013% 33.81% 327ms 4.33% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 33.82% 326ms 4.32% AbstractCentreBasedCellPopulation::GetDampingConstant 15ms 0.2% 34.02% 325ms 4.31% std::_Rb_tree::_M_insert_ (inline) 4ms 0.053% 34.07% 315ms 4.17% std::set::set (inline) 11ms 0.15% 34.22% 305ms 4.04% std::less::operator() (inline) 10ms 0.13% 34.35% 304ms 4.03% AbstractCellPopulation::IsCellAttachedToLocationIndex 53ms 0.7% 35.05% 299ms 3.96% std::_Rb_tree::_M_copy (inline) 294ms 3.90% 38.95% 294ms 3.90% std::operator< (inline) 23ms 0.3% 39.25% 293ms 3.88% std::num_put::_M_insert_float 6ms 0.08% 39.33% 292ms 3.87% Element::Element 5ms 0.066% 39.40% 288ms 3.82% Cell::ReadyToDivide 94ms 1.25% 40.64% 275ms 3.64% __GI___libc_free 0 0% 40.64% 264ms 3.50% std::_Rb_tree::_M_drop_node (inline) 6ms 0.08% 40.72% 256ms 3.39% divconqrecurse 169ms 2.24% 42.96% 254ms 3.37% _int_malloc 6ms 0.08% 43.04% 253ms 3.35% std::__new_allocator::deallocate (inline) 0 0% 43.04% 248ms 3.29% std::allocator_traits::deallocate (inline) 57ms 0.76% 43.80% 244ms 3.23% mergehulls 65ms 0.86% 44.66% 242ms 3.21% std::_Rb_tree::_M_clone_node (inline) 3ms 0.04% 44.70% 234ms 3.10% std::__cxx11::collate::do_transform 1ms 0.013% 44.71% 233ms 3.09% CellProliferativeTypesWriter::VisitCell 4ms 0.053% 44.77% 220ms 2.92% ___vsnprintf 0 0% 44.77% 216ms 2.86% __vsnprintf_internal (inline) 31ms 0.41% 45.18% 213ms 2.82% __printf_buffer 0 0% 45.18% 210ms 2.78% std::_Rb_tree::_M_put_node (inline) 4ms 0.053% 45.23% 206ms 2.73% AbstractCellProperty::IsType (inline) 1ms 0.013% 45.24% 205ms 2.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 16ms 0.21% 45.45% 199ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.093% 45.55% 197ms 2.61% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.053% 45.60% 194ms 2.57% CellPropertyCollection::HasProperty 0 0% 45.60% 193ms 2.56% Cell::HasCellProperty (inline) 24ms 0.32% 45.92% 185ms 2.45% TetrahedralMesh::Clear 161ms 2.13% 48.05% 180ms 2.39% _int_free 0 0% 48.05% 179ms 2.37% Element::RegisterWithNodes (inline) 1ms 0.013% 48.07% 177ms 2.35% Node::AddElement 40ms 0.53% 48.60% 176ms 2.33% TetrahedralMesh::EdgesEnd (partial-inline) 68ms 0.9% 49.50% 174ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.093% 49.59% 165ms 2.19% __printf_fp_l_buffer 0 0% 49.59% 165ms 2.19% __printf_fp_spec (inline) 45ms 0.6% 50.19% 164ms 2.17% AbstractCellProperty::IsSame 4ms 0.053% 50.24% 155ms 2.05% boost::numeric::ublas::vector_assign (inline) 82ms 1.09% 51.33% 153ms 2.03% __printf_fp_buffer_1 15ms 0.2% 51.52% 152ms 2.01% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.52% 148ms 1.96% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 7ms 0.093% 51.62% 148ms 1.96% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 51.63% 146ms 1.93% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.63% 143ms 1.90% OutputFileHandler::OpenOutputFile 0 0% 51.63% 139ms 1.84% std::basic_ofstream::basic_ofstream (inline) 3ms 0.04% 51.67% 136ms 1.80% std::basic_filebuf::open 0 0% 51.67% 136ms 1.80% std::basic_ofstream::open (inline) 0 0% 51.67% 134ms 1.78% OutputFileHandler::CommonConstructor 0 0% 51.67% 134ms 1.78% OutputFileHandler::OutputFileHandler 2ms 0.027% 51.70% 131ms 1.74% OutputFileHandler::MakeFoldersAndReturnFullPath 58ms 0.77% 52.46% 131ms 1.74% std::__ostream_insert 35ms 0.46% 52.93% 129ms 1.71% std::num_put::_M_insert_int 0 0% 52.93% 128ms 1.70% AbstractCellBasedWriter::CloseFile 0 0% 52.93% 128ms 1.70% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.027% 52.96% 128ms 1.70% std::basic_filebuf::close 0 0% 52.96% 128ms 1.70% std::basic_ofstream::close (inline) 1ms 0.013% 52.97% 125ms 1.66% alternateaxes 0 0% 52.97% 124ms 1.64% AbstractCellPopulation::Iterator::operator++ (inline) 21ms 0.28% 53.25% 123ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 117ms 1.55% 54.80% 123ms 1.63% vertexmedian 19ms 0.25% 55.05% 122ms 1.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 10ms 0.13% 55.18% 121ms 1.60% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 55.19% 119ms 1.58% TetrahedralMesh::RefreshJacobianCachedData 38ms 0.5% 55.70% 119ms 1.58% boost::numeric::ublas::indexing_vector_assign 119ms 1.58% 57.28% 119ms 1.58% std::_Rb_tree_increment 31ms 0.41% 57.69% 119ms 1.58% std::type_info::operator== (inline) 85ms 1.13% 58.81% 115ms 1.52% TetrahedralMesh::EdgeIterator::EdgeIterator 114ms 1.51% 60.32% 114ms 1.51% incircle 6ms 0.08% 60.40% 112ms 1.48% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.08% 60.48% 111ms 1.47% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.17% 60.65% 110ms 1.46% boost::detail::shared_count::~shared_count (inline) 0 0% 60.65% 110ms 1.46% boost::shared_ptr::~shared_ptr (inline) 110ms 1.46% 62.11% 110ms 1.46% std::_Rb_tree_insert_and_rebalance 2ms 0.027% 62.14% 110ms 1.46% std::operator<< (inline) 47ms 0.62% 62.76% 105ms 1.39% boost::shared_ptr::shared_ptr (inline) 5ms 0.066% 62.83% 104ms 1.38% Node::~Node 2ms 0.027% 62.85% 104ms 1.38% std::_Vector_base::_M_allocate (inline) 2ms 0.027% 62.88% 102ms 1.35% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 6ms 0.08% 62.96% 102ms 1.35% std::vector::push_back (inline) 19ms 0.25% 63.21% 101ms 1.34% AbstractTetrahedralElement::RefreshJacobian 0 0% 63.21% 101ms 1.34% _IO_new_file_fopen 0 0% 63.21% 101ms 1.34% _IO_new_fopen 0 0% 63.21% 101ms 1.34% __fopen_internal (inline) 0 0% 63.21% 101ms 1.34% std::__basic_file::open 0 0% 63.21% 98ms 1.30% __GI__IO_file_open 94ms 1.25% 64.46% 94ms 1.25% boost::detail::sp_counted_base::release 1ms 0.013% 64.47% 92ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 64.48% 92ms 1.22% std::basic_filebuf::_M_terminate_output 1ms 0.013% 64.50% 92ms 1.22% std::basic_filebuf::overflow 0 0% 64.50% 91ms 1.21% Cell::GetCellId 12ms 0.16% 64.66% 91ms 1.21% std::vector::_M_realloc_insert 1ms 0.013% 64.67% 90ms 1.19% std::basic_filebuf::_M_convert_to_external 88ms 1.17% 65.84% 89ms 1.18% __libc_open64 0 0% 65.84% 89ms 1.18% std::__basic_file::xsputn 88ms 1.17% 67.00% 88ms 1.17% [libchaste_cell_based.so] 88ms 1.17% 68.17% 88ms 1.17% __GI___libc_write 3ms 0.04% 68.21% 84ms 1.11% AbstractCellPopulation::GetLocationIndexUsingCell 82ms 1.09% 69.29% 82ms 1.09% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.04% 69.33% 71ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 0.7% 70.04% 71ms 0.94% std::basic_streambuf::xsputn 70ms 0.93% 70.96% 70ms 0.93% Node::GetIndex 67ms 0.89% 71.85% 70ms 0.93% vertexsort 28ms 0.37% 72.22% 69ms 0.91% AbstractElement::GetNodeLocation 45ms 0.6% 72.82% 68ms 0.9% AbstractElement::GetNodeGlobalIndex 68ms 0.9% 73.72% 68ms 0.9% counterclockwise 49ms 0.65% 74.37% 67ms 0.89% malloc_consolidate 8ms 0.11% 74.48% 66ms 0.87% CellPropertyCollection::AddProperty 0 0% 74.48% 66ms 0.87% std::filesystem::create_directory 2ms 0.027% 74.50% 64ms 0.85% std::_Rb_tree::_M_emplace_hint_unique 62ms 0.82% 75.32% 62ms 0.82% __memcpy_avx_unaligned_erms 37ms 0.49% 75.82% 62ms 0.82% std::basic_filebuf::xsputn 56ms 0.74% 76.56% 61ms 0.81% std::num_put::do_put 61ms 0.81% 77.37% 61ms 0.81% std::vector::size (inline) 2ms 0.027% 77.39% 60ms 0.8% Node::ConstructNodeAttributes (inline) 0 0% 77.39% 59ms 0.78% tcache_get (inline) 59ms 0.78% 78.17% 59ms 0.78% tcache_get_n (inline) 0 0% 78.17% 58ms 0.77% Node::ClearAppliedForce 58ms 0.77% 78.94% 58ms 0.77% [libchaste_mesh.so] 57ms 0.76% 79.70% 58ms 0.77% boost::detail::shared_count::shared_count (inline) 30ms 0.4% 80.10% 57ms 0.76% AbstractTetrahedralMesh::GetElement 2ms 0.027% 80.12% 57ms 0.76% std::filesystem::status 56ms 0.74% 80.86% 56ms 0.74% __GI___fstatat64 0 0% 80.86% 54ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.86% 54ms 0.72% std::__new_allocator::destroy (inline) 0 0% 80.86% 54ms 0.72% std::allocator_traits::destroy (inline) 37ms 0.49% 81.35% 53ms 0.7% boost::numeric::ublas::c_matrix::operator() 0 0% 81.35% 51ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeA 17ms 0.23% 81.58% 48ms 0.64% AbstractCellCycleModel::GetAge 0 0% 81.58% 48ms 0.64% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 81.58% 47ms 0.62% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.58% 47ms 0.62% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.58% 46ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.053% 81.63% 46ms 0.61% NodeAttributes::NodeAttributes 2ms 0.027% 81.66% 45ms 0.6% BoundaryNodeWriter::Visit 13ms 0.17% 81.83% 45ms 0.6% Determinant (inline) 0 0% 81.83% 45ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.83% 44ms 0.58% CellPropertyCollection::~CellPropertyCollection (inline) 44ms 0.58% 82.41% 44ms 0.58% [libstdc++.so.6.0.33] 43ms 0.57% 82.98% 43ms 0.57% boost::numeric::ublas::c_vector::operator() 0 0% 82.98% 43ms 0.57% std::vector::vector (inline) 0 0% 82.98% 42ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.98% 42ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.54% 83.53% 41ms 0.54% Node::IsDeleted 0 0% 83.53% 41ms 0.54% std::_Vector_base::_Vector_base (inline) 2ms 0.027% 83.55% 41ms 0.54% std::__new_allocator::construct (inline) 0 0% 83.55% 41ms 0.54% std::allocator_traits::construct (inline) 0 0% 83.55% 41ms 0.54% std::map::find (inline) 1ms 0.013% 83.57% 39ms 0.52% std::_Vector_base::_M_create_storage (inline) 2ms 0.027% 83.59% 39ms 0.52% std::_Vector_base::_M_deallocate (inline) 0 0% 83.59% 39ms 0.52% std::map::map (inline) 38ms 0.5% 84.10% 38ms 0.5% std::ostream::sentry::sentry