File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6626ms, 85.13% of 7783ms total Dropped 603 nodes (cum <= 38.91ms) flat flat% sum% cum cum% 0 0% 0% 7747ms 99.54% __libc_start_call_main 0 0% 0% 7747ms 99.54% __libc_start_main_impl 0 0% 0% 7747ms 99.54% _start 0 0% 0% 7729ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7729ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7729ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7729ms 99.31% main 0 0% 0% 7689ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7689ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7689ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7687ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0% 3394ms 43.61% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2997ms 38.51% MeshBasedCellPopulation::Update 1ms 0.013% 0.026% 2676ms 34.38% AbstractCellPopulation::WriteResultsToFiles 2ms 0.026% 0.051% 1607ms 20.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1535ms 19.72% MutableMesh::ReMesh 0 0% 0.051% 1450ms 18.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.064% 1407ms 18.08% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.1% 0.17% 1404ms 18.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.21% 0.37% 1202ms 15.44% MeshBasedCellPopulation::SpringIterator::operator++ 105ms 1.35% 1.72% 966ms 12.41% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 1.75% 961ms 12.35% AbstractTwoBodyInteractionForce::AddForceContribution 327ms 4.20% 5.95% 958ms 12.31% __dynamic_cast 4ms 0.051% 6.00% 937ms 12.04% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 422ms 5.42% 11.42% 933ms 11.99% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.15% 11.58% 918ms 11.79% CellPropertyCollection::GetPropertiesType (inline) 32ms 0.41% 11.99% 869ms 11.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.12% 12.10% 861ms 11.06% CellPopulationElementWriter::Visit 5ms 0.064% 12.17% 782ms 10.05% MeshBasedCellPopulation::AcceptCellWriter 25ms 0.32% 12.49% 775ms 9.96% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.039% 12.53% 751ms 9.65% AbstractCellProperty::IsSubType (inline) 9ms 0.12% 12.64% 741ms 9.52% TetrahedralMesh::ImportFromMesher 0 0% 12.64% 607ms 7.80% triangulate 54ms 0.69% 13.34% 582ms 7.48% std::map::operator[] (partial-inline) 39ms 0.5% 13.84% 572ms 7.35% operator new 0 0% 13.84% 558ms 7.17% std::ostream::operator<< (inline) 93ms 1.19% 15.03% 557ms 7.16% std::ostream::_M_insert 0 0% 15.03% 547ms 7.03% delaunay 4ms 0.051% 15.08% 547ms 7.03% divconqdelaunay 529ms 6.80% 21.88% 529ms 6.80% __strcmp_avx2 178ms 2.29% 24.17% 528ms 6.78% __GI___libc_malloc 33ms 0.42% 24.59% 523ms 6.72% std::__new_allocator::allocate (inline) 0 0% 24.59% 520ms 6.68% std::allocator_traits::allocate (inline) 6ms 0.077% 24.67% 513ms 6.59% std::set::insert (inline) 6ms 0.077% 24.75% 509ms 6.54% Cell::GetCellProliferativeType 4ms 0.051% 24.80% 507ms 6.51% std::_Rb_tree::_M_insert_unique 21ms 0.27% 25.07% 501ms 6.44% std::_Rb_tree::find (inline) 2ms 0.026% 25.09% 490ms 6.30% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 25.09% 474ms 6.09% std::_Rb_tree::lower_bound (inline) 0 0% 25.09% 474ms 6.09% std::map::lower_bound (inline) 0 0% 25.09% 457ms 5.87% std::set::count (inline) 38ms 0.49% 25.58% 445ms 5.72% std::_Rb_tree::~_Rb_tree (inline) 199ms 2.56% 28.14% 430ms 5.52% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.14% 429ms 5.51% std::_Rb_tree::_M_create_node (inline) 0 0% 28.14% 413ms 5.31% std::set::~set (inline) 0 0% 28.14% 406ms 5.22% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.14% 403ms 5.18% std::_Rb_tree::_M_get_node (inline) 90ms 1.16% 29.29% 401ms 5.15% std::_Rb_tree::_M_erase 1ms 0.013% 29.31% 395ms 5.08% Cell::GetMutationState 5ms 0.064% 29.37% 378ms 4.86% AbstractCellBasedSimulation::DoCellBirth 24ms 0.31% 29.68% 373ms 4.79% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.1% 29.78% 352ms 4.52% std::less::operator() (inline) 1ms 0.013% 29.80% 350ms 4.50% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 29.85% 348ms 4.47% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.064% 29.91% 346ms 4.45% std::set::set (inline) 344ms 4.42% 34.33% 344ms 4.42% std::operator< (inline) 10ms 0.13% 34.46% 333ms 4.28% divconqrecurse 2ms 0.026% 34.49% 331ms 4.25% NodeLocationWriter::Visit 1ms 0.013% 34.50% 330ms 4.24% Element::Element 18ms 0.23% 34.73% 320ms 4.11% std::_Rb_tree::_M_insert_ (inline) 92ms 1.18% 35.91% 312ms 4.01% mergehulls 11ms 0.14% 36.05% 310ms 3.98% AbstractCellPopulation::IsCellAttachedToLocationIndex 44ms 0.57% 36.62% 308ms 3.96% std::_Rb_tree::_M_copy (inline) 84ms 1.08% 37.70% 294ms 3.78% __GI___libc_free 28ms 0.36% 38.06% 291ms 3.74% std::num_put::_M_insert_float 286ms 3.67% 41.73% 286ms 3.67% std::_Rb_tree::_S_right (inline) 185ms 2.38% 44.11% 283ms 3.64% _int_malloc 0 0% 44.11% 281ms 3.61% std::_Rb_tree::_M_drop_node (inline) 9ms 0.12% 44.22% 270ms 3.47% std::__new_allocator::deallocate (inline) 0 0% 44.22% 265ms 3.40% std::allocator_traits::deallocate (inline) 4ms 0.051% 44.28% 261ms 3.35% Cell::ReadyToDivide 66ms 0.85% 45.12% 260ms 3.34% std::_Rb_tree::_M_clone_node (inline) 4ms 0.051% 45.18% 251ms 3.22% CellProliferativeTypesWriter::VisitCell 6ms 0.077% 45.25% 240ms 3.08% std::__cxx11::collate::do_transform 4ms 0.051% 45.30% 233ms 2.99% CellPropertyCollection::HasProperty 0 0% 45.30% 231ms 2.97% Cell::HasCellProperty (inline) 0 0% 45.30% 231ms 2.97% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 45.37% 223ms 2.87% ___vsnprintf 4ms 0.051% 45.42% 222ms 2.85% AbstractCellProperty::IsType (inline) 24ms 0.31% 45.73% 218ms 2.80% __printf_buffer 0 0% 45.73% 218ms 2.80% __vsnprintf_internal (inline) 10ms 0.13% 45.86% 212ms 2.72% MeshBasedCellPopulation::SpringsEnd (inline) 179ms 2.30% 48.16% 209ms 2.69% _int_free 3ms 0.039% 48.19% 208ms 2.67% Element::RegisterWithNodes (inline) 7ms 0.09% 48.28% 207ms 2.66% TetrahedralMesh::Clear 5ms 0.064% 48.35% 197ms 2.53% Node::AddElement 13ms 0.17% 48.52% 188ms 2.42% AbstractTetrahedralElement::CalculateJacobian 8ms 0.1% 48.62% 183ms 2.35% __printf_fp_l_buffer 0 0% 48.62% 183ms 2.35% __printf_fp_spec (inline) 65ms 0.84% 49.45% 183ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.026% 49.48% 176ms 2.26% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.013% 49.49% 173ms 2.22% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.064% 49.56% 172ms 2.21% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 49.56% 170ms 2.18% AbstractCellBasedWriter::OpenOutputFileForAppend 31ms 0.4% 49.96% 170ms 2.18% AbstractCellProperty::IsSame 39ms 0.5% 50.46% 169ms 2.17% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.46% 168ms 2.16% OutputFileHandler::OpenOutputFile 79ms 1.02% 51.47% 165ms 2.12% __printf_fp_buffer_1 0 0% 51.47% 164ms 2.11% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 51.48% 162ms 2.08% std::basic_ofstream::open (inline) 2ms 0.026% 51.51% 161ms 2.07% std::basic_filebuf::open 0 0% 51.51% 160ms 2.06% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.51% 155ms 1.99% AbstractCellBasedWriter::CloseFile 0 0% 51.51% 155ms 1.99% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 51.52% 155ms 1.99% std::basic_filebuf::close 0 0% 51.52% 155ms 1.99% std::basic_ofstream::close (inline) 11ms 0.14% 51.66% 150ms 1.93% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.19% 51.86% 149ms 1.91% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 51.86% 140ms 1.80% OutputFileHandler::CommonConstructor 0 0% 51.86% 140ms 1.80% OutputFileHandler::OutputFileHandler 23ms 0.3% 52.15% 139ms 1.79% std::type_info::operator== (inline) 1ms 0.013% 52.16% 137ms 1.76% OutputFileHandler::MakeFoldersAndReturnFullPath 137ms 1.76% 53.93% 137ms 1.76% incircle 3ms 0.039% 53.96% 132ms 1.70% alternateaxes 0 0% 53.96% 131ms 1.68% std::__basic_file::open 0 0% 53.96% 130ms 1.67% _IO_new_fopen 2ms 0.026% 53.99% 130ms 1.67% __fopen_internal (inline) 119ms 1.53% 55.52% 129ms 1.66% vertexmedian 24ms 0.31% 55.83% 128ms 1.64% AbstractTetrahedralElement::RefreshJacobian 6ms 0.077% 55.90% 127ms 1.63% Node::~Node 2ms 0.026% 55.93% 126ms 1.62% _IO_new_file_fopen 2ms 0.026% 55.96% 125ms 1.61% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.039% 55.99% 123ms 1.58% __GI__IO_file_open 2ms 0.026% 56.02% 120ms 1.54% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 56.03% 119ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 45ms 0.58% 56.61% 119ms 1.53% std::__ostream_insert 14ms 0.18% 56.79% 118ms 1.52% boost::detail::shared_count::~shared_count (inline) 0 0% 56.79% 118ms 1.52% boost::shared_ptr::~shared_ptr (inline) 0 0% 56.79% 117ms 1.50% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 56.80% 116ms 1.49% std::basic_filebuf::_M_terminate_output 1ms 0.013% 56.82% 116ms 1.49% std::basic_filebuf::overflow 77ms 0.99% 57.81% 115ms 1.48% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 57.82% 115ms 1.48% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 57.83% 114ms 1.46% std::__basic_file::xsputn 28ms 0.36% 58.19% 113ms 1.45% std::num_put::_M_insert_int 111ms 1.43% 59.62% 112ms 1.44% __GI___libc_write 110ms 1.41% 61.03% 110ms 1.41% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.026% 61.06% 106ms 1.36% std::vector::push_back (inline) 105ms 1.35% 62.41% 105ms 1.35% [libchaste_cell_based.so] 100ms 1.28% 63.69% 100ms 1.28% __libc_open64 100ms 1.28% 64.97% 100ms 1.28% std::_Rb_tree_insert_and_rebalance 49ms 0.63% 65.60% 99ms 1.27% boost::shared_ptr::shared_ptr (inline) 10ms 0.13% 65.73% 97ms 1.25% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.73% 96ms 1.23% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.73% 96ms 1.23% std::operator<< (inline) 90ms 1.16% 66.89% 95ms 1.22% boost::detail::sp_counted_base::release 10ms 0.13% 67.02% 95ms 1.22% std::vector::_M_realloc_insert 28ms 0.36% 67.38% 89ms 1.14% AbstractElement::GetNodeLocation 89ms 1.14% 68.52% 89ms 1.14% counterclockwise 89ms 1.14% 69.66% 89ms 1.14% std::_Rb_tree_increment 2ms 0.026% 69.69% 85ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 25ms 0.32% 70.01% 84ms 1.08% boost::numeric::ublas::indexing_vector_assign 4ms 0.051% 70.06% 84ms 1.08% std::_Rb_tree_const_iterator::operator++ (inline) 37ms 0.48% 70.54% 81ms 1.04% std::basic_filebuf::xsputn 76ms 0.98% 71.51% 76ms 0.98% __GI___fstatat64 1ms 0.013% 71.53% 75ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 75ms 0.96% 72.49% 75ms 0.96% std::vector::size (inline) 1ms 0.013% 72.50% 74ms 0.95% std::filesystem::create_directory 0 0% 72.50% 74ms 0.95% std::filesystem::status 66ms 0.85% 73.35% 74ms 0.95% vertexsort 5ms 0.064% 73.42% 71ms 0.91% AbstractCellPopulation::GetLocationIndexUsingCell 70ms 0.9% 74.32% 70ms 0.9% Node::GetIndex 47ms 0.6% 74.92% 70ms 0.9% malloc_consolidate 1ms 0.013% 74.93% 67ms 0.86% Cell::GetCellId 1ms 0.013% 74.95% 67ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 74.95% 66ms 0.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.95% 66ms 0.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.064% 75.01% 65ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 61ms 0.78% 75.79% 61ms 0.78% Node::rGetLocation 41ms 0.53% 76.32% 61ms 0.78% boost::numeric::ublas::c_matrix::operator() (partial-inline) 48ms 0.62% 76.94% 61ms 0.78% std::num_put::do_put 41ms 0.53% 77.46% 60ms 0.77% AbstractElement::GetNodeGlobalIndex 0 0% 77.46% 60ms 0.77% tcache_get (inline) 60ms 0.77% 78.23% 60ms 0.77% tcache_get_n (inline) 21ms 0.27% 78.50% 58ms 0.75% Determinant (inline) 4ms 0.051% 78.56% 57ms 0.73% CellPropertyCollection::AddProperty 30ms 0.39% 78.94% 56ms 0.72% AbstractTetrahedralMesh::GetElement 56ms 0.72% 79.66% 56ms 0.72% [libchaste_mesh.so] 0 0% 79.66% 55ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.051% 79.71% 54ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.71% 54ms 0.69% std::vector::vector (inline) 53ms 0.68% 80.39% 53ms 0.68% __memcpy_avx_unaligned_erms 28ms 0.36% 80.75% 53ms 0.68% hack_digit 0 0% 80.75% 52ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.75% 51ms 0.66% boost::numeric::ublas::norm_2 (inline) 18ms 0.23% 80.98% 51ms 0.66% boost::numeric::ublas::vector_norm_2::apply (inline) 48ms 0.62% 81.60% 50ms 0.64% boost::detail::shared_count::shared_count (inline) 0 0% 81.60% 50ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.60% 50ms 0.64% std::__new_allocator::destroy (inline) 0 0% 81.60% 50ms 0.64% std::allocator_traits::destroy (inline) 2ms 0.026% 81.63% 47ms 0.6% Node::ConstructNodeAttributes (inline) 47ms 0.6% 82.23% 47ms 0.6% boost::shared_ptr::operator-> (inline) 1ms 0.013% 82.24% 46ms 0.59% Node::ClearAppliedForce 46ms 0.59% 82.83% 46ms 0.59% [libstdc++.so.6.0.33] 0 0% 82.83% 45ms 0.58% std::_Vector_base::_Vector_base (inline) 14ms 0.18% 83.01% 43ms 0.55% Inverse 0 0% 83.01% 43ms 0.55% std::_Vector_base::_M_create_storage (inline) 0 0% 83.01% 41ms 0.53% BoundaryNodeWriter::Visit 27ms 0.35% 83.36% 41ms 0.53% std::basic_streambuf::xsputn 21ms 0.27% 83.63% 40ms 0.51% AbstractMesh::GetNode 0 0% 83.63% 39ms 0.5% AbstractCentreBasedCellPopulation::CreateCellPair 39ms 0.5% 84.13% 39ms 0.5% boost::numeric::ublas::c_vector::operator() 39ms 0.5% 84.63% 39ms 0.5% operator delete 39ms 0.5% 85.13% 39ms 0.5% unlink_chunk