File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6556ms, 84.06% of 7799ms total Dropped 575 nodes (cum <= 38.99ms) flat flat% sum% cum cum% 0 0% 0% 7761ms 99.51% __libc_start_call_main 0 0% 0% 7761ms 99.51% __libc_start_main_impl 0 0% 0% 7761ms 99.51% _start 0 0% 0% 7744ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7744ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7744ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7744ms 99.29% main 0 0% 0% 7707ms 98.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7707ms 98.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7707ms 98.82% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7706ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3339ms 42.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2881ms 36.94% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.051% 2856ms 36.62% MeshBasedCellPopulation::Update 1ms 0.013% 0.064% 1473ms 18.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.064% 1437ms 18.43% MutableMesh::ReMesh 0 0% 0.064% 1356ms 17.39% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.077% 1341ms 17.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.026% 0.1% 1288ms 16.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 12ms 0.15% 0.26% 1169ms 14.99% MeshBasedCellPopulation::SpringIterator::operator++ 419ms 5.37% 5.63% 954ms 12.23% std::_Rb_tree::_M_lower_bound (inline) 97ms 1.24% 6.87% 940ms 12.05% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.013% 6.89% 921ms 11.81% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.01% 904ms 11.59% CellPopulationElementWriter::Visit 10ms 0.13% 7.14% 889ms 11.40% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.038% 7.18% 858ms 11.00% AbstractTwoBodyInteractionForce::AddForceContribution 245ms 3.14% 10.32% 814ms 10.44% __dynamic_cast 34ms 0.44% 10.76% 766ms 9.82% AbstractCellPopulation::GetCellUsingLocationIndex 53ms 0.68% 11.44% 764ms 9.80% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.1% 11.54% 762ms 9.77% TetrahedralMesh::ImportFromMesher 2ms 0.026% 11.57% 757ms 9.71% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.026% 11.59% 652ms 8.36% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.60% 623ms 7.99% std::ostream::operator<< (inline) 103ms 1.32% 12.92% 622ms 7.98% std::ostream::_M_insert 39ms 0.5% 13.42% 598ms 7.67% std::map::operator[] (partial-inline) 49ms 0.63% 14.05% 592ms 7.59% operator new 3ms 0.038% 14.09% 560ms 7.18% std::set::insert (inline) 7ms 0.09% 14.18% 557ms 7.14% std::_Rb_tree::_M_insert_unique 183ms 2.35% 16.53% 539ms 6.91% __GI___libc_malloc 6ms 0.077% 16.60% 531ms 6.81% Cell::GetCellProliferativeType 31ms 0.4% 17.00% 521ms 6.68% std::__new_allocator::allocate (inline) 0 0% 17.00% 519ms 6.65% std::_Rb_tree::lower_bound (inline) 0 0% 17.00% 519ms 6.65% std::map::lower_bound (inline) 2ms 0.026% 17.03% 519ms 6.65% triangulate 0 0% 17.03% 517ms 6.63% std::allocator_traits::allocate (inline) 478ms 6.13% 23.16% 478ms 6.13% __strcmp_avx2 19ms 0.24% 23.40% 474ms 6.08% std::_Rb_tree::find (inline) 3ms 0.038% 23.44% 467ms 5.99% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.44% 463ms 5.94% delaunay 0 0% 23.44% 463ms 5.94% divconqdelaunay 4ms 0.051% 23.49% 456ms 5.85% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.49% 428ms 5.49% std::_Rb_tree::_M_create_node (inline) 0 0% 23.49% 426ms 5.46% std::set::count (inline) 0 0% 23.49% 409ms 5.24% std::_Rb_tree::_Alloc_node::operator() (inline) 181ms 2.32% 25.81% 407ms 5.22% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.53% 26.34% 405ms 5.19% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.34% 395ms 5.06% std::_Rb_tree::_M_get_node (inline) 3ms 0.038% 26.38% 393ms 5.04% NodeLocationWriter::Visit 21ms 0.27% 26.64% 393ms 5.04% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.051% 26.70% 376ms 4.82% Cell::GetMutationState 0 0% 26.70% 375ms 4.81% std::set::~set (inline) 2ms 0.026% 26.72% 365ms 4.68% std::set::set (inline) 85ms 1.09% 27.81% 360ms 4.62% std::_Rb_tree::_M_erase 20ms 0.26% 28.07% 348ms 4.46% std::_Rb_tree::_M_insert_ (inline) 347ms 4.45% 32.52% 347ms 4.45% std::_Rb_tree::_S_right (inline) 1ms 0.013% 32.53% 345ms 4.42% MeshBasedCellPopulation::GetDampingConstant 12ms 0.15% 32.68% 345ms 4.42% std::num_put::_M_insert_float 2ms 0.026% 32.71% 344ms 4.41% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.09% 32.80% 338ms 4.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.22% 33.02% 334ms 4.28% std::less::operator() (inline) 3ms 0.038% 33.06% 331ms 4.24% Cell::ReadyToDivide 37ms 0.47% 33.53% 327ms 4.19% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 33.54% 319ms 4.09% Element::Element 317ms 4.06% 37.61% 317ms 4.06% std::operator< (inline) 104ms 1.33% 38.94% 302ms 3.87% __GI___libc_free 1ms 0.013% 38.95% 299ms 3.83% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.95% 297ms 3.81% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.95% 293ms 3.76% OutputFileHandler::OpenOutputFile 9ms 0.12% 39.07% 292ms 3.74% std::__cxx11::collate::do_transform 98ms 1.26% 40.33% 289ms 3.71% std::_Rb_tree::_M_clone_node (inline) 183ms 2.35% 42.67% 283ms 3.63% _int_malloc 2ms 0.026% 42.70% 272ms 3.49% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 42.74% 268ms 3.44% ___vsnprintf 0 0% 42.74% 265ms 3.40% __vsnprintf_internal (inline) 16ms 0.21% 42.94% 264ms 3.39% divconqrecurse 6ms 0.077% 43.02% 256ms 3.28% AbstractCellProperty::IsType (inline) 34ms 0.44% 43.45% 253ms 3.24% __printf_buffer 0 0% 43.45% 253ms 3.24% std::_Rb_tree::_M_drop_node (inline) 7ms 0.09% 43.54% 252ms 3.23% std::__new_allocator::deallocate (inline) 0 0% 43.54% 251ms 3.22% std::allocator_traits::deallocate (inline) 10ms 0.13% 43.67% 244ms 3.13% CellPropertyCollection::HasProperty 72ms 0.92% 44.60% 244ms 3.13% mergehulls 0 0% 44.60% 239ms 3.06% Cell::HasCellProperty (inline) 5ms 0.064% 44.66% 221ms 2.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 12ms 0.15% 44.81% 211ms 2.71% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.051% 44.86% 210ms 2.69% Element::RegisterWithNodes (inline) 0 0% 44.86% 206ms 2.64% std::_Rb_tree::_M_put_node (inline) 1ms 0.013% 44.88% 204ms 2.62% Node::AddElement 11ms 0.14% 45.02% 203ms 2.60% __printf_fp_l_buffer 0 0% 45.02% 203ms 2.60% __printf_fp_spec (inline) 76ms 0.97% 45.99% 203ms 2.60% std::_Rb_tree::_M_get_insert_unique_pos (inline) 22ms 0.28% 46.28% 202ms 2.59% TetrahedralMesh::Clear 172ms 2.21% 48.48% 198ms 2.54% _int_free 50ms 0.64% 49.12% 196ms 2.51% AbstractCellProperty::IsSame 101ms 1.30% 50.42% 187ms 2.40% __printf_fp_buffer_1 44ms 0.56% 50.98% 181ms 2.32% TetrahedralMesh::EdgesEnd (partial-inline) 8ms 0.1% 51.08% 179ms 2.30% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.064% 51.15% 162ms 2.08% AbstractTetrahedralElement::CalculateJacobian 36ms 0.46% 51.61% 146ms 1.87% std::type_info::operator== (inline) 0 0% 51.61% 145ms 1.86% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.61% 142ms 1.82% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 51.62% 142ms 1.82% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.62% 141ms 1.81% AbstractCellBasedWriter::CloseFile 4ms 0.051% 51.67% 141ms 1.81% std::basic_filebuf::close 0 0% 51.67% 141ms 1.81% std::basic_ofstream::close (inline) 140ms 1.80% 53.47% 140ms 1.80% std::_Rb_tree_increment 1ms 0.013% 53.48% 138ms 1.77% std::basic_ofstream::open (inline) 8ms 0.1% 53.58% 137ms 1.76% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.038% 53.62% 137ms 1.76% std::basic_filebuf::open 1ms 0.013% 53.64% 133ms 1.71% OutputFileHandler::OutputFileHandler 1ms 0.013% 53.65% 132ms 1.69% OutputFileHandler::CommonConstructor 6ms 0.077% 53.72% 129ms 1.65% alternateaxes 7ms 0.09% 53.81% 127ms 1.63% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.038% 53.85% 124ms 1.59% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 53.87% 123ms 1.58% std::_Vector_base::_M_allocate (inline) 109ms 1.40% 55.26% 123ms 1.58% vertexmedian 25ms 0.32% 55.58% 119ms 1.53% AbstractTetrahedralElement::RefreshJacobian 0 0% 55.58% 119ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 0 0% 55.58% 119ms 1.53% OutputFileHandler::MakeFoldersAndReturnFullPath 119ms 1.53% 57.11% 119ms 1.53% __GI_fchmodat 0 0% 57.11% 119ms 1.53% std::filesystem::permissions 31ms 0.4% 57.51% 119ms 1.53% std::num_put::_M_insert_int 4ms 0.051% 57.56% 118ms 1.51% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.077% 57.64% 118ms 1.51% std::vector::push_back (inline) 117ms 1.50% 59.14% 117ms 1.50% incircle 59ms 0.76% 59.89% 117ms 1.50% std::__ostream_insert 116ms 1.49% 61.38% 116ms 1.49% std::_Rb_tree_insert_and_rebalance 15ms 0.19% 61.57% 115ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 61.57% 112ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.026% 61.60% 112ms 1.44% AbstractTetrahedralElement::AbstractTetrahedralElement 73ms 0.94% 62.53% 110ms 1.41% TetrahedralMesh::EdgeIterator::EdgeIterator 10ms 0.13% 62.66% 108ms 1.38% std::vector::_M_realloc_insert 5ms 0.064% 62.73% 106ms 1.36% Node::~Node 19ms 0.24% 62.97% 104ms 1.33% MeshBasedCellPopulation::SpringIterator::SpringIterator 11ms 0.14% 63.11% 104ms 1.33% boost::detail::shared_count::~shared_count (inline) 0 0% 63.11% 104ms 1.33% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 63.12% 102ms 1.31% std::__basic_file::open 0 0% 63.12% 100ms 1.28% _IO_new_fopen 1ms 0.013% 63.14% 100ms 1.28% __fopen_internal (inline) 7ms 0.09% 63.23% 99ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 63.23% 98ms 1.26% std::basic_filebuf::_M_terminate_output 2ms 0.026% 63.25% 98ms 1.26% std::basic_filebuf::overflow 96ms 1.23% 64.48% 96ms 1.23% __GI___libc_write 0 0% 64.48% 96ms 1.23% std::__basic_file::xsputn 0 0% 64.48% 96ms 1.23% std::basic_filebuf::_M_convert_to_external 0 0% 64.48% 95ms 1.22% _IO_new_file_fopen 0 0% 64.48% 94ms 1.21% __GI__IO_file_open 57ms 0.73% 65.21% 93ms 1.19% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 65.25% 93ms 1.19% std::operator<< (inline) 92ms 1.18% 66.43% 92ms 1.18% boost::detail::sp_counted_base::release 0 0% 66.43% 91ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 84ms 1.08% 67.51% 84ms 1.08% __libc_open64 35ms 0.45% 67.96% 82ms 1.05% AbstractElement::GetNodeLocation 27ms 0.35% 68.30% 82ms 1.05% boost::numeric::ublas::indexing_vector_assign 11ms 0.14% 68.44% 80ms 1.03% CellPropertyCollection::AddProperty 56ms 0.72% 69.16% 78ms 1.00% malloc_consolidate 8ms 0.1% 69.27% 76ms 0.97% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 69.27% 74ms 0.95% AbstractCellPopulation::GetLocationIndexUsingCell 74ms 0.95% 70.21% 74ms 0.95% [libchaste_cell_based.so] 73ms 0.94% 71.15% 73ms 0.94% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 71.15% 72ms 0.92% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 71.16% 72ms 0.92% std::filesystem::create_directory 49ms 0.63% 71.79% 67ms 0.86% std::basic_streambuf::xsputn 0 0% 71.79% 65ms 0.83% tcache_get (inline) 65ms 0.83% 72.62% 65ms 0.83% tcache_get_n (inline) 4ms 0.051% 72.68% 63ms 0.81% Node::ConstructNodeAttributes (inline) 63ms 0.81% 73.48% 63ms 0.81% Node::GetIndex 1ms 0.013% 73.50% 62ms 0.79% Cell::GetCellId 37ms 0.47% 73.97% 62ms 0.79% std::basic_filebuf::xsputn 1ms 0.013% 73.98% 61ms 0.78% Node::ClearAppliedForce 60ms 0.77% 74.75% 60ms 0.77% std::vector::size (inline) 54ms 0.69% 75.45% 60ms 0.77% vertexsort 7ms 0.09% 75.54% 58ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 43ms 0.55% 76.09% 57ms 0.73% AbstractElement::GetNodeGlobalIndex 36ms 0.46% 76.55% 57ms 0.73% boost::numeric::ublas::c_matrix::operator() (partial-inline) 23ms 0.29% 76.84% 56ms 0.72% Determinant (inline) 56ms 0.72% 77.56% 56ms 0.72% __GI___fstatat64 47ms 0.6% 78.16% 56ms 0.72% std::num_put::do_put 0 0% 78.16% 55ms 0.71% std::filesystem::status 54ms 0.69% 78.86% 54ms 0.69% __memcpy_avx_unaligned_erms 28ms 0.36% 79.22% 53ms 0.68% AbstractTetrahedralMesh::GetElement 53ms 0.68% 79.89% 53ms 0.68% counterclockwise 0 0% 79.89% 52ms 0.67% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 79.89% 51ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 51ms 0.65% 80.55% 51ms 0.65% [libchaste_mesh.so] 51ms 0.65% 81.20% 51ms 0.65% [libstdc++.so.6.0.33] 0 0% 81.20% 51ms 0.65% std::vector::vector (inline) 25ms 0.32% 81.52% 50ms 0.64% AbstractCellCycleModel::GetAge 0 0% 81.52% 49ms 0.63% std::_Vector_base::_M_create_storage (inline) 0 0% 81.52% 49ms 0.63% std::_Vector_base::_Vector_base (inline) 48ms 0.62% 82.14% 48ms 0.62% boost::shared_ptr::operator-> (inline) 28ms 0.36% 82.50% 48ms 0.62% hack_digit 4ms 0.051% 82.55% 47ms 0.6% NodeAttributes::NodeAttributes 0 0% 82.55% 47ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.026% 82.57% 47ms 0.6% std::_Vector_base::_M_deallocate (inline) 0 0% 82.57% 47ms 0.6% std::__new_allocator::destroy (inline) 0 0% 82.57% 47ms 0.6% std::allocator_traits::destroy (inline) 22ms 0.28% 82.86% 46ms 0.59% AbstractTetrahedralMesh::GetNumAllElements 0 0% 82.86% 45ms 0.58% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.013% 82.87% 44ms 0.56% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 1ms 0.013% 82.88% 44ms 0.56% BoundaryNodeWriter::Visit 4ms 0.051% 82.93% 44ms 0.56% Element::~Element 0 0% 82.93% 44ms 0.56% std::map::find (inline) 0 0% 82.93% 42ms 0.54% AbstractCentreBasedCellPopulation::CreateCellPair 41ms 0.53% 83.46% 41ms 0.53% __GI___mkdir 40ms 0.51% 83.97% 40ms 0.51% Node::IsDeleted 0 0% 83.97% 40ms 0.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.97% 40ms 0.51% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.97% 40ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.97% 40ms 0.51% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 7ms 0.09% 84.06% 40ms 0.51% std::_Rb_tree_header::_Rb_tree_header (inline)