File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6054ms, 86.39% of 7008ms total Dropped 517 nodes (cum <= 35.04ms) flat flat% sum% cum cum% 0 0% 0% 6976ms 99.54% __libc_start_call_main 0 0% 0% 6976ms 99.54% __libc_start_main_impl 0 0% 0% 6976ms 99.54% _start 0 0% 0% 6959ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6959ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6959ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6959ms 99.30% main 0 0% 0% 6929ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6929ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6929ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6926ms 98.83% AbstractCellBasedSimulation::Solve 1ms 0.014% 0.014% 3246ms 46.32% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.029% 0.043% 2831ms 40.40% MeshBasedCellPopulation::Update 1ms 0.014% 0.057% 2262ms 32.28% AbstractCellPopulation::WriteResultsToFiles 1ms 0.014% 0.071% 1455ms 20.76% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.071% 1413ms 20.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.071% 1321ms 18.85% MutableMesh::ReMesh 3ms 0.043% 0.11% 1235ms 17.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 26ms 0.37% 0.49% 1235ms 17.62% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.014% 0.5% 1184ms 16.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 100ms 1.43% 1.93% 982ms 14.01% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.086% 2.01% 882ms 12.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.071% 2.08% 848ms 12.10% AbstractTwoBodyInteractionForce::AddForceContribution 225ms 3.21% 5.29% 791ms 11.29% __dynamic_cast 32ms 0.46% 5.75% 783ms 11.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.029% 5.78% 760ms 10.84% CellPropertyCollection::GetPropertiesType (inline) 367ms 5.24% 11.02% 760ms 10.84% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.26% 11.27% 745ms 10.63% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.1% 11.37% 740ms 10.56% CellPopulationElementWriter::Visit 12ms 0.17% 11.54% 721ms 10.29% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.1% 11.64% 648ms 9.25% TetrahedralMesh::ImportFromMesher 3ms 0.043% 11.69% 633ms 9.03% AbstractCellProperty::IsSubType (inline) 40ms 0.57% 12.26% 604ms 8.62% operator new 100ms 1.43% 13.68% 565ms 8.06% std::_Rb_tree::~_Rb_tree (inline) 218ms 3.11% 16.80% 551ms 7.86% __GI___libc_malloc 5ms 0.071% 16.87% 527ms 7.52% std::set::insert (inline) 0 0% 16.87% 526ms 7.51% std::set::~set (inline) 6ms 0.086% 16.95% 522ms 7.45% std::_Rb_tree::_M_insert_unique 4ms 0.057% 17.01% 513ms 7.32% std::__new_allocator::allocate (inline) 0 0% 17.01% 512ms 7.31% triangulate 0 0% 17.01% 510ms 7.28% std::allocator_traits::allocate (inline) 18ms 0.26% 17.27% 509ms 7.26% std::_Rb_tree::find (inline) 3ms 0.043% 17.31% 498ms 7.11% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.057% 17.37% 484ms 6.91% Cell::GetCellProliferativeType 0 0% 17.37% 478ms 6.82% std::ostream::operator<< (inline) 70ms 1% 18.36% 474ms 6.76% std::ostream::_M_insert 0 0% 18.36% 474ms 6.76% std::set::count (inline) 62ms 0.88% 19.25% 465ms 6.64% std::_Rb_tree::_M_erase 0 0% 19.25% 447ms 6.38% delaunay 0 0% 19.25% 447ms 6.38% divconqdelaunay 431ms 6.15% 25.40% 431ms 6.15% __strcmp_evex 0 0% 25.40% 431ms 6.15% std::_Rb_tree::_M_create_node (inline) 64ms 0.91% 26.31% 418ms 5.96% std::map::operator[] (partial-inline) 0 0% 26.31% 414ms 5.91% std::_Rb_tree::_M_get_node (inline) 1ms 0.014% 26.33% 409ms 5.84% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.33% 405ms 5.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.33% 400ms 5.71% std::_Rb_tree::_M_drop_node (inline) 15ms 0.21% 26.54% 399ms 5.69% std::_Rb_tree::_Rb_tree (partial-inline) 167ms 2.38% 28.92% 379ms 5.41% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.043% 28.97% 369ms 5.27% std::set::set (inline) 74ms 1.06% 30.02% 348ms 4.97% __GI___libc_free 32ms 0.46% 30.48% 347ms 4.95% std::_Rb_tree::_M_copy (inline) 34ms 0.49% 30.96% 347ms 4.95% std::_Rb_tree::_M_insert_ (inline) 3ms 0.043% 31.01% 329ms 4.69% Cell::GetMutationState 15ms 0.21% 31.22% 321ms 4.58% std::__new_allocator::deallocate (inline) 0 0% 31.22% 320ms 4.57% NodeLocationWriter::Visit 0 0% 31.22% 318ms 4.54% std::allocator_traits::deallocate (inline) 126ms 1.80% 33.02% 300ms 4.28% std::_Rb_tree::_M_clone_node (inline) 0 0% 33.02% 292ms 4.17% std::_Rb_tree::lower_bound (inline) 0 0% 33.02% 292ms 4.17% std::map::lower_bound (inline) 2ms 0.029% 33.05% 291ms 4.15% boost::detail::shared_count::~shared_count (inline) 0 0% 33.05% 291ms 4.15% boost::shared_ptr::~shared_ptr (inline) 5ms 0.071% 33.12% 288ms 4.11% Element::Element 281ms 4.01% 37.13% 283ms 4.04% boost::detail::sp_counted_base::release 3ms 0.043% 37.17% 276ms 3.94% MeshBasedCellPopulation::GetDampingConstant 1ms 0.014% 37.19% 273ms 3.90% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.19% 273ms 3.90% std::_Rb_tree::_M_put_node (inline) 25ms 0.36% 37.54% 272ms 3.88% std::num_put::_M_insert_float 234ms 3.34% 40.88% 268ms 3.82% _int_free 4ms 0.057% 40.94% 260ms 3.71% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.2% 41.14% 255ms 3.64% std::less::operator() (inline) 8ms 0.11% 41.25% 252ms 3.60% divconqrecurse 2ms 0.029% 41.28% 251ms 3.58% Cell::ReadyToDivide 167ms 2.38% 43.66% 243ms 3.47% _int_malloc 241ms 3.44% 47.10% 241ms 3.44% std::operator< (inline) 84ms 1.20% 48.30% 239ms 3.41% mergehulls 223ms 3.18% 51.48% 223ms 3.18% [libchaste_cell_based.so] 7ms 0.1% 51.58% 220ms 3.14% std::__cxx11::collate::do_transform 3ms 0.043% 51.63% 212ms 3.03% Element::RegisterWithNodes (inline) 0 0% 51.63% 208ms 2.97% ___vsnprintf 0 0% 51.63% 208ms 2.97% __vsnprintf_internal (inline) 8ms 0.11% 51.74% 206ms 2.94% Node::AddElement 29ms 0.41% 52.15% 204ms 2.91% __printf_buffer 204ms 2.91% 55.07% 204ms 2.91% std::_Rb_tree::_S_right (inline) 4ms 0.057% 55.12% 194ms 2.77% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.1% 55.22% 193ms 2.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 10ms 0.14% 55.37% 187ms 2.67% AbstractCellProperty::IsType (inline) 1ms 0.014% 55.38% 186ms 2.65% CellProliferativeTypesWriter::VisitCell 0 0% 55.38% 185ms 2.64% Cell::HasCellProperty (inline) 3ms 0.043% 55.42% 183ms 2.61% CellPropertyCollection::HasProperty 8ms 0.11% 55.54% 181ms 2.58% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 64ms 0.91% 56.45% 169ms 2.41% std::_Rb_tree::_M_get_insert_unique_pos (inline) 20ms 0.29% 56.74% 166ms 2.37% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.014% 56.75% 157ms 2.24% __printf_fp_spec (inline) 5ms 0.071% 56.82% 156ms 2.23% __printf_fp_l_buffer 2ms 0.029% 56.85% 152ms 2.17% TetrahedralMesh::Clear 1ms 0.014% 56.86% 149ms 2.13% TetrahedralMesh::RefreshJacobianCachedData 0 0% 56.86% 146ms 2.08% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 56.86% 146ms 2.08% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.014% 56.88% 144ms 2.05% OutputFileHandler::OpenOutputFile 80ms 1.14% 58.02% 144ms 2.05% __printf_fp_buffer_1 4ms 0.057% 58.08% 141ms 2.01% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.16% 58.23% 135ms 1.93% AbstractTetrahedralElement::CalculateJacobian 135ms 1.93% 60.16% 135ms 1.93% [libchaste_mesh.so] 27ms 0.39% 60.55% 130ms 1.86% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.029% 60.57% 129ms 1.84% boost::numeric::ublas::vector_assign (inline) 0 0% 60.57% 127ms 1.81% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 60.57% 127ms 1.81% std::_Rb_tree::_M_destroy_node (inline) 0 0% 60.57% 127ms 1.81% std::__new_allocator::destroy (inline) 0 0% 60.57% 127ms 1.81% std::allocator_traits::destroy (inline) 14ms 0.2% 60.77% 125ms 1.78% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 60.77% 124ms 1.77% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.043% 60.82% 120ms 1.71% alternateaxes 49ms 0.7% 61.52% 118ms 1.68% std::__ostream_insert 101ms 1.44% 62.96% 117ms 1.67% vertexmedian 27ms 0.39% 63.34% 110ms 1.57% AbstractCellProperty::IsSame 83ms 1.18% 64.53% 109ms 1.56% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 64.53% 104ms 1.48% std::operator<< (inline) 2ms 0.029% 64.55% 103ms 1.47% std::vector::push_back (inline) 30ms 0.43% 64.98% 100ms 1.43% std::num_put::_M_insert_int 99ms 1.41% 66.40% 99ms 1.41% [libstdc++.so.6.0.33] 14ms 0.2% 66.60% 97ms 1.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 66.60% 96ms 1.37% std::_Vector_base::_M_allocate (inline) 29ms 0.41% 67.01% 95ms 1.36% boost::numeric::ublas::indexing_vector_assign 4ms 0.057% 67.07% 95ms 1.36% std::vector::_M_realloc_insert 13ms 0.19% 67.25% 93ms 1.33% AbstractTetrahedralElement::RefreshJacobian 93ms 1.33% 68.58% 93ms 1.33% std::_Rb_tree_insert_and_rebalance 92ms 1.31% 69.89% 92ms 1.31% incircle 1ms 0.014% 69.91% 91ms 1.30% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 12ms 0.17% 70.08% 83ms 1.18% std::type_info::operator== (inline) 3ms 0.043% 70.12% 82ms 1.17% AbstractTetrahedralElement::AbstractTetrahedralElement 78ms 1.11% 71.23% 78ms 1.11% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 71.23% 78ms 1.11% tcache_get (inline) 78ms 1.11% 72.35% 78ms 1.11% tcache_get_n (inline) 1ms 0.014% 72.36% 77ms 1.10% Node::~Node 11ms 0.16% 72.52% 73ms 1.04% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 72.52% 73ms 1.04% std::basic_ofstream::basic_ofstream (inline) 0 0% 72.52% 72ms 1.03% std::basic_filebuf::open 0 0% 72.52% 72ms 1.03% std::basic_ofstream::open (inline) 71ms 1.01% 73.53% 71ms 1.01% std::vector::size (inline) 3ms 0.043% 73.57% 70ms 1% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.13% 73.70% 70ms 1% TetrahedralMesh::EdgeIterator::GetNodeA 7ms 0.1% 73.80% 69ms 0.98% std::_Rb_tree_const_iterator::operator++ (inline) 25ms 0.36% 74.16% 68ms 0.97% AbstractElement::GetNodeLocation 0 0% 74.16% 68ms 0.97% Cell::GetCellId 62ms 0.88% 75.04% 68ms 0.97% vertexsort 6ms 0.086% 75.13% 66ms 0.94% CellPropertyCollection::AddProperty 2ms 0.029% 75.16% 62ms 0.88% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.16% 61ms 0.87% AbstractCellBasedWriter::CloseFile 0 0% 75.16% 61ms 0.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 75.16% 61ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 75.16% 61ms 0.87% std::basic_filebuf::close 0 0% 75.16% 61ms 0.87% std::basic_ofstream::close (inline) 59ms 0.84% 76.00% 59ms 0.84% std::_Rb_tree::_S_left (inline) 34ms 0.49% 76.48% 59ms 0.84% std::basic_filebuf::xsputn 43ms 0.61% 77.10% 59ms 0.84% std::basic_streambuf::xsputn 0 0% 77.10% 57ms 0.81% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 14ms 0.2% 77.30% 55ms 0.78% Determinant (inline) 1ms 0.014% 77.31% 53ms 0.76% OutputFileHandler::CommonConstructor 0 0% 77.31% 53ms 0.76% OutputFileHandler::OutputFileHandler 53ms 0.76% 78.07% 53ms 0.76% counterclockwise 0 0% 78.07% 51ms 0.73% OutputFileHandler::MakeFoldersAndReturnFullPath 41ms 0.59% 78.65% 51ms 0.73% malloc_consolidate 51ms 0.73% 79.38% 51ms 0.73% std::_Rb_tree_increment 42ms 0.6% 79.98% 50ms 0.71% CellPropertyCollection::GetProperty 49ms 0.7% 80.68% 49ms 0.7% __memcpy_avx512_unaligned_erms 1ms 0.014% 80.69% 49ms 0.7% std::__basic_file::open 0 0% 80.69% 48ms 0.68% _IO_new_fopen 0 0% 80.69% 48ms 0.68% __fopen_internal (inline) 34ms 0.49% 81.18% 48ms 0.68% boost::numeric::ublas::c_matrix::operator() 0 0% 81.18% 48ms 0.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.18% 48ms 0.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.18% 47ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.057% 81.24% 47ms 0.67% Node::ConstructNodeAttributes (inline) 0 0% 81.24% 47ms 0.67% _IO_new_file_fopen 0 0% 81.24% 47ms 0.67% __GI__IO_file_open 0 0% 81.24% 46ms 0.66% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 45ms 0.64% 81.88% 46ms 0.66% __libc_open64 1ms 0.014% 81.89% 46ms 0.66% std::_Vector_base::_M_deallocate (inline) 24ms 0.34% 82.23% 45ms 0.64% AbstractTetrahedralMesh::GetElement 0 0% 82.23% 45ms 0.64% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 45ms 0.64% 82.88% 45ms 0.64% Node::rGetLocation 31ms 0.44% 83.32% 45ms 0.64% boost::shared_ptr::shared_ptr (inline) 7ms 0.1% 83.42% 44ms 0.63% Inverse 0 0% 83.42% 44ms 0.63% Node::ClearAppliedForce 1ms 0.014% 83.43% 44ms 0.63% std::basic_filebuf::_M_terminate_output 1ms 0.014% 83.45% 44ms 0.63% std::basic_filebuf::overflow 13ms 0.19% 83.63% 43ms 0.61% AbstractElement::GetNodeGlobalIndex 0 0% 83.63% 43ms 0.61% FilesystemPermissions::SetFilePermissions (inline) 43ms 0.61% 84.25% 43ms 0.61% Node::GetIndex 42ms 0.6% 84.85% 43ms 0.61% __GI___libc_write 43ms 0.61% 85.46% 43ms 0.61% __GI_fchmodat 0 0% 85.46% 43ms 0.61% std::__basic_file::xsputn 0 0% 85.46% 43ms 0.61% std::basic_filebuf::_M_convert_to_external 0 0% 85.46% 43ms 0.61% std::filesystem::permissions 29ms 0.41% 85.87% 41ms 0.59% std::num_put::do_put 0 0% 85.87% 40ms 0.57% std::vector::vector (inline) 0 0% 85.87% 39ms 0.56% std::map::map (inline) 0 0% 85.87% 39ms 0.56% std::map::~map (inline) 0 0% 85.87% 37ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.87% 37ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 36ms 0.51% 86.39% 36ms 0.51% tcache_put (inline)