File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6811ms, 84.91% of 8021ms total Dropped 599 nodes (cum <= 40.10ms) flat flat% sum% cum cum% 0 0% 0% 7985ms 99.55% __libc_start_call_main 0 0% 0% 7985ms 99.55% __libc_start_main_impl 0 0% 0% 7985ms 99.55% _start 0 0% 0% 7968ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7968ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7968ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7968ms 99.34% main 0 0% 0% 7924ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7924ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7924ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7920ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3392ms 42.29% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2946ms 36.73% MeshBasedCellPopulation::Update 0 0% 0% 2934ms 36.58% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 1588ms 19.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.012% 1455ms 18.14% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.012% 1435ms 17.89% MutableMesh::ReMesh 1ms 0.012% 0.025% 1427ms 17.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.037% 0.062% 1375ms 17.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.3% 1257ms 15.67% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.41% 1.71% 1011ms 12.60% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.73% 1001ms 12.48% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.037% 1.77% 967ms 12.06% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 412ms 5.14% 6.91% 958ms 11.94% std::_Rb_tree::_M_lower_bound (inline) 289ms 3.60% 10.51% 954ms 11.89% __dynamic_cast 11ms 0.14% 10.65% 900ms 11.22% CellPropertyCollection::GetPropertiesType (inline) 43ms 0.54% 11.18% 873ms 10.88% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.11% 11.30% 839ms 10.46% CellPopulationElementWriter::Visit 6ms 0.075% 11.37% 807ms 10.06% MeshBasedCellPopulation::AcceptCellWriter 25ms 0.31% 11.68% 782ms 9.75% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.73% 743ms 9.26% AbstractCellProperty::IsSubType (inline) 12ms 0.15% 11.88% 709ms 8.84% TetrahedralMesh::ImportFromMesher 60ms 0.75% 12.63% 600ms 7.48% std::map::operator[] (partial-inline) 2ms 0.025% 12.65% 594ms 7.41% std::ostream::operator<< (inline) 107ms 1.33% 13.99% 589ms 7.34% std::ostream::_M_insert 28ms 0.35% 14.34% 576ms 7.18% operator new 2ms 0.025% 14.36% 557ms 6.94% triangulate 177ms 2.21% 16.57% 541ms 6.74% __GI___libc_malloc 2ms 0.025% 16.59% 534ms 6.66% Cell::GetCellProliferativeType 30ms 0.37% 16.97% 523ms 6.52% std::_Rb_tree::find (inline) 8ms 0.1% 17.07% 512ms 6.38% std::set::insert (inline) 510ms 6.36% 23.43% 510ms 6.36% __strcmp_avx2 5ms 0.062% 23.49% 509ms 6.35% LegacyCellProliferativeTypesWriter::VisitCell 28ms 0.35% 23.84% 508ms 6.33% std::__new_allocator::allocate (inline) 11ms 0.14% 23.97% 504ms 6.28% std::_Rb_tree::_M_insert_unique 0 0% 23.97% 502ms 6.26% std::allocator_traits::allocate (inline) 0 0% 23.97% 501ms 6.25% delaunay 0 0% 23.97% 499ms 6.22% divconqdelaunay 0 0% 23.97% 488ms 6.08% std::_Rb_tree::lower_bound (inline) 0 0% 23.97% 488ms 6.08% std::map::lower_bound (inline) 242ms 3.02% 26.99% 484ms 6.03% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.99% 465ms 5.80% std::set::count (inline) 3ms 0.037% 27.03% 424ms 5.29% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.03% 406ms 5.06% std::_Rb_tree::_M_create_node (inline) 37ms 0.46% 27.49% 389ms 4.85% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.49% 379ms 4.73% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.49% 373ms 4.65% std::_Rb_tree::_M_get_node (inline) 0 0% 27.49% 366ms 4.56% std::set::~set (inline) 30ms 0.37% 27.86% 365ms 4.55% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.012% 27.88% 357ms 4.45% Cell::GetMutationState 1ms 0.012% 27.89% 357ms 4.45% NodeLocationWriter::Visit 8ms 0.1% 27.99% 356ms 4.44% std::less::operator() (inline) 348ms 4.34% 32.33% 348ms 4.34% std::operator< (inline) 66ms 0.82% 33.15% 347ms 4.33% std::_Rb_tree::_M_erase 337ms 4.20% 37.35% 337ms 4.20% std::_Rb_tree::_S_right (inline) 0 0% 37.35% 331ms 4.13% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.35% 331ms 4.13% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.35% 329ms 4.10% OutputFileHandler::OpenOutputFile 31ms 0.39% 37.74% 327ms 4.08% std::num_put::_M_insert_float 1ms 0.012% 37.75% 322ms 4.01% std::set::set (inline) 17ms 0.21% 37.96% 314ms 3.91% std::_Rb_tree::_M_insert_ (inline) 38ms 0.47% 38.44% 304ms 3.79% std::_Rb_tree::_M_copy (inline) 8ms 0.1% 38.54% 303ms 3.78% Element::Element 8ms 0.1% 38.64% 293ms 3.65% Cell::ReadyToDivide 189ms 2.36% 40.99% 289ms 3.60% _int_malloc 9ms 0.11% 41.10% 289ms 3.60% divconqrecurse 2ms 0.025% 41.13% 281ms 3.50% MeshBasedCellPopulation::GetDampingConstant 88ms 1.10% 42.23% 281ms 3.50% __GI___libc_free 2ms 0.025% 42.25% 279ms 3.48% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.087% 42.34% 270ms 3.37% AbstractCellPopulation::IsCellAttachedToLocationIndex 78ms 0.97% 43.31% 263ms 3.28% mergehulls 82ms 1.02% 44.33% 260ms 3.24% std::_Rb_tree::_M_clone_node (inline) 4ms 0.05% 44.38% 252ms 3.14% std::__cxx11::collate::do_transform 3ms 0.037% 44.42% 251ms 3.13% CellProliferativeTypesWriter::VisitCell 0 0% 44.42% 251ms 3.13% std::_Rb_tree::_M_drop_node (inline) 10ms 0.12% 44.55% 250ms 3.12% std::__new_allocator::deallocate (inline) 0 0% 44.55% 244ms 3.04% std::allocator_traits::deallocate (inline) 1ms 0.012% 44.56% 235ms 2.93% ___vsnprintf 2ms 0.025% 44.58% 234ms 2.92% __vsnprintf_internal (inline) 33ms 0.41% 44.99% 228ms 2.84% __printf_buffer 4ms 0.05% 45.04% 225ms 2.81% AbstractCellProperty::IsType (inline) 9ms 0.11% 45.16% 224ms 2.79% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.012% 45.17% 223ms 2.78% CellPropertyCollection::HasProperty 0 0% 45.17% 221ms 2.76% Cell::HasCellProperty (inline) 4ms 0.05% 45.22% 207ms 2.58% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 45.36% 202ms 2.52% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 45.36% 200ms 2.49% std::_Rb_tree::_M_put_node (inline) 155ms 1.93% 47.29% 193ms 2.41% _int_free 34ms 0.42% 47.71% 189ms 2.36% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.15% 47.86% 188ms 2.34% TetrahedralMesh::Clear 10ms 0.12% 47.99% 186ms 2.32% AbstractTetrahedralElement::CalculateJacobian 12ms 0.15% 48.14% 184ms 2.29% __printf_fp_l_buffer 0 0% 48.14% 184ms 2.29% __printf_fp_spec (inline) 6ms 0.075% 48.21% 180ms 2.24% Element::RegisterWithNodes (inline) 2ms 0.025% 48.24% 180ms 2.24% OutputFileHandler::OutputFileHandler 58ms 0.72% 48.96% 179ms 2.23% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.012% 48.97% 178ms 2.22% OutputFileHandler::CommonConstructor 43ms 0.54% 49.51% 174ms 2.17% AbstractCellProperty::IsSame 0 0% 49.51% 173ms 2.16% std::basic_ofstream::basic_ofstream (inline) 3ms 0.037% 49.54% 171ms 2.13% Node::AddElement 102ms 1.27% 50.82% 169ms 2.11% __printf_fp_buffer_1 1ms 0.012% 50.83% 168ms 2.09% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.037% 50.87% 168ms 2.09% std::basic_filebuf::open 0 0% 50.87% 168ms 2.09% std::basic_ofstream::open (inline) 110ms 1.37% 52.24% 163ms 2.03% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.012% 52.25% 159ms 1.98% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.25% 157ms 1.96% AbstractCellBasedWriter::CloseFile 2ms 0.025% 52.28% 157ms 1.96% std::basic_filebuf::close 0 0% 52.28% 157ms 1.96% std::basic_ofstream::close (inline) 4ms 0.05% 52.33% 150ms 1.87% boost::numeric::ublas::vector_assign (inline) 9ms 0.11% 52.44% 149ms 1.86% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 52.44% 145ms 1.81% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.12% 52.56% 141ms 1.76% AbstractTetrahedralElement::CalculateInverseJacobian 25ms 0.31% 52.87% 141ms 1.76% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.012% 52.89% 141ms 1.76% alternateaxes 130ms 1.62% 54.51% 140ms 1.75% vertexmedian 17ms 0.21% 54.72% 136ms 1.70% AbstractTetrahedralElement::RefreshJacobian 0 0% 54.72% 131ms 1.63% FilesystemPermissions::SetFilePermissions (inline) 53ms 0.66% 55.38% 131ms 1.63% std::__ostream_insert 2ms 0.025% 55.40% 131ms 1.63% std::filesystem::permissions 29ms 0.36% 55.77% 131ms 1.63% std::type_info::operator== (inline) 1ms 0.012% 55.78% 130ms 1.62% std::_Vector_base::_M_allocate (inline) 129ms 1.61% 57.39% 129ms 1.61% __GI_fchmodat 1ms 0.012% 57.40% 128ms 1.60% std::__basic_file::open 6ms 0.075% 57.47% 127ms 1.58% Node::~Node 2ms 0.025% 57.50% 127ms 1.58% _IO_new_fopen 0 0% 57.50% 125ms 1.56% __fopen_internal (inline) 4ms 0.05% 57.55% 124ms 1.55% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.025% 57.57% 123ms 1.53% _IO_new_file_fopen 1ms 0.012% 57.59% 121ms 1.51% __GI__IO_file_open 2ms 0.025% 57.61% 119ms 1.48% std::basic_filebuf::_M_convert_to_external 0 0% 57.61% 119ms 1.48% std::basic_filebuf::_M_terminate_output 0 0% 57.61% 119ms 1.48% std::basic_filebuf::overflow 65ms 0.81% 58.42% 117ms 1.46% boost::shared_ptr::shared_ptr (inline) 117ms 1.46% 59.88% 117ms 1.46% incircle 0 0% 59.88% 117ms 1.46% std::__basic_file::xsputn 115ms 1.43% 61.31% 116ms 1.45% __GI___libc_write 109ms 1.36% 62.67% 110ms 1.37% __libc_open64 1ms 0.012% 62.69% 106ms 1.32% std::operator<< (inline) 36ms 0.45% 63.13% 105ms 1.31% boost::numeric::ublas::indexing_vector_assign 104ms 1.30% 64.43% 104ms 1.30% std::_Rb_tree_insert_and_rebalance 45ms 0.56% 64.99% 103ms 1.28% AbstractElement::GetNodeLocation 8ms 0.1% 65.09% 103ms 1.28% std::vector::push_back (inline) 8ms 0.1% 65.19% 102ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 65.19% 102ms 1.27% boost::shared_ptr::~shared_ptr (inline) 6ms 0.075% 65.27% 98ms 1.22% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.27% 65.54% 97ms 1.21% std::num_put::_M_insert_int 96ms 1.20% 66.74% 96ms 1.20% [libchaste_cell_based.so] 0 0% 66.74% 95ms 1.18% AbstractCellPopulation::Iterator::operator++ (inline) 69ms 0.86% 67.60% 94ms 1.17% malloc_consolidate 10ms 0.12% 67.72% 92ms 1.15% std::vector::_M_realloc_insert 6ms 0.075% 67.80% 91ms 1.13% std::_Rb_tree_const_iterator::operator++ (inline) 91ms 1.13% 68.93% 91ms 1.13% std::_Rb_tree_increment 88ms 1.10% 70.03% 88ms 1.10% __GI___fstatat64 84ms 1.05% 71.08% 88ms 1.10% boost::detail::sp_counted_base::release 4ms 0.05% 71.13% 87ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.012% 71.14% 86ms 1.07% std::filesystem::status 0 0% 71.14% 85ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 71.16% 85ms 1.06% std::filesystem::create_directory 1ms 0.012% 71.18% 81ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 79ms 0.98% 72.16% 79ms 0.98% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 36ms 0.45% 72.61% 76ms 0.95% std::basic_filebuf::xsputn 0 0% 72.61% 75ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.61% 73ms 0.91% tcache_get (inline) 73ms 0.91% 73.52% 73ms 0.91% tcache_get_n (inline) 1ms 0.012% 73.53% 72ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.012% 73.54% 71ms 0.89% Cell::GetCellId 71ms 0.89% 74.43% 71ms 0.89% counterclockwise 69ms 0.86% 75.29% 69ms 0.86% Node::GetIndex 53ms 0.66% 75.95% 68ms 0.85% AbstractElement::GetNodeGlobalIndex 43ms 0.54% 76.49% 66ms 0.82% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.012% 76.50% 64ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.50% 64ms 0.8% std::vector::vector (inline) 0 0% 76.50% 62ms 0.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.50% 62ms 0.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 76.50% 61ms 0.76% std::_Vector_base::_Vector_base (inline) 60ms 0.75% 77.25% 60ms 0.75% [libchaste_mesh.so] 46ms 0.57% 77.82% 60ms 0.75% std::num_put::do_put 60ms 0.75% 78.57% 60ms 0.75% std::vector::size (inline) 0 0% 78.57% 59ms 0.74% std::_Vector_base::_M_create_storage (inline) 5ms 0.062% 78.63% 58ms 0.72% Node::ConstructNodeAttributes (inline) 51ms 0.64% 79.27% 57ms 0.71% vertexsort 1ms 0.012% 79.28% 56ms 0.7% BoundaryNodeWriter::Visit 13ms 0.16% 79.44% 54ms 0.67% Determinant (inline) 1ms 0.012% 79.45% 54ms 0.67% Node::ClearAppliedForce 51ms 0.64% 80.09% 52ms 0.65% boost::detail::shared_count::shared_count (inline) 3ms 0.037% 80.13% 52ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.062% 80.19% 51ms 0.64% CellPropertyCollection::AddProperty 51ms 0.64% 80.83% 51ms 0.64% boost::numeric::ublas::c_vector::operator() 0 0% 80.83% 51ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.83% 51ms 0.64% std::__new_allocator::destroy (inline) 0 0% 80.83% 51ms 0.64% std::allocator_traits::destroy (inline) 49ms 0.61% 81.44% 49ms 0.61% __memcpy_avx_unaligned_erms 33ms 0.41% 81.85% 49ms 0.61% std::basic_streambuf::xsputn 0 0% 81.85% 48ms 0.6% std::map::find (inline) 46ms 0.57% 82.42% 46ms 0.57% Node::rGetLocation 0 0% 82.42% 46ms 0.57% std::map::map (inline) 21ms 0.26% 82.68% 45ms 0.56% AbstractTetrahedralMesh::GetElement 45ms 0.56% 83.24% 45ms 0.56% [libstdc++.so.6.0.33] 45ms 0.56% 83.81% 45ms 0.56% __GI___mkdir 2ms 0.025% 83.83% 45ms 0.56% std::_Vector_base::_M_deallocate (inline) 0 0% 83.83% 43ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 43ms 0.54% 84.37% 43ms 0.54% boost::shared_ptr::operator-> (inline) 23ms 0.29% 84.65% 43ms 0.54% hack_digit 0 0% 84.65% 42ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 84.65% 42ms 0.52% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.012% 84.67% 42ms 0.52% NodeAttributes::NodeAttributes 0 0% 84.67% 42ms 0.52% _dl_init 0 0% 84.67% 42ms 0.52% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 84.91% 42ms 0.52% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.91% 42ms 0.52% call_init (inline)