File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6552ms, 85.23% of 7687ms total Dropped 560 nodes (cum <= 38.44ms) flat flat% sum% cum cum% 0 0% 0% 7651ms 99.53% __libc_start_call_main 0 0% 0% 7651ms 99.53% __libc_start_main_impl 0 0% 0% 7651ms 99.53% _start 0 0% 0% 7636ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7636ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7636ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7636ms 99.34% main 0 0% 0% 7597ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7597ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7597ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7595ms 98.80% AbstractCellBasedSimulation::Solve 0 0% 0% 3309ms 43.05% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2949ms 38.36% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.026% 2851ms 37.09% MeshBasedCellPopulation::Update 0 0% 0.026% 1413ms 18.38% MutableMesh::ReMesh 1ms 0.013% 0.039% 1384ms 18.00% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.052% 1330ms 17.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.25% 0.3% 1223ms 15.91% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.013% 0.31% 1160ms 15.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.039% 0.35% 1117ms 14.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 10ms 0.13% 0.48% 1072ms 13.95% CellPropertyCollection::GetPropertiesType (inline) 113ms 1.47% 1.95% 1016ms 13.22% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 1.98% 1006ms 13.09% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 459ms 5.97% 7.95% 904ms 11.76% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.052% 8.00% 896ms 11.66% CellPopulationElementWriter::Visit 5ms 0.065% 8.07% 870ms 11.32% AbstractCellProperty::IsSubType (inline) 206ms 2.68% 10.75% 869ms 11.30% __dynamic_cast 7ms 0.091% 10.84% 856ms 11.14% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.1% 10.94% 739ms 9.61% TetrahedralMesh::ImportFromMesher 39ms 0.51% 11.45% 721ms 9.38% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.026% 11.47% 706ms 9.18% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.026% 11.50% 650ms 8.46% Cell::GetCellProliferativeType 32ms 0.42% 11.92% 623ms 8.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.026% 11.94% 618ms 8.04% std::ostream::operator<< (inline) 112ms 1.46% 13.40% 616ms 8.01% std::ostream::_M_insert 42ms 0.55% 13.95% 563ms 7.32% operator new 239ms 3.11% 17.05% 544ms 7.08% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.25% 17.30% 531ms 6.91% std::_Rb_tree::find (inline) 36ms 0.47% 17.77% 525ms 6.83% std::__new_allocator::allocate (inline) 0 0% 17.77% 521ms 6.78% std::allocator_traits::allocate (inline) 6ms 0.078% 17.85% 515ms 6.70% LegacyCellProliferativeTypesWriter::VisitCell 49ms 0.64% 18.49% 514ms 6.69% std::map::operator[] (partial-inline) 7ms 0.091% 18.58% 513ms 6.67% std::set::insert (inline) 183ms 2.38% 20.96% 510ms 6.63% __GI___libc_malloc 8ms 0.1% 21.06% 506ms 6.58% std::_Rb_tree::_M_insert_unique 1ms 0.013% 21.07% 503ms 6.54% triangulate 0 0% 21.07% 487ms 6.34% std::set::count (inline) 0 0% 21.07% 461ms 6.00% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 21.09% 445ms 5.79% AbstractCellBasedSimulation::DoCellBirth 7ms 0.091% 21.18% 443ms 5.76% Cell::GetMutationState 0 0% 21.18% 434ms 5.65% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 21.18% 426ms 5.54% delaunay 0 0% 21.18% 426ms 5.54% std::_Rb_tree::_M_get_node (inline) 0 0% 21.18% 425ms 5.53% divconqdelaunay 422ms 5.49% 26.67% 422ms 5.49% __strcmp_avx2 0 0% 26.67% 412ms 5.36% std::_Rb_tree::lower_bound (inline) 0 0% 26.67% 412ms 5.36% std::map::lower_bound (inline) 35ms 0.46% 27.12% 400ms 5.20% std::_Rb_tree::~_Rb_tree (inline) 24ms 0.31% 27.44% 385ms 5.01% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.44% 366ms 4.76% std::set::~set (inline) 84ms 1.09% 28.53% 363ms 4.72% std::_Rb_tree::_M_erase 3ms 0.039% 28.57% 357ms 4.64% NodeLocationWriter::Visit 14ms 0.18% 28.75% 346ms 4.50% std::less::operator() (inline) 2ms 0.026% 28.78% 339ms 4.41% std::set::set (inline) 1ms 0.013% 28.79% 336ms 4.37% MeshBasedCellPopulation::GetDampingConstant 0 0% 28.79% 335ms 4.36% AbstractCentreBasedCellPopulation::GetDampingConstant 332ms 4.32% 33.11% 332ms 4.32% std::operator< (inline) 41ms 0.53% 33.64% 324ms 4.21% std::_Rb_tree::_M_copy (inline) 15ms 0.2% 33.84% 320ms 4.16% std::_Rb_tree::_M_insert_ (inline) 10ms 0.13% 33.97% 317ms 4.12% Element::Element 129ms 1.68% 35.64% 317ms 4.12% __GI___libc_free 0 0% 35.64% 315ms 4.10% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 35.64% 315ms 4.10% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 28ms 0.36% 36.01% 312ms 4.06% std::num_put::_M_insert_float 0 0% 36.01% 310ms 4.03% OutputFileHandler::OpenOutputFile 7ms 0.091% 36.10% 307ms 3.99% Cell::ReadyToDivide 4ms 0.052% 36.15% 296ms 3.85% CellProliferativeTypesWriter::VisitCell 64ms 0.83% 36.98% 279ms 3.63% std::_Rb_tree::_M_clone_node (inline) 3ms 0.039% 37.02% 265ms 3.45% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.21% 37.23% 263ms 3.42% std::__new_allocator::deallocate (inline) 0 0% 37.23% 260ms 3.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 37.23% 260ms 3.38% std::allocator_traits::deallocate (inline) 182ms 2.37% 39.60% 247ms 3.21% _int_malloc 6ms 0.078% 39.68% 239ms 3.11% std::__cxx11::collate::do_transform 230ms 2.99% 42.67% 230ms 2.99% std::_Rb_tree::_S_right (inline) 5ms 0.065% 42.73% 226ms 2.94% ___vsnprintf 10ms 0.13% 42.86% 225ms 2.93% divconqrecurse 0 0% 42.86% 221ms 2.87% __vsnprintf_internal (inline) 26ms 0.34% 43.20% 220ms 2.86% __printf_buffer 6ms 0.078% 43.28% 217ms 2.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 43.28% 212ms 2.76% std::_Rb_tree::_M_put_node (inline) 67ms 0.87% 44.15% 209ms 2.72% mergehulls 6ms 0.078% 44.23% 208ms 2.71% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.22% 44.45% 208ms 2.71% TetrahedralMesh::Clear 6ms 0.078% 44.53% 190ms 2.47% Element::RegisterWithNodes (inline) 166ms 2.16% 46.69% 188ms 2.45% _int_free 1ms 0.013% 46.70% 181ms 2.35% Node::AddElement 5ms 0.065% 46.77% 181ms 2.35% __printf_fp_l_buffer 0 0% 46.77% 181ms 2.35% __printf_fp_spec (inline) 67ms 0.87% 47.64% 178ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 10ms 0.13% 47.77% 173ms 2.25% AbstractTetrahedralElement::CalculateJacobian 96ms 1.25% 49.02% 172ms 2.24% __printf_fp_buffer_1 12ms 0.16% 49.17% 159ms 2.07% CellPropertyCollection::HasProperty 0 0% 49.17% 157ms 2.04% Cell::HasCellProperty (inline) 11ms 0.14% 49.32% 150ms 1.95% MeshBasedCellPopulation::SpringsEnd (inline) 63ms 0.82% 50.14% 149ms 1.94% std::__ostream_insert 2ms 0.026% 50.16% 148ms 1.93% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.091% 50.25% 146ms 1.90% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 50.25% 146ms 1.90% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 50.27% 145ms 1.89% boost::numeric::ublas::vector_assign (inline) 35ms 0.46% 50.72% 143ms 1.86% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.72% 142ms 1.85% AbstractCellPopulation::CloseRoundRobinWritersFiles 11ms 0.14% 50.87% 141ms 1.83% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 50.88% 141ms 1.83% std::basic_filebuf::close 1ms 0.013% 50.89% 140ms 1.82% std::basic_filebuf::open 0 0% 50.89% 140ms 1.82% std::basic_ofstream::open (inline) 0 0% 50.89% 139ms 1.81% AbstractCellBasedWriter::CloseFile 139ms 1.81% 52.70% 139ms 1.81% std::_Rb_tree_increment 0 0% 52.70% 139ms 1.81% std::basic_ofstream::close (inline) 16ms 0.21% 52.91% 137ms 1.78% AbstractTetrahedralElement::RefreshJacobian 5ms 0.065% 52.97% 136ms 1.77% AbstractTetrahedralElement::CalculateInverseJacobian 37ms 0.48% 53.45% 134ms 1.74% std::num_put::_M_insert_int 0 0% 53.45% 133ms 1.73% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 53.47% 133ms 1.73% std::filesystem::permissions 132ms 1.72% 55.18% 132ms 1.72% __GI_fchmodat 0 0% 55.18% 130ms 1.69% OutputFileHandler::OutputFileHandler 0 0% 55.18% 129ms 1.68% OutputFileHandler::CommonConstructor 0 0% 55.18% 124ms 1.61% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.026% 55.21% 123ms 1.60% AbstractTetrahedralElement::AbstractTetrahedralElement 24ms 0.31% 55.52% 120ms 1.56% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 55.54% 117ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 55.54% 117ms 1.52% std::operator<< (inline) 3ms 0.039% 55.57% 116ms 1.51% alternateaxes 17ms 0.22% 55.80% 115ms 1.50% boost::detail::shared_count::~shared_count (inline) 0 0% 55.80% 115ms 1.50% boost::shared_ptr::~shared_ptr (inline) 27ms 0.35% 56.15% 114ms 1.48% boost::numeric::ublas::indexing_vector_assign 5ms 0.065% 56.21% 114ms 1.48% std::vector::push_back (inline) 104ms 1.35% 57.56% 113ms 1.47% vertexmedian 10ms 0.13% 57.69% 112ms 1.46% Node::~Node 1ms 0.013% 57.71% 112ms 1.46% std::__basic_file::open 0 0% 57.71% 111ms 1.44% _IO_new_fopen 0 0% 57.71% 111ms 1.44% __fopen_internal (inline) 0 0% 57.71% 110ms 1.43% _IO_new_file_fopen 2ms 0.026% 57.73% 110ms 1.43% __GI__IO_file_open 54ms 0.7% 58.44% 107ms 1.39% AbstractCellProperty::IsType (inline) 60ms 0.78% 59.22% 106ms 1.38% AbstractElement::GetNodeLocation 11ms 0.14% 59.36% 102ms 1.33% std::vector::_M_realloc_insert 97ms 1.26% 60.62% 97ms 1.26% __libc_open64 1ms 0.013% 60.63% 97ms 1.26% std::basic_filebuf::_M_terminate_output 1ms 0.013% 60.65% 97ms 1.26% std::basic_filebuf::overflow 45ms 0.59% 61.23% 96ms 1.25% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 61.25% 96ms 1.25% std::_Vector_base::_M_allocate (inline) 2ms 0.026% 61.27% 96ms 1.25% std::__basic_file::xsputn 0 0% 61.27% 96ms 1.25% std::basic_filebuf::_M_convert_to_external 14ms 0.18% 61.45% 95ms 1.24% MeshBasedCellPopulation::SpringIterator::SpringIterator 94ms 1.22% 62.68% 94ms 1.22% boost::detail::sp_counted_base::release 94ms 1.22% 63.90% 94ms 1.22% incircle 94ms 1.22% 65.12% 94ms 1.22% std::_Rb_tree_insert_and_rebalance 71ms 0.92% 66.05% 93ms 1.21% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 93ms 1.21% 67.26% 93ms 1.21% __GI___libc_write 4ms 0.052% 67.31% 85ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 63ms 0.82% 68.13% 85ms 1.11% std::basic_streambuf::xsputn 84ms 1.09% 69.22% 84ms 1.09% [libchaste_cell_based.so] 1ms 0.013% 69.23% 82ms 1.07% Cell::GetCellId 0 0% 69.23% 80ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 44ms 0.57% 69.81% 79ms 1.03% std::basic_filebuf::xsputn 73ms 0.95% 70.76% 79ms 1.03% vertexsort 11ms 0.14% 70.90% 73ms 0.95% CellPropertyCollection::AddProperty 56ms 0.73% 71.63% 71ms 0.92% AbstractElement::GetNodeGlobalIndex 0 0% 71.63% 70ms 0.91% tcache_get (inline) 70ms 0.91% 72.54% 70ms 0.91% tcache_get_n (inline) 65ms 0.85% 73.38% 65ms 0.85% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 73.40% 63ms 0.82% AbstractCellPopulation::GetLocationIndexUsingCell 5ms 0.065% 73.46% 63ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 63ms 0.82% 74.28% 63ms 0.82% __GI___fstatat64 1ms 0.013% 74.29% 63ms 0.82% std::filesystem::status 31ms 0.4% 74.70% 62ms 0.81% AbstractTetrahedralMesh::GetElement 0 0% 74.70% 61ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.70% 61ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.039% 74.74% 60ms 0.78% AbstractCentreBasedCellPopulation::CreateCellPair 59ms 0.77% 75.50% 59ms 0.77% Node::GetIndex 59ms 0.77% 76.27% 59ms 0.77% __memcpy_avx_unaligned_erms 0 0% 76.27% 58ms 0.75% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 3ms 0.039% 76.31% 58ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.31% 58ms 0.75% std::filesystem::create_directory 43ms 0.56% 76.87% 58ms 0.75% std::num_put::do_put 57ms 0.74% 77.61% 57ms 0.74% [libchaste_mesh.so] 54ms 0.7% 78.31% 54ms 0.7% boost::numeric::ublas::c_vector::operator() (partial-inline) 53ms 0.69% 79.00% 53ms 0.69% CellProperty::GetTypeId 2ms 0.026% 79.03% 53ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.03% 52ms 0.68% std::map::map (inline) 52ms 0.68% 79.71% 52ms 0.68% std::vector::size (inline) 1ms 0.013% 79.72% 51ms 0.66% BoundaryNodeWriter::Visit 49ms 0.64% 80.36% 51ms 0.66% boost::detail::shared_count::shared_count (inline) 12ms 0.16% 80.51% 48ms 0.62% AbstractMesh::GetVectorFromAtoB 36ms 0.47% 80.98% 48ms 0.62% CellPropertyCollection::GetProperty 1ms 0.013% 80.99% 48ms 0.62% Node::ConstructNodeAttributes (inline) 0 0% 80.99% 48ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.039% 81.03% 48ms 0.62% std::_Vector_base::_M_deallocate (inline) 0 0% 81.03% 48ms 0.62% std::__new_allocator::destroy (inline) 0 0% 81.03% 48ms 0.62% std::allocator_traits::destroy (inline) 0 0% 81.03% 47ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.03% 47ms 0.61% Node::ClearAppliedForce 25ms 0.33% 81.36% 47ms 0.61% boost::numeric::ublas::c_matrix::operator() (partial-inline) 47ms 0.61% 81.97% 47ms 0.61% std::ostream::sentry::sentry 45ms 0.59% 82.55% 45ms 0.59% counterclockwise 31ms 0.4% 82.96% 45ms 0.59% malloc_consolidate 1ms 0.013% 82.97% 44ms 0.57% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 0 0% 82.97% 44ms 0.57% boost::numeric::ublas::norm_2 (inline) 44ms 0.57% 83.54% 44ms 0.57% boost::numeric::ublas::same_impl_ex 15ms 0.2% 83.74% 44ms 0.57% boost::numeric::ublas::vector_norm_2::apply (inline) 43ms 0.56% 84.30% 43ms 0.56% boost::shared_ptr::operator-> (inline) 2ms 0.026% 84.32% 41ms 0.53% Element::~Element 29ms 0.38% 84.70% 41ms 0.53% hack_digit 40ms 0.52% 85.22% 40ms 0.52% [libstdc++.so.6.0.33] 0 0% 85.22% 40ms 0.52% std::vector::vector (inline) 0 0% 85.22% 39ms 0.51% _IO_new_fclose 0 0% 85.22% 39ms 0.51% std::__basic_file::close 1ms 0.013% 85.23% 39ms 0.51% std::__new_allocator::construct (inline) 0 0% 85.23% 39ms 0.51% std::allocator_traits::construct (inline)