File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6812ms, 85.41% of 7976ms total Dropped 601 nodes (cum <= 39.88ms) flat flat% sum% cum cum% 0 0% 0% 7940ms 99.55% __libc_start_call_main 0 0% 0% 7940ms 99.55% __libc_start_main_impl 0 0% 0% 7940ms 99.55% _start 0 0% 0% 7925ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7925ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7925ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7925ms 99.36% main 0 0% 0% 7887ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7887ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7887ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7884ms 98.85% AbstractCellBasedSimulation::Solve 0 0% 0% 3317ms 41.59% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2976ms 37.31% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.013% 2846ms 35.68% MeshBasedCellPopulation::Update 4ms 0.05% 0.063% 1579ms 19.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.088% 1437ms 18.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.088% 1401ms 17.57% MutableMesh::ReMesh 8ms 0.1% 0.19% 1381ms 17.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.2% 1378ms 17.28% MeshBasedCellPopulation::UpdateNodePairs 19ms 0.24% 0.44% 1190ms 14.92% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.05% 0.49% 989ms 12.40% AbstractTwoBodyInteractionForce::AddForceContribution 472ms 5.92% 6.41% 989ms 12.40% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 6.42% 981ms 12.30% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 90ms 1.13% 7.55% 971ms 12.17% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.05% 7.60% 910ms 11.41% CellPopulationElementWriter::Visit 12ms 0.15% 7.75% 898ms 11.26% CellPropertyCollection::GetPropertiesType (inline) 255ms 3.20% 10.95% 879ms 11.02% __dynamic_cast 45ms 0.56% 11.51% 876ms 10.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.088% 11.60% 816ms 10.23% MeshBasedCellPopulation::AcceptCellWriter 39ms 0.49% 12.09% 808ms 10.13% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 12.22% 704ms 8.83% TetrahedralMesh::ImportFromMesher 10ms 0.13% 12.35% 696ms 8.73% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.36% 665ms 8.34% std::ostream::operator<< (inline) 89ms 1.12% 13.48% 663ms 8.31% std::ostream::_M_insert 52ms 0.65% 14.13% 613ms 7.69% std::map::operator[] (partial-inline) 42ms 0.53% 14.66% 555ms 6.96% operator new 7ms 0.088% 14.74% 536ms 6.72% Cell::GetCellProliferativeType 2ms 0.025% 14.77% 525ms 6.58% triangulate 0 0% 14.77% 524ms 6.57% std::_Rb_tree::lower_bound (inline) 0 0% 14.77% 524ms 6.57% std::map::lower_bound (inline) 24ms 0.3% 15.07% 518ms 6.49% std::_Rb_tree::find (inline) 4ms 0.05% 15.12% 504ms 6.32% std::set::insert (inline) 501ms 6.28% 21.40% 501ms 6.28% __strcmp_avx2 169ms 2.12% 23.52% 500ms 6.27% __GI___libc_malloc 14ms 0.18% 23.70% 500ms 6.27% std::_Rb_tree::_M_insert_unique 34ms 0.43% 24.12% 493ms 6.18% std::__new_allocator::allocate (inline) 0 0% 24.12% 492ms 6.17% std::allocator_traits::allocate (inline) 2ms 0.025% 24.15% 474ms 5.94% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.15% 474ms 5.94% std::set::count (inline) 0 0% 24.15% 462ms 5.79% delaunay 2ms 0.025% 24.17% 460ms 5.77% divconqdelaunay 0 0% 24.17% 455ms 5.70% AbstractCellBasedSimulation::DoCellBirth 201ms 2.52% 26.69% 450ms 5.64% __cxxabiv1::__si_class_type_info::__do_dyncast 39ms 0.49% 27.18% 442ms 5.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.18% 417ms 5.23% std::_Rb_tree::_M_create_node (inline) 0 0% 27.18% 413ms 5.18% std::set::~set (inline) 0 0% 27.18% 395ms 4.95% std::_Rb_tree::_Alloc_node::operator() (inline) 73ms 0.92% 28.10% 394ms 4.94% std::_Rb_tree::_M_erase 0 0% 28.10% 379ms 4.75% std::_Rb_tree::_M_get_node (inline) 0 0% 28.10% 378ms 4.74% NodeLocationWriter::Visit 1ms 0.013% 28.11% 363ms 4.55% Cell::GetMutationState 12ms 0.15% 28.26% 346ms 4.34% std::_Rb_tree::_Rb_tree (partial-inline) 16ms 0.2% 28.46% 346ms 4.34% std::less::operator() (inline) 0 0% 28.46% 338ms 4.24% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.46% 338ms 4.24% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 28.47% 332ms 4.16% OutputFileHandler::OpenOutputFile 330ms 4.14% 32.61% 330ms 4.14% std::operator< (inline) 325ms 4.07% 36.69% 325ms 4.07% std::_Rb_tree::_S_right (inline) 26ms 0.33% 37.01% 324ms 4.06% std::num_put::_M_insert_float 2ms 0.025% 37.04% 312ms 3.91% std::set::set (inline) 4ms 0.05% 37.09% 311ms 3.90% Cell::ReadyToDivide 11ms 0.14% 37.22% 305ms 3.82% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 37.24% 304ms 3.81% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.24% 304ms 3.81% MeshBasedCellPopulation::GetDampingConstant 103ms 1.29% 38.53% 303ms 3.80% __GI___libc_free 6ms 0.075% 38.60% 301ms 3.77% Element::Element 0 0% 38.60% 295ms 3.70% std::_Rb_tree::_M_drop_node (inline) 31ms 0.39% 38.99% 294ms 3.69% std::_Rb_tree::_M_copy (inline) 5ms 0.063% 39.05% 287ms 3.60% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 39.09% 283ms 3.55% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.088% 39.18% 273ms 3.42% divconqrecurse 171ms 2.14% 41.32% 263ms 3.30% _int_malloc 4ms 0.05% 41.37% 263ms 3.30% std::__new_allocator::deallocate (inline) 0 0% 41.37% 261ms 3.27% std::allocator_traits::deallocate (inline) 79ms 0.99% 42.36% 259ms 3.25% std::_Rb_tree::_M_clone_node (inline) 86ms 1.08% 43.44% 255ms 3.20% mergehulls 5ms 0.063% 43.51% 239ms 3.00% std::__cxx11::collate::do_transform 2ms 0.025% 43.53% 227ms 2.85% ___vsnprintf 0 0% 43.53% 225ms 2.82% __vsnprintf_internal (inline) 0 0% 43.53% 225ms 2.82% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 43.56% 222ms 2.78% AbstractCellProperty::IsType (inline) 33ms 0.41% 43.97% 221ms 2.77% __printf_buffer 0 0% 43.97% 219ms 2.75% Cell::HasCellProperty (inline) 2ms 0.025% 43.99% 218ms 2.73% CellPropertyCollection::HasProperty 3ms 0.038% 44.03% 205ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.1% 44.13% 202ms 2.53% Element::RegisterWithNodes (inline) 181ms 2.27% 46.40% 200ms 2.51% _int_free 8ms 0.1% 46.50% 197ms 2.47% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.088% 46.59% 193ms 2.42% Node::AddElement 6ms 0.075% 46.66% 192ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 17ms 0.21% 46.88% 188ms 2.36% TetrahedralMesh::Clear 0 0% 46.88% 186ms 2.33% std::basic_ofstream::basic_ofstream (inline) 55ms 0.69% 47.57% 182ms 2.28% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 47.57% 180ms 2.26% std::basic_filebuf::open 0 0% 47.57% 180ms 2.26% std::basic_ofstream::open (inline) 38ms 0.48% 48.04% 178ms 2.23% std::num_put::_M_insert_int 11ms 0.14% 48.18% 174ms 2.18% __printf_fp_l_buffer 0 0% 48.18% 174ms 2.18% __printf_fp_spec (inline) 69ms 0.87% 49.05% 171ms 2.14% std::__ostream_insert 42ms 0.53% 49.57% 163ms 2.04% AbstractCellProperty::IsSame 45ms 0.56% 50.14% 161ms 2.02% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.14% 50.28% 157ms 1.97% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.28% 153ms 1.92% TetrahedralMesh::RefreshJacobianCachedData 78ms 0.98% 51.25% 150ms 1.88% __printf_fp_buffer_1 0 0% 51.25% 149ms 1.87% std::__basic_file::open 1ms 0.013% 51.27% 148ms 1.86% _IO_new_fopen 0 0% 51.27% 147ms 1.84% __fopen_internal (inline) 8ms 0.1% 51.37% 145ms 1.82% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.025% 51.39% 144ms 1.81% _IO_new_file_fopen 2ms 0.025% 51.42% 139ms 1.74% __GI__IO_file_open 1ms 0.013% 51.43% 138ms 1.73% AbstractCellBasedWriter::CloseFile 0 0% 51.43% 138ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 11ms 0.14% 51.57% 138ms 1.73% boost::detail::shared_count::~shared_count (inline) 0 0% 51.57% 138ms 1.73% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 51.58% 138ms 1.73% std::basic_ofstream::close (inline) 1ms 0.013% 51.59% 137ms 1.72% std::basic_filebuf::close 3ms 0.038% 51.63% 136ms 1.71% boost::numeric::ublas::vector_assign (inline) 4ms 0.05% 51.68% 133ms 1.67% std::operator<< (inline) 1ms 0.013% 51.69% 129ms 1.62% OutputFileHandler::OutputFileHandler 0 0% 51.69% 127ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.69% 127ms 1.59% OutputFileHandler::CommonConstructor 124ms 1.55% 53.25% 126ms 1.58% boost::detail::sp_counted_base::release 9ms 0.11% 53.36% 126ms 1.58% boost::numeric::ublas::c_vector::c_vector (inline) 17ms 0.21% 53.57% 125ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.29% 53.86% 125ms 1.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 12ms 0.15% 54.01% 125ms 1.57% std::_Rb_tree_const_iterator::operator++ (inline) 124ms 1.55% 55.57% 124ms 1.55% std::_Rb_tree_increment 0 0% 55.57% 123ms 1.54% OutputFileHandler::MakeFoldersAndReturnFullPath 25ms 0.31% 55.88% 121ms 1.52% std::type_info::operator== (inline) 119ms 1.49% 57.37% 119ms 1.49% __libc_open64 19ms 0.24% 57.61% 116ms 1.45% AbstractTetrahedralElement::RefreshJacobian 3ms 0.038% 57.65% 116ms 1.45% std::_Vector_base::_M_allocate (inline) 2ms 0.025% 57.67% 116ms 1.45% std::vector::push_back (inline) 1ms 0.013% 57.69% 115ms 1.44% alternateaxes 101ms 1.27% 58.95% 114ms 1.43% vertexmedian 7ms 0.088% 59.04% 112ms 1.40% std::vector::_M_realloc_insert 0 0% 59.04% 111ms 1.39% FilesystemPermissions::SetFilePermissions (inline) 111ms 1.39% 60.43% 111ms 1.39% __GI_fchmodat 0 0% 60.43% 111ms 1.39% std::filesystem::permissions 12ms 0.15% 60.58% 108ms 1.35% Node::~Node 39ms 0.49% 61.07% 105ms 1.32% boost::numeric::ublas::indexing_vector_assign 5ms 0.063% 61.13% 104ms 1.30% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 75ms 0.94% 62.07% 103ms 1.29% std::basic_filebuf::xsputn 100ms 1.25% 63.33% 100ms 1.25% [libchaste_cell_based.so] 34ms 0.43% 63.75% 100ms 1.25% boost::shared_ptr::shared_ptr (inline) 100ms 1.25% 65.01% 100ms 1.25% incircle 0 0% 65.01% 98ms 1.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 98ms 1.23% 66.24% 98ms 1.23% __GI___libc_write 1ms 0.013% 66.25% 98ms 1.23% std::basic_filebuf::overflow 62ms 0.78% 67.03% 97ms 1.22% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 67.03% 97ms 1.22% std::__basic_file::xsputn 0 0% 67.03% 97ms 1.22% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 67.04% 97ms 1.22% std::basic_filebuf::_M_terminate_output 2ms 0.025% 67.06% 95ms 1.19% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.025% 67.09% 92ms 1.15% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.44% 67.53% 88ms 1.10% AbstractElement::GetNodeLocation 63ms 0.79% 68.32% 85ms 1.07% std::basic_streambuf::xsputn 1ms 0.013% 68.33% 82ms 1.03% Cell::GetCellId 80ms 1.00% 69.33% 80ms 1.00% std::_Rb_tree_insert_and_rebalance 77ms 0.97% 70.30% 77ms 0.97% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 56ms 0.7% 71.00% 74ms 0.93% std::num_put::do_put 52ms 0.65% 71.65% 70ms 0.88% AbstractElement::GetNodeGlobalIndex 0 0% 71.65% 70ms 0.88% std::_Rb_tree::_M_destroy_node (inline) 0 0% 71.65% 70ms 0.88% std::__new_allocator::destroy (inline) 0 0% 71.65% 70ms 0.88% std::allocator_traits::destroy (inline) 69ms 0.87% 72.52% 69ms 0.87% Node::GetIndex 50ms 0.63% 73.14% 69ms 0.87% malloc_consolidate 1ms 0.013% 73.16% 67ms 0.84% BoundaryNodeWriter::Visit 64ms 0.8% 73.96% 66ms 0.83% boost::detail::shared_count::shared_count (inline) 66ms 0.83% 74.79% 66ms 0.83% counterclockwise 64ms 0.8% 75.59% 64ms 0.8% std::ostream::sentry::sentry 63ms 0.79% 76.38% 63ms 0.79% __GI___fstatat64 63ms 0.79% 77.17% 63ms 0.79% __memcpy_avx_unaligned_erms 0 0% 77.17% 62ms 0.78% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 46ms 0.58% 77.75% 62ms 0.78% boost::numeric::ublas::c_matrix::operator() 0 0% 77.75% 62ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.75% 62ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 77.76% 62ms 0.78% std::filesystem::create_directory 0 0% 77.76% 62ms 0.78% std::filesystem::status 61ms 0.76% 78.52% 61ms 0.76% [libchaste_mesh.so] 61ms 0.76% 79.29% 61ms 0.76% std::vector::size (inline) 2ms 0.025% 79.31% 59ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 6ms 0.075% 79.39% 58ms 0.73% CellPropertyCollection::AddProperty 0 0% 79.39% 57ms 0.71% tcache_get (inline) 57ms 0.71% 80.10% 57ms 0.71% tcache_get_n (inline) 51ms 0.64% 80.74% 56ms 0.7% vertexsort 7ms 0.088% 80.83% 55ms 0.69% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 80.83% 55ms 0.69% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 80.83% 53ms 0.66% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.83% 52ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 52ms 0.65% 81.48% 52ms 0.65% [libstdc++.so.6.0.33] 0 0% 81.48% 51ms 0.64% std::vector::vector (inline) 50ms 0.63% 82.11% 50ms 0.63% Node::IsDeleted 24ms 0.3% 82.41% 49ms 0.61% AbstractCellCycleModel::GetAge 0 0% 82.41% 49ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 12ms 0.15% 82.56% 49ms 0.61% Determinant (inline) 7ms 0.088% 82.65% 49ms 0.61% Inverse 48ms 0.6% 83.25% 48ms 0.6% boost::numeric::ublas::c_vector::operator() 30ms 0.38% 83.63% 47ms 0.59% AbstractTetrahedralMesh::GetElement 5ms 0.063% 83.69% 47ms 0.59% Node::ConstructNodeAttributes (inline) 47ms 0.59% 84.28% 47ms 0.59% Node::rGetLocation 2ms 0.025% 84.30% 45ms 0.56% Node::ClearAppliedForce 0 0% 84.30% 45ms 0.56% boost::numeric::ublas::norm_2 (inline) 10ms 0.13% 84.43% 45ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.43% 43ms 0.54% std::_Vector_base::_Vector_base (inline) 37ms 0.46% 84.89% 42ms 0.53% std::__numpunct_cache::_M_cache 1ms 0.013% 84.90% 41ms 0.51% std::_Vector_base::_M_create_storage (inline) 0 0% 84.90% 41ms 0.51% std::map::find (inline) 40ms 0.5% 85.41% 40ms 0.5% boost::shared_ptr::operator-> (inline)