File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6616ms, 84.06% of 7871ms total Dropped 588 nodes (cum <= 39.35ms) flat flat% sum% cum cum% 0 0% 0% 7835ms 99.54% __libc_start_call_main 0 0% 0% 7835ms 99.54% __libc_start_main_impl 0 0% 0% 7835ms 99.54% _start 0 0% 0% 7820ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7820ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7820ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7820ms 99.35% main 0 0% 0% 7783ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7783ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7783ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7779ms 98.83% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.025% 3347ms 42.52% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.051% 2891ms 36.73% MeshBasedCellPopulation::Update 1ms 0.013% 0.064% 2884ms 36.64% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.076% 1542ms 19.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.076% 1436ms 18.24% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.076% 1405ms 17.85% MutableMesh::ReMesh 1ms 0.013% 0.089% 1404ms 17.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.051% 0.14% 1342ms 17.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.38% 1258ms 15.98% MeshBasedCellPopulation::SpringIterator::operator++ 107ms 1.36% 1.74% 1047ms 13.30% TetrahedralMesh::EdgeIterator::operator++ 466ms 5.92% 7.66% 1016ms 12.91% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.064% 7.72% 933ms 11.85% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 16ms 0.2% 7.93% 930ms 11.82% CellPopulationElementWriter::Visit 4ms 0.051% 7.98% 911ms 11.57% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.13% 8.11% 904ms 11.49% CellPropertyCollection::GetPropertiesType (inline) 283ms 3.60% 11.70% 899ms 11.42% __dynamic_cast 40ms 0.51% 12.21% 810ms 10.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.025% 12.23% 772ms 9.81% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.27% 12.50% 764ms 9.71% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 12.59% 735ms 9.34% TetrahedralMesh::ImportFromMesher 5ms 0.064% 12.65% 698ms 8.87% AbstractCellProperty::IsSubType (inline) 55ms 0.7% 13.35% 612ms 7.78% std::map::operator[] (partial-inline) 86ms 1.09% 14.45% 602ms 7.65% std::ostream::_M_insert 0 0% 14.45% 602ms 7.65% std::ostream::operator<< (inline) 47ms 0.6% 15.04% 582ms 7.39% operator new 28ms 0.36% 15.40% 559ms 7.10% std::_Rb_tree::find (inline) 8ms 0.1% 15.50% 547ms 6.95% std::set::insert (inline) 11ms 0.14% 15.64% 539ms 6.85% std::_Rb_tree::_M_insert_unique 1ms 0.013% 15.65% 533ms 6.77% triangulate 2ms 0.025% 15.68% 531ms 6.75% Cell::GetCellProliferativeType 197ms 2.50% 18.18% 531ms 6.75% __GI___libc_malloc 30ms 0.38% 18.56% 523ms 6.64% std::__new_allocator::allocate (inline) 0 0% 18.56% 519ms 6.59% std::allocator_traits::allocate (inline) 0 0% 18.56% 516ms 6.56% std::set::count (inline) 0 0% 18.56% 515ms 6.54% std::_Rb_tree::lower_bound (inline) 0 0% 18.56% 515ms 6.54% std::map::lower_bound (inline) 504ms 6.40% 24.97% 504ms 6.40% __strcmp_avx2 7ms 0.089% 25.05% 488ms 6.20% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 25.05% 474ms 6.02% delaunay 2ms 0.025% 25.08% 472ms 6.00% divconqdelaunay 207ms 2.63% 27.71% 454ms 5.77% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.71% 446ms 5.67% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.71% 440ms 5.59% std::_Rb_tree::_M_create_node (inline) 0 0% 27.71% 416ms 5.29% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.71% 403ms 5.12% std::_Rb_tree::_M_get_node (inline) 34ms 0.43% 28.14% 394ms 5.01% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.22% 28.36% 387ms 4.92% std::_Rb_tree::_Rb_tree (partial-inline) 12ms 0.15% 28.51% 375ms 4.76% std::less::operator() (inline) 2ms 0.025% 28.54% 372ms 4.73% Cell::GetMutationState 1ms 0.013% 28.55% 371ms 4.71% NodeLocationWriter::Visit 363ms 4.61% 33.16% 363ms 4.61% std::operator< (inline) 0 0% 33.16% 362ms 4.60% std::set::~set (inline) 1ms 0.013% 33.17% 358ms 4.55% std::set::set (inline) 65ms 0.83% 34.00% 355ms 4.51% std::_Rb_tree::_M_erase 1ms 0.013% 34.01% 340ms 4.32% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 34.05% 339ms 4.31% AbstractCentreBasedCellPopulation::GetDampingConstant 336ms 4.27% 38.32% 336ms 4.27% std::_Rb_tree::_S_right (inline) 16ms 0.2% 38.52% 335ms 4.26% std::_Rb_tree::_M_insert_ (inline) 28ms 0.36% 38.88% 328ms 4.17% std::num_put::_M_insert_float 8ms 0.1% 38.98% 326ms 4.14% AbstractCellPopulation::IsCellAttachedToLocationIndex 43ms 0.55% 39.52% 325ms 4.13% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 39.55% 321ms 4.08% Element::Element 5ms 0.064% 39.61% 307ms 3.90% Cell::ReadyToDivide 108ms 1.37% 40.99% 301ms 3.82% __GI___libc_free 0 0% 40.99% 296ms 3.76% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 40.99% 294ms 3.74% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 41.00% 290ms 3.68% OutputFileHandler::OpenOutputFile 84ms 1.07% 42.07% 277ms 3.52% std::_Rb_tree::_M_clone_node (inline) 11ms 0.14% 42.21% 268ms 3.40% divconqrecurse 0 0% 42.21% 266ms 3.38% std::_Rb_tree::_M_drop_node (inline) 5ms 0.064% 42.27% 265ms 3.37% std::__new_allocator::deallocate (inline) 0 0% 42.27% 263ms 3.34% std::allocator_traits::deallocate (inline) 3ms 0.038% 42.31% 259ms 3.29% CellPropertyCollection::HasProperty 0 0% 42.31% 258ms 3.28% Cell::HasCellProperty (inline) 178ms 2.26% 44.57% 257ms 3.27% _int_malloc 6ms 0.076% 44.64% 255ms 3.24% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 44.68% 249ms 3.16% AbstractCellProperty::IsType (inline) 84ms 1.07% 45.75% 248ms 3.15% mergehulls 1ms 0.013% 45.76% 248ms 3.15% std::__cxx11::collate::do_transform 5ms 0.064% 45.83% 239ms 3.04% ___vsnprintf 0 0% 45.83% 234ms 2.97% __vsnprintf_internal (inline) 22ms 0.28% 46.11% 227ms 2.88% __printf_buffer 3ms 0.038% 46.14% 209ms 2.66% Element::RegisterWithNodes (inline) 0 0% 46.14% 209ms 2.66% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 46.18% 205ms 2.60% Node::AddElement 2ms 0.025% 46.21% 197ms 2.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 60ms 0.76% 46.97% 193ms 2.45% std::_Rb_tree::_M_get_insert_unique_pos (inline) 170ms 2.16% 49.13% 192ms 2.44% _int_free 3ms 0.038% 49.17% 191ms 2.43% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.13% 49.29% 188ms 2.39% TetrahedralMesh::Clear 1ms 0.013% 49.31% 181ms 2.30% __printf_fp_spec (inline) 8ms 0.1% 49.41% 180ms 2.29% __printf_fp_l_buffer 42ms 0.53% 49.94% 178ms 2.26% AbstractCellProperty::IsSame 9ms 0.11% 50.06% 174ms 2.21% MeshBasedCellPopulation::SpringsEnd (inline) 93ms 1.18% 51.24% 167ms 2.12% __printf_fp_buffer_1 36ms 0.46% 51.70% 148ms 1.88% TetrahedralMesh::EdgesEnd (partial-inline) 34ms 0.43% 52.13% 144ms 1.83% std::num_put::_M_insert_int 1ms 0.013% 52.14% 142ms 1.80% OutputFileHandler::OutputFileHandler 8ms 0.1% 52.24% 141ms 1.79% AbstractTetrahedralElement::CalculateJacobian 0 0% 52.24% 141ms 1.79% OutputFileHandler::CommonConstructor 0 0% 52.24% 140ms 1.78% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 52.26% 137ms 1.74% std::basic_filebuf::open 0 0% 52.26% 137ms 1.74% std::basic_ofstream::open (inline) 3ms 0.038% 52.29% 136ms 1.73% boost::numeric::ublas::vector_assign (inline) 33ms 0.42% 52.71% 136ms 1.73% std::type_info::operator== (inline) 12ms 0.15% 52.86% 133ms 1.69% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 52.86% 132ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 52.89% 132ms 1.68% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 52.89% 129ms 1.64% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 52.90% 128ms 1.63% AbstractCellBasedWriter::CloseFile 0 0% 52.90% 128ms 1.63% std::basic_filebuf::close 0 0% 52.90% 127ms 1.61% std::basic_ofstream::close (inline) 14ms 0.18% 53.08% 123ms 1.56% boost::detail::shared_count::~shared_count (inline) 0 0% 53.08% 123ms 1.56% boost::shared_ptr::~shared_ptr (inline) 57ms 0.72% 53.81% 121ms 1.54% std::__ostream_insert 4ms 0.051% 53.86% 119ms 1.51% AbstractTetrahedralElement::AbstractTetrahedralElement 119ms 1.51% 55.37% 119ms 1.51% std::_Rb_tree_increment 7ms 0.089% 55.46% 119ms 1.51% std::vector::push_back (inline) 1ms 0.013% 55.47% 117ms 1.49% std::_Vector_base::_M_allocate (inline) 0 0% 55.47% 116ms 1.47% TetrahedralMesh::RefreshJacobianCachedData 0 0% 55.47% 115ms 1.46% FilesystemPermissions::SetFilePermissions (inline) 115ms 1.46% 56.93% 115ms 1.46% __GI_fchmodat 0 0% 56.93% 115ms 1.46% std::filesystem::permissions 18ms 0.23% 57.16% 114ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 57.17% 112ms 1.42% alternateaxes 0 0% 57.17% 111ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 99ms 1.26% 58.43% 111ms 1.41% vertexmedian 110ms 1.40% 59.83% 110ms 1.40% incircle 13ms 0.17% 59.99% 109ms 1.38% Node::~Node 3ms 0.038% 60.03% 108ms 1.37% std::vector::_M_realloc_insert 9ms 0.11% 60.14% 106ms 1.35% AbstractTetrahedralElement::RefreshJacobian 5ms 0.064% 60.21% 105ms 1.33% AbstractTetrahedralElement::CalculateInverseJacobian 102ms 1.30% 61.50% 104ms 1.32% boost::detail::sp_counted_base::release 0 0% 61.50% 103ms 1.31% std::__basic_file::open 0 0% 61.50% 102ms 1.30% _IO_new_fopen 0 0% 61.50% 102ms 1.30% __fopen_internal (inline) 102ms 1.30% 62.80% 102ms 1.30% std::_Rb_tree_insert_and_rebalance 4ms 0.051% 62.85% 102ms 1.30% std::operator<< (inline) 22ms 0.28% 63.13% 100ms 1.27% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 63.13% 100ms 1.27% _IO_new_file_fopen 1ms 0.013% 63.14% 97ms 1.23% __GI__IO_file_open 27ms 0.34% 63.49% 97ms 1.23% boost::numeric::ublas::indexing_vector_assign 51ms 0.65% 64.13% 96ms 1.22% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 64.15% 95ms 1.21% std::basic_filebuf::_M_terminate_output 93ms 1.18% 65.33% 94ms 1.19% __GI___libc_write 0 0% 65.33% 94ms 1.19% std::__basic_file::xsputn 0 0% 65.33% 94ms 1.19% std::basic_filebuf::_M_convert_to_external 0 0% 65.33% 94ms 1.19% std::basic_filebuf::overflow 6ms 0.076% 65.40% 90ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 51ms 0.65% 66.05% 90ms 1.14% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 66.05% 88ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 38ms 0.48% 66.54% 88ms 1.12% AbstractElement::GetNodeLocation 88ms 1.12% 67.65% 88ms 1.12% __libc_open64 87ms 1.11% 68.76% 87ms 1.11% [libchaste_cell_based.so] 85ms 1.08% 69.84% 85ms 1.08% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 74ms 0.94% 70.78% 80ms 1.02% vertexsort 48ms 0.61% 71.39% 78ms 0.99% std::basic_filebuf::xsputn 0 0% 71.39% 77ms 0.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.39% 77ms 0.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.95% 72.34% 75ms 0.95% __GI___fstatat64 54ms 0.69% 73.03% 75ms 0.95% std::basic_streambuf::xsputn 1ms 0.013% 73.04% 74ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.04% 74ms 0.94% std::filesystem::status 7ms 0.089% 73.13% 69ms 0.88% CellPropertyCollection::AddProperty 4ms 0.051% 73.18% 69ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.013% 73.19% 66ms 0.84% Cell::GetCellId 48ms 0.61% 73.80% 65ms 0.83% std::num_put::do_put 65ms 0.83% 74.63% 65ms 0.83% std::vector::size (inline) 53ms 0.67% 75.30% 64ms 0.81% AbstractElement::GetNodeGlobalIndex 63ms 0.8% 76.10% 63ms 0.8% Node::GetIndex 46ms 0.58% 76.69% 63ms 0.8% malloc_consolidate 0 0% 76.69% 63ms 0.8% tcache_get (inline) 63ms 0.8% 77.49% 63ms 0.8% tcache_get_n (inline) 1ms 0.013% 77.50% 60ms 0.76% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 60ms 0.76% 78.26% 60ms 0.76% __memcpy_avx_unaligned_erms 60ms 0.76% 79.02% 60ms 0.76% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 79.02% 59ms 0.75% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 79.28% 59ms 0.75% boost::numeric::ublas::vector_norm_2::apply (inline) 1ms 0.013% 79.29% 59ms 0.75% std::filesystem::create_directory 0 0% 79.29% 57ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.29% 57ms 0.72% std::__new_allocator::destroy (inline) 0 0% 79.29% 57ms 0.72% std::allocator_traits::destroy (inline) 6ms 0.076% 79.37% 55ms 0.7% Node::ConstructNodeAttributes (inline) 24ms 0.3% 79.67% 54ms 0.69% AbstractTetrahedralMesh::GetElement 3ms 0.038% 79.71% 52ms 0.66% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 79.72% 51ms 0.65% Node::ClearAppliedForce 0 0% 79.72% 51ms 0.65% std::vector::vector (inline) 0 0% 79.72% 49ms 0.62% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.051% 79.77% 49ms 0.62% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 79.77% 49ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 49ms 0.62% 80.40% 49ms 0.62% [libchaste_mesh.so] 48ms 0.61% 81.01% 48ms 0.61% counterclockwise 0 0% 81.01% 47ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.01% 46ms 0.58% BoundaryNodeWriter::Visit 46ms 0.58% 81.59% 46ms 0.58% Node::IsDeleted 44ms 0.56% 82.15% 45ms 0.57% boost::detail::shared_count::shared_count (inline) 20ms 0.25% 82.40% 44ms 0.56% AbstractCellCycleModel::GetAge 17ms 0.22% 82.62% 43ms 0.55% AbstractTetrahedralMesh::GetNumAllElements 25ms 0.32% 82.94% 43ms 0.55% boost::numeric::ublas::c_matrix::operator() 0 0% 82.94% 42ms 0.53% CellPropertyCollection::~CellPropertyCollection (inline) 42ms 0.53% 83.47% 42ms 0.53% Node::rGetLocation 42ms 0.53% 84.00% 42ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 84.00% 42ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.013% 84.02% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 84.02% 42ms 0.53% std::allocator_traits::construct (inline) 0 0% 84.02% 41ms 0.52% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.038% 84.06% 41ms 0.52% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 84.06% 41ms 0.52% std::_Vector_base::_Vector_base (inline) 0 0% 84.06% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline)