File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6606ms, 83.79% of 7884ms total Dropped 578 nodes (cum <= 39.42ms) flat flat% sum% cum cum% 0 0% 0% 7846ms 99.52% __libc_start_call_main 0 0% 0% 7846ms 99.52% __libc_start_main_impl 0 0% 0% 7846ms 99.52% _start 0 0% 0% 7829ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7829ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7829ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7829ms 99.30% main 0 0% 0% 7789ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7789ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7789ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7787ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0% 3340ms 42.36% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2920ms 37.04% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.051% 2879ms 36.52% MeshBasedCellPopulation::Update 0 0% 0.051% 1518ms 19.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1442ms 18.29% MutableMesh::ReMesh 0 0% 0.051% 1393ms 17.67% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.051% 1384ms 17.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.089% 0.14% 1334ms 16.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.34% 1195ms 15.16% MeshBasedCellPopulation::SpringIterator::operator++ 102ms 1.29% 1.64% 970ms 12.30% TetrahedralMesh::EdgeIterator::operator++ 455ms 5.77% 7.41% 956ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.46% 926ms 11.75% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.051% 7.51% 926ms 11.75% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.16% 7.67% 923ms 11.71% CellPopulationElementWriter::Visit 11ms 0.14% 7.81% 899ms 11.40% CellPropertyCollection::GetPropertiesType (inline) 271ms 3.44% 11.25% 837ms 10.62% __dynamic_cast 55ms 0.7% 11.95% 807ms 10.24% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.063% 12.01% 794ms 10.07% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 12.35% 759ms 9.63% AbstractCellPopulation::GetCellUsingLocationIndex 14ms 0.18% 12.53% 745ms 9.45% TetrahedralMesh::ImportFromMesher 6ms 0.076% 12.61% 679ms 8.61% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 12.63% 625ms 7.93% std::ostream::operator<< (inline) 90ms 1.14% 13.77% 623ms 7.90% std::ostream::_M_insert 54ms 0.68% 14.46% 598ms 7.58% std::map::operator[] (partial-inline) 38ms 0.48% 14.94% 581ms 7.37% operator new 201ms 2.55% 17.49% 547ms 6.94% __GI___libc_malloc 32ms 0.41% 17.90% 538ms 6.82% std::__new_allocator::allocate (inline) 5ms 0.063% 17.96% 538ms 6.82% std::set::insert (inline) 0 0% 17.96% 538ms 6.82% triangulate 0 0% 17.96% 534ms 6.77% std::allocator_traits::allocate (inline) 16ms 0.2% 18.16% 533ms 6.76% std::_Rb_tree::_M_insert_unique 4ms 0.051% 18.21% 521ms 6.61% Cell::GetCellProliferativeType 0 0% 18.21% 506ms 6.42% std::_Rb_tree::lower_bound (inline) 0 0% 18.21% 506ms 6.42% std::map::lower_bound (inline) 23ms 0.29% 18.51% 504ms 6.39% std::_Rb_tree::find (inline) 6ms 0.076% 18.58% 493ms 6.25% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.013% 18.59% 462ms 5.86% delaunay 1ms 0.013% 18.61% 459ms 5.82% divconqdelaunay 0 0% 18.61% 457ms 5.80% std::set::count (inline) 455ms 5.77% 24.38% 455ms 5.77% __strcmp_avx2 5ms 0.063% 24.44% 451ms 5.72% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.44% 426ms 5.40% std::_Rb_tree::_M_create_node (inline) 31ms 0.39% 24.84% 420ms 5.33% std::_Rb_tree::~_Rb_tree (inline) 184ms 2.33% 27.17% 403ms 5.11% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.17% 402ms 5.10% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.17% 402ms 5.10% std::_Rb_tree::_M_get_node (inline) 0 0% 27.17% 389ms 4.93% std::set::~set (inline) 83ms 1.05% 28.22% 383ms 4.86% std::_Rb_tree::_M_erase 3ms 0.038% 28.26% 374ms 4.74% Cell::GetMutationState 0 0% 28.26% 369ms 4.68% NodeLocationWriter::Visit 33ms 0.42% 28.68% 352ms 4.46% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.14% 28.82% 343ms 4.35% std::less::operator() (inline) 28ms 0.36% 29.17% 340ms 4.31% std::_Rb_tree::_M_insert_ (inline) 0 0% 29.17% 335ms 4.25% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 37ms 0.47% 29.64% 334ms 4.24% std::num_put::_M_insert_float 332ms 4.21% 33.85% 332ms 4.21% std::operator< (inline) 0 0% 33.85% 330ms 4.19% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 33.87% 325ms 4.12% std::set::set (inline) 0 0% 33.87% 324ms 4.11% OutputFileHandler::OpenOutputFile 1ms 0.013% 33.88% 320ms 4.06% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.88% 319ms 4.05% AbstractCentreBasedCellPopulation::GetDampingConstant 107ms 1.36% 35.24% 315ms 4.00% __GI___libc_free 310ms 3.93% 39.17% 310ms 3.93% std::_Rb_tree::_S_right (inline) 4ms 0.051% 39.22% 302ms 3.83% Cell::ReadyToDivide 2ms 0.025% 39.24% 302ms 3.83% Element::Element 36ms 0.46% 39.70% 288ms 3.65% std::_Rb_tree::_M_copy (inline) 11ms 0.14% 39.84% 281ms 3.56% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 39.84% 275ms 3.49% std::_Rb_tree::_M_drop_node (inline) 8ms 0.1% 39.94% 266ms 3.37% std::__new_allocator::deallocate (inline) 0 0% 39.94% 262ms 3.32% std::allocator_traits::deallocate (inline) 9ms 0.11% 40.06% 261ms 3.31% std::__cxx11::collate::do_transform 160ms 2.03% 42.09% 259ms 3.29% _int_malloc 2ms 0.025% 42.11% 258ms 3.27% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 42.25% 248ms 3.15% divconqrecurse 57ms 0.72% 42.97% 248ms 3.15% std::_Rb_tree::_M_clone_node (inline) 4ms 0.051% 43.02% 242ms 3.07% AbstractCellProperty::IsType (inline) 4ms 0.051% 43.07% 241ms 3.06% ___vsnprintf 9ms 0.11% 43.19% 240ms 3.04% CellPropertyCollection::HasProperty 0 0% 43.19% 237ms 3.01% __vsnprintf_internal (inline) 0 0% 43.19% 236ms 2.99% Cell::HasCellProperty (inline) 26ms 0.33% 43.52% 232ms 2.94% __printf_buffer 76ms 0.96% 44.48% 229ms 2.90% mergehulls 19ms 0.24% 44.72% 219ms 2.78% TetrahedralMesh::Clear 0 0% 44.72% 219ms 2.78% std::_Rb_tree::_M_put_node (inline) 179ms 2.27% 46.99% 208ms 2.64% _int_free 2ms 0.025% 47.02% 200ms 2.54% Element::RegisterWithNodes (inline) 4ms 0.051% 47.07% 195ms 2.47% Node::AddElement 5ms 0.063% 47.13% 192ms 2.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.076% 47.21% 187ms 2.37% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.11% 47.32% 183ms 2.32% __printf_fp_l_buffer 0 0% 47.32% 183ms 2.32% __printf_fp_spec (inline) 9ms 0.11% 47.44% 181ms 2.30% MeshBasedCellPopulation::SpringsEnd (inline) 63ms 0.8% 48.24% 178ms 2.26% std::_Rb_tree::_M_get_insert_unique_pos (inline) 52ms 0.66% 48.90% 175ms 2.22% AbstractCellProperty::IsSame 91ms 1.15% 50.05% 171ms 2.17% __printf_fp_buffer_1 0 0% 50.05% 165ms 2.09% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 50.06% 159ms 2.02% std::basic_filebuf::open 0 0% 50.06% 159ms 2.02% std::basic_ofstream::open (inline) 64ms 0.81% 50.88% 153ms 1.94% std::__ostream_insert 13ms 0.16% 51.04% 150ms 1.90% AbstractTetrahedralElement::CalculateJacobian 33ms 0.42% 51.46% 146ms 1.85% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.46% 141ms 1.79% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.46% 141ms 1.79% alternateaxes 37ms 0.47% 51.93% 141ms 1.79% std::num_put::_M_insert_int 6ms 0.076% 52.00% 140ms 1.78% boost::numeric::ublas::vector_assign (inline) 129ms 1.64% 53.64% 140ms 1.78% vertexmedian 1ms 0.013% 53.65% 136ms 1.73% AbstractCellBasedWriter::CloseFile 0 0% 53.65% 136ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 4ms 0.051% 53.70% 136ms 1.73% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 53.72% 135ms 1.71% std::basic_ofstream::close (inline) 0 0% 53.72% 134ms 1.70% std::basic_filebuf::close 0 0% 53.72% 132ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.038% 53.75% 132ms 1.67% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 53.78% 132ms 1.67% std::filesystem::permissions 0 0% 53.78% 131ms 1.66% std::__basic_file::open 9ms 0.11% 53.89% 130ms 1.65% AbstractTetrahedralElement::CalculateInverseJacobian 8ms 0.1% 54.00% 130ms 1.65% Node::~Node 0 0% 54.00% 130ms 1.65% _IO_new_fopen 130ms 1.65% 55.64% 130ms 1.65% __GI_fchmodat 0 0% 55.64% 130ms 1.65% __fopen_internal (inline) 8ms 0.1% 55.75% 129ms 1.64% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 55.77% 127ms 1.61% _IO_new_file_fopen 18ms 0.23% 56.00% 126ms 1.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 126ms 1.60% 57.60% 126ms 1.60% std::_Rb_tree_increment 0 0% 57.60% 125ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 57.60% 125ms 1.59% OutputFileHandler::OutputFileHandler 0 0% 57.60% 124ms 1.57% OutputFileHandler::CommonConstructor 1ms 0.013% 57.61% 124ms 1.57% __GI__IO_file_open 26ms 0.33% 57.94% 123ms 1.56% std::type_info::operator== (inline) 2ms 0.025% 57.97% 122ms 1.55% std::operator<< (inline) 0 0% 57.97% 120ms 1.52% OutputFileHandler::MakeFoldersAndReturnFullPath 7ms 0.089% 58.05% 117ms 1.48% std::vector::push_back (inline) 11ms 0.14% 58.19% 116ms 1.47% MeshBasedCellPopulation::SpringIterator::SpringIterator 114ms 1.45% 59.64% 115ms 1.46% __libc_open64 15ms 0.19% 59.83% 112ms 1.42% AbstractTetrahedralElement::RefreshJacobian 5ms 0.063% 59.89% 109ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 73ms 0.93% 60.82% 108ms 1.37% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 10ms 0.13% 60.95% 106ms 1.34% std::vector::_M_realloc_insert 13ms 0.16% 61.11% 102ms 1.29% boost::detail::shared_count::~shared_count (inline) 0 0% 61.11% 102ms 1.29% boost::shared_ptr::~shared_ptr (inline) 102ms 1.29% 62.40% 102ms 1.29% std::_Rb_tree_insert_and_rebalance 29ms 0.37% 62.77% 101ms 1.28% boost::numeric::ublas::indexing_vector_assign 100ms 1.27% 64.04% 100ms 1.27% incircle 1ms 0.013% 64.05% 95ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 45ms 0.57% 64.62% 95ms 1.20% boost::shared_ptr::shared_ptr (inline) 0 0% 64.62% 94ms 1.19% std::basic_filebuf::_M_terminate_output 1ms 0.013% 64.64% 94ms 1.19% std::basic_filebuf::overflow 93ms 1.18% 65.82% 93ms 1.18% [libchaste_cell_based.so] 2ms 0.025% 65.84% 93ms 1.18% std::basic_filebuf::_M_convert_to_external 91ms 1.15% 67.00% 91ms 1.15% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 67.01% 91ms 1.15% std::__basic_file::xsputn 2ms 0.025% 67.03% 89ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 88ms 1.12% 68.15% 88ms 1.12% __GI___libc_write 85ms 1.08% 69.23% 86ms 1.09% boost::detail::sp_counted_base::release 37ms 0.47% 69.70% 82ms 1.04% AbstractElement::GetNodeLocation 61ms 0.77% 70.47% 81ms 1.03% std::basic_streambuf::xsputn 2ms 0.025% 70.50% 79ms 1.00% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 70.51% 79ms 1.00% Cell::GetCellId 54ms 0.68% 71.19% 79ms 1.00% malloc_consolidate 49ms 0.62% 71.82% 78ms 0.99% std::basic_filebuf::xsputn 78ms 0.99% 72.81% 78ms 0.99% std::vector::size (inline) 0 0% 72.81% 76ms 0.96% tcache_get (inline) 76ms 0.96% 73.77% 76ms 0.96% tcache_get_n (inline) 50ms 0.63% 74.40% 74ms 0.94% AbstractElement::GetNodeGlobalIndex 10ms 0.13% 74.53% 74ms 0.94% CellPropertyCollection::AddProperty 57ms 0.72% 75.25% 72ms 0.91% std::num_put::do_put 66ms 0.84% 76.09% 66ms 0.84% __GI___fstatat64 2ms 0.025% 76.12% 65ms 0.82% std::filesystem::status 4ms 0.051% 76.17% 64ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 76.17% 64ms 0.81% std::vector::vector (inline) 63ms 0.8% 76.97% 63ms 0.8% Node::GetIndex 0 0% 76.97% 63ms 0.8% std::_Vector_base::_Vector_base (inline) 62ms 0.79% 77.75% 62ms 0.79% [libchaste_mesh.so] 1ms 0.013% 77.77% 61ms 0.77% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.77% 60ms 0.76% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 60ms 0.76% 78.53% 60ms 0.76% __memcpy_avx_unaligned_erms 0 0% 78.53% 60ms 0.76% std::filesystem::create_directory 0 0% 78.53% 59ms 0.75% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 78.53% 59ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 78.54% 59ms 0.75% std::_Vector_base::_M_create_storage (inline) 51ms 0.65% 79.19% 58ms 0.74% vertexsort 0 0% 79.19% 57ms 0.72% BoundaryNodeWriter::Visit 0 0% 79.19% 56ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.19% 56ms 0.71% std::__new_allocator::destroy (inline) 0 0% 79.19% 56ms 0.71% std::allocator_traits::destroy (inline) 26ms 0.33% 79.52% 55ms 0.7% AbstractTetrahedralMesh::GetElement 4ms 0.051% 79.57% 52ms 0.66% Node::ConstructNodeAttributes (inline) 28ms 0.36% 79.92% 51ms 0.65% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.013% 79.93% 50ms 0.63% Node::ClearAppliedForce 50ms 0.63% 80.57% 50ms 0.63% boost::detail::shared_count::shared_count (inline) 50ms 0.63% 81.20% 50ms 0.63% counterclockwise 7ms 0.089% 81.29% 49ms 0.62% std::_Vector_base::_M_deallocate (inline) 23ms 0.29% 81.58% 48ms 0.61% AbstractCellCycleModel::GetAge 48ms 0.61% 82.19% 48ms 0.61% boost::numeric::ublas::c_vector::operator() (inline) 0 0% 82.19% 47ms 0.6% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.19% 47ms 0.6% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 82.20% 45ms 0.57% AbstractCentreBasedCellPopulation::CreateCellPair 45ms 0.57% 82.78% 45ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 82.78% 43ms 0.55% AbstractCentreBasedCellPopulation::IsMarkedSpring 15ms 0.19% 82.97% 42ms 0.53% Determinant (inline) 25ms 0.32% 83.28% 42ms 0.53% hack_digit 0 0% 83.28% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 83.28% 40ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 40ms 0.51% 83.79% 40ms 0.51% Node::rGetLocation