File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6624ms, 84.54% of 7835ms total Dropped 563 nodes (cum <= 39.17ms) flat flat% sum% cum cum% 0 0% 0% 7796ms 99.50% __libc_start_call_main 0 0% 0% 7796ms 99.50% __libc_start_main_impl 0 0% 0% 7796ms 99.50% _start 0 0% 0% 7779ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7779ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7779ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7779ms 99.29% main 0 0% 0% 7740ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7740ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7740ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7737ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0% 3451ms 44.05% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.038% 2973ms 37.95% MeshBasedCellPopulation::Update 1ms 0.013% 0.051% 2674ms 34.13% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.089% 1603ms 20.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.089% 1496ms 19.09% MutableMesh::ReMesh 1ms 0.013% 0.1% 1444ms 18.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.11% 1412ms 18.02% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.13% 0.24% 1380ms 17.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.42% 1219ms 15.56% MeshBasedCellPopulation::SpringIterator::operator++ 120ms 1.53% 1.95% 985ms 12.57% TetrahedralMesh::EdgeIterator::operator++ 249ms 3.18% 5.13% 968ms 12.35% __dynamic_cast 1ms 0.013% 5.14% 962ms 12.28% AbstractTwoBodyInteractionForce::AddForceContribution 429ms 5.48% 10.62% 941ms 12.01% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 10.67% 938ms 11.97% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 6ms 0.077% 10.75% 917ms 11.70% CellPropertyCollection::GetPropertiesType (inline) 40ms 0.51% 11.26% 872ms 11.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 12ms 0.15% 11.41% 861ms 10.99% CellPopulationElementWriter::Visit 6ms 0.077% 11.49% 798ms 10.19% MeshBasedCellPopulation::AcceptCellWriter 1ms 0.013% 11.50% 765ms 9.76% AbstractCellProperty::IsSubType (inline) 31ms 0.4% 11.90% 743ms 9.48% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.05% 722ms 9.22% TetrahedralMesh::ImportFromMesher 71ms 0.91% 12.95% 621ms 7.93% std::map::operator[] (partial-inline) 2ms 0.026% 12.98% 614ms 7.84% triangulate 578ms 7.38% 20.36% 578ms 7.38% __strcmp_avx2 26ms 0.33% 20.69% 558ms 7.12% operator new 6ms 0.077% 20.77% 554ms 7.07% Cell::GetCellProliferativeType 0 0% 20.77% 554ms 7.07% std::ostream::operator<< (inline) 111ms 1.42% 22.18% 552ms 7.05% std::ostream::_M_insert 0 0% 22.18% 536ms 6.84% delaunay 2ms 0.026% 22.21% 536ms 6.84% divconqdelaunay 180ms 2.30% 24.51% 530ms 6.76% __GI___libc_malloc 4ms 0.051% 24.56% 510ms 6.51% LegacyCellProliferativeTypesWriter::VisitCell 224ms 2.86% 27.42% 507ms 6.47% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.4% 27.81% 505ms 6.45% std::__new_allocator::allocate (inline) 0 0% 27.81% 501ms 6.39% std::allocator_traits::allocate (inline) 0 0% 27.81% 499ms 6.37% std::_Rb_tree::lower_bound (inline) 0 0% 27.81% 499ms 6.37% std::map::lower_bound (inline) 29ms 0.37% 28.18% 496ms 6.33% std::_Rb_tree::find (inline) 3ms 0.038% 28.22% 488ms 6.23% std::set::insert (inline) 7ms 0.089% 28.31% 485ms 6.19% std::_Rb_tree::_M_insert_unique 4ms 0.051% 28.36% 465ms 5.93% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.36% 437ms 5.58% std::set::count (inline) 45ms 0.57% 28.93% 433ms 5.53% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.93% 406ms 5.18% std::set::~set (inline) 0 0% 28.93% 398ms 5.08% std::_Rb_tree::_M_create_node (inline) 84ms 1.07% 30.01% 380ms 4.85% std::_Rb_tree::_M_erase 0 0% 30.01% 376ms 4.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 30.01% 375ms 4.79% std::_Rb_tree::_M_get_node (inline) 3ms 0.038% 30.04% 365ms 4.66% Cell::GetMutationState 18ms 0.23% 30.27% 340ms 4.34% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.077% 30.35% 333ms 4.25% std::less::operator() (inline) 0 0% 30.35% 328ms 4.19% NodeLocationWriter::Visit 327ms 4.17% 34.52% 327ms 4.17% std::operator< (inline) 325ms 4.15% 38.67% 325ms 4.15% std::_Rb_tree::_S_right (inline) 4ms 0.051% 38.72% 318ms 4.06% Cell::ReadyToDivide 4ms 0.051% 38.77% 312ms 3.98% Element::Element 5ms 0.064% 38.84% 309ms 3.94% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 38.85% 307ms 3.92% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 38.86% 306ms 3.91% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.051% 38.92% 304ms 3.88% std::set::set (inline) 35ms 0.45% 39.36% 293ms 3.74% std::num_put::_M_insert_float 86ms 1.10% 40.46% 286ms 3.65% __GI___libc_free 31ms 0.4% 40.86% 284ms 3.62% std::_Rb_tree::_M_copy (inline) 25ms 0.32% 41.17% 284ms 3.62% std::_Rb_tree::_M_insert_ (inline) 6ms 0.077% 41.25% 281ms 3.59% divconqrecurse 0 0% 41.25% 274ms 3.50% std::_Rb_tree::_M_drop_node (inline) 167ms 2.13% 43.38% 265ms 3.38% _int_malloc 20ms 0.26% 43.64% 265ms 3.38% std::__new_allocator::deallocate (inline) 67ms 0.86% 44.49% 264ms 3.37% mergehulls 0 0% 44.49% 263ms 3.36% std::allocator_traits::deallocate (inline) 1ms 0.013% 44.51% 251ms 3.20% CellProliferativeTypesWriter::VisitCell 58ms 0.74% 45.25% 242ms 3.09% std::_Rb_tree::_M_clone_node (inline) 7ms 0.089% 45.34% 239ms 3.05% CellPropertyCollection::HasProperty 0 0% 45.34% 236ms 3.01% Cell::HasCellProperty (inline) 2ms 0.026% 45.36% 233ms 2.97% AbstractCellProperty::IsType (inline) 0 0% 45.36% 227ms 2.90% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 45.40% 224ms 2.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.064% 45.46% 219ms 2.80% std::__cxx11::collate::do_transform 4ms 0.051% 45.51% 216ms 2.76% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.026% 45.54% 208ms 2.65% ___vsnprintf 0 0% 45.54% 207ms 2.64% __vsnprintf_internal (inline) 13ms 0.17% 45.71% 205ms 2.62% TetrahedralMesh::Clear 29ms 0.37% 46.08% 203ms 2.59% __printf_buffer 172ms 2.20% 48.27% 199ms 2.54% _int_free 68ms 0.87% 49.14% 194ms 2.48% std::_Rb_tree::_M_get_insert_unique_pos (inline) 6ms 0.077% 49.22% 192ms 2.45% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.038% 49.25% 186ms 2.37% Element::RegisterWithNodes (inline) 46ms 0.59% 49.84% 177ms 2.26% AbstractCellProperty::IsSame 1ms 0.013% 49.85% 175ms 2.23% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.026% 49.88% 175ms 2.23% Node::AddElement 0 0% 49.88% 174ms 2.22% AbstractCellBasedWriter::OpenOutputFileForAppend 11ms 0.14% 50.02% 170ms 2.17% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.02% 170ms 2.17% OutputFileHandler::OpenOutputFile 0 0% 50.02% 165ms 2.11% std::basic_ofstream::basic_ofstream (inline) 2ms 0.026% 50.04% 162ms 2.07% alternateaxes 2ms 0.026% 50.07% 161ms 2.05% std::basic_filebuf::open 0 0% 50.07% 161ms 2.05% std::basic_ofstream::open (inline) 145ms 1.85% 51.92% 160ms 2.04% vertexmedian 8ms 0.1% 52.02% 159ms 2.03% __printf_fp_l_buffer 0 0% 52.02% 159ms 2.03% __printf_fp_spec (inline) 42ms 0.54% 52.56% 154ms 1.97% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 52.56% 152ms 1.94% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 52.57% 150ms 1.91% AbstractCellBasedWriter::CloseFile 0 0% 52.57% 149ms 1.90% std::basic_filebuf::close 0 0% 52.57% 149ms 1.90% std::basic_ofstream::close (inline) 79ms 1.01% 53.58% 144ms 1.84% __printf_fp_buffer_1 2ms 0.026% 53.61% 142ms 1.81% OutputFileHandler::OutputFileHandler 0 0% 53.61% 141ms 1.80% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.038% 53.64% 141ms 1.80% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 53.66% 140ms 1.79% OutputFileHandler::CommonConstructor 137ms 1.75% 55.41% 137ms 1.75% incircle 3ms 0.038% 55.44% 136ms 1.74% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 55.46% 135ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.064% 55.52% 132ms 1.68% Node::~Node 26ms 0.33% 55.85% 131ms 1.67% AbstractTetrahedralElement::RefreshJacobian 28ms 0.36% 56.21% 131ms 1.67% std::type_info::operator== (inline) 9ms 0.11% 56.32% 129ms 1.65% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.077% 56.40% 128ms 1.63% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 56.40% 126ms 1.61% std::_Vector_base::_M_allocate (inline) 12ms 0.15% 56.55% 124ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 56.57% 123ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.026% 56.59% 120ms 1.53% std::__basic_file::open 41ms 0.52% 57.12% 120ms 1.53% std::__ostream_insert 1ms 0.013% 57.13% 118ms 1.51% _IO_new_fopen 15ms 0.19% 57.32% 117ms 1.49% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 57.33% 117ms 1.49% __fopen_internal (inline) 1ms 0.013% 57.35% 116ms 1.48% _IO_new_file_fopen 1ms 0.013% 57.36% 115ms 1.47% std::basic_filebuf::overflow 12ms 0.15% 57.51% 114ms 1.46% boost::detail::shared_count::~shared_count (inline) 0 0% 57.51% 114ms 1.46% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 57.52% 114ms 1.46% std::__basic_file::xsputn 0 0% 57.52% 114ms 1.46% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 57.54% 114ms 1.46% std::basic_filebuf::_M_terminate_output 113ms 1.44% 58.98% 113ms 1.44% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 58.98% 113ms 1.44% __GI__IO_file_open 113ms 1.44% 60.42% 113ms 1.44% __GI___libc_write 76ms 0.97% 61.39% 107ms 1.37% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 61.40% 104ms 1.33% std::operator<< (inline) 21ms 0.27% 61.67% 101ms 1.29% std::num_put::_M_insert_int 2ms 0.026% 61.70% 100ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 7ms 0.089% 61.79% 99ms 1.26% std::vector::push_back (inline) 3ms 0.038% 61.83% 98ms 1.25% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.37% 62.20% 98ms 1.25% boost::numeric::ublas::indexing_vector_assign 97ms 1.24% 63.43% 97ms 1.24% [libchaste_cell_based.so] 88ms 1.12% 64.56% 96ms 1.23% boost::detail::sp_counted_base::release 43ms 0.55% 65.11% 94ms 1.20% AbstractElement::GetNodeLocation 40ms 0.51% 65.62% 94ms 1.20% boost::shared_ptr::shared_ptr (inline) 91ms 1.16% 66.78% 91ms 1.16% __libc_open64 60ms 0.77% 67.54% 88ms 1.12% malloc_consolidate 87ms 1.11% 68.65% 87ms 1.11% std::_Rb_tree_increment 4ms 0.051% 68.70% 84ms 1.07% AbstractCellPopulation::GetLocationIndexUsingCell 6ms 0.077% 68.78% 84ms 1.07% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.064% 68.84% 84ms 1.07% std::vector::_M_realloc_insert 74ms 0.94% 69.79% 84ms 1.07% vertexsort 61ms 0.78% 70.57% 78ms 1% AbstractElement::GetNodeGlobalIndex 50ms 0.64% 71.21% 77ms 0.98% std::basic_filebuf::xsputn 0 0% 71.21% 76ms 0.97% Cell::GetCellId 0 0% 71.21% 76ms 0.97% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.21% 76ms 0.97% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.026% 71.23% 76ms 0.97% std::filesystem::create_directory 1ms 0.013% 71.24% 76ms 0.97% std::filesystem::status 3ms 0.038% 71.28% 74ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeA 74ms 0.94% 72.23% 74ms 0.94% __GI___fstatat64 0 0% 72.23% 74ms 0.94% tcache_get (inline) 74ms 0.94% 73.17% 74ms 0.94% tcache_get_n (inline) 73ms 0.93% 74.10% 73ms 0.93% __memcpy_avx_unaligned_erms 73ms 0.93% 75.04% 73ms 0.93% std::_Rb_tree_insert_and_rebalance 73ms 0.93% 75.97% 73ms 0.93% std::vector::size (inline) 4ms 0.051% 76.02% 70ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 76.03% 65ms 0.83% Node::ClearAppliedForce 2ms 0.026% 76.06% 65ms 0.83% Node::ConstructNodeAttributes (inline) 61ms 0.78% 76.83% 61ms 0.78% Node::GetIndex 23ms 0.29% 77.13% 60ms 0.77% AbstractCellCycleModel::GetAge 60ms 0.77% 77.89% 60ms 0.77% counterclockwise 0 0% 77.89% 60ms 0.77% std::vector::vector (inline) 0 0% 77.89% 59ms 0.75% boost::numeric::ublas::norm_2 (inline) 17ms 0.22% 78.11% 59ms 0.75% boost::numeric::ublas::vector_norm_2::apply (inline) 28ms 0.36% 78.47% 58ms 0.74% AbstractTetrahedralMesh::GetElement 0 0% 78.47% 56ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 34ms 0.43% 78.90% 56ms 0.71% std::basic_streambuf::xsputn 54ms 0.69% 79.59% 54ms 0.69% boost::detail::shared_count::shared_count (inline) 2ms 0.026% 79.62% 53ms 0.68% CellPropertyCollection::AddProperty 53ms 0.68% 80.29% 53ms 0.68% [libchaste_mesh.so] 0 0% 80.29% 52ms 0.66% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.29% 52ms 0.66% std::_Vector_base::_Vector_base (inline) 3ms 0.038% 80.33% 52ms 0.66% std::__copy_move::__copy_m (inline) 0 0% 80.33% 52ms 0.66% std::__copy_move_a (inline) 0 0% 80.33% 52ms 0.66% std::__copy_move_a1 (inline) 0 0% 80.33% 52ms 0.66% std::__copy_move_a2 (inline) 0 0% 80.33% 52ms 0.66% std::copy (inline) 5ms 0.064% 80.40% 51ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.077% 80.47% 49ms 0.63% NodeAttributes::NodeAttributes 48ms 0.61% 81.08% 48ms 0.61% [libstdc++.so.6.0.33] 0 0% 81.08% 48ms 0.61% std::_Vector_base::_M_create_storage (inline) 0 0% 81.08% 47ms 0.6% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 81.08% 47ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.08% 47ms 0.6% std::__new_allocator::destroy (inline) 0 0% 81.08% 47ms 0.6% std::allocator_traits::destroy (inline) 0 0% 81.08% 47ms 0.6% std::map::find (inline) 46ms 0.59% 81.67% 46ms 0.59% boost::shared_ptr::operator-> (inline) 45ms 0.57% 82.25% 45ms 0.57% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.25% 44ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 44ms 0.56% 82.81% 44ms 0.56% Node::IsDeleted 0 0% 82.81% 43ms 0.55% CellPropertyCollection::~CellPropertyCollection (inline) 24ms 0.31% 83.11% 43ms 0.55% hack_digit 39ms 0.5% 83.61% 43ms 0.55% std::num_put::do_put 32ms 0.41% 84.02% 42ms 0.54% boost::numeric::ublas::c_matrix::operator() 41ms 0.52% 84.54% 41ms 0.52% boost::numeric::ublas::same_impl_ex 0 0% 84.54% 41ms 0.52% std::map::map (inline)