File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6623ms, 84.01% of 7884ms total Dropped 588 nodes (cum <= 39.42ms) flat flat% sum% cum cum% 0 0% 0% 7844ms 99.49% __libc_start_call_main 0 0% 0% 7844ms 99.49% __libc_start_main_impl 0 0% 0% 7844ms 99.49% _start 0 0% 0% 7827ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7827ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7827ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7827ms 99.28% main 0 0% 0% 7788ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7788ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7788ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7785ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3300ms 41.86% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2895ms 36.72% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.025% 2802ms 35.54% MeshBasedCellPopulation::Update 2ms 0.025% 0.051% 1581ms 20.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.063% 1438ms 18.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.11% 0.18% 1383ms 17.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.19% 1372ms 17.40% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.038% 0.23% 1369ms 17.36% MutableMesh::ReMesh 16ms 0.2% 0.43% 1201ms 15.23% MeshBasedCellPopulation::SpringIterator::operator++ 454ms 5.76% 6.19% 999ms 12.67% std::_Rb_tree::_M_lower_bound (inline) 102ms 1.29% 7.48% 968ms 12.28% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.038% 7.52% 952ms 12.08% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 7.55% 922ms 11.69% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.22% 7.76% 912ms 11.57% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.2% 7.97% 902ms 11.44% CellPopulationElementWriter::Visit 291ms 3.69% 11.66% 872ms 11.06% __dynamic_cast 46ms 0.58% 12.24% 807ms 10.24% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 8ms 0.1% 12.34% 791ms 10.03% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.33% 12.67% 775ms 9.83% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.71% 689ms 8.74% AbstractCellProperty::IsSubType (inline) 9ms 0.11% 12.82% 682ms 8.65% TetrahedralMesh::ImportFromMesher 6ms 0.076% 12.90% 616ms 7.81% std::ostream::operator<< (inline) 89ms 1.13% 14.03% 610ms 7.74% std::ostream::_M_insert 47ms 0.6% 14.62% 603ms 7.65% std::map::operator[] (partial-inline) 34ms 0.43% 15.06% 558ms 7.08% operator new 5ms 0.063% 15.12% 543ms 6.89% Cell::GetCellProliferativeType 2ms 0.025% 15.14% 541ms 6.86% triangulate 7ms 0.089% 15.23% 536ms 6.80% std::set::insert (inline) 16ms 0.2% 15.44% 529ms 6.71% std::_Rb_tree::_M_insert_unique 187ms 2.37% 17.81% 525ms 6.66% __GI___libc_malloc 15ms 0.19% 18.00% 523ms 6.63% std::_Rb_tree::find (inline) 36ms 0.46% 18.46% 513ms 6.51% std::__new_allocator::allocate (inline) 0 0% 18.46% 512ms 6.49% std::allocator_traits::allocate (inline) 0 0% 18.46% 509ms 6.46% std::_Rb_tree::lower_bound (inline) 0 0% 18.46% 509ms 6.46% std::map::lower_bound (inline) 6ms 0.076% 18.53% 484ms 6.14% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.025% 18.56% 479ms 6.08% AbstractCellBasedSimulation::DoCellBirth 473ms 6.00% 24.56% 473ms 6.00% __strcmp_avx2 0 0% 24.56% 473ms 6.00% std::set::count (inline) 0 0% 24.56% 462ms 5.86% delaunay 3ms 0.038% 24.59% 459ms 5.82% divconqdelaunay 0 0% 24.59% 438ms 5.56% std::_Rb_tree::_M_create_node (inline) 0 0% 24.59% 412ms 5.23% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 24.59% 405ms 5.14% std::_Rb_tree::_M_get_node (inline) 195ms 2.47% 27.07% 402ms 5.10% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.038% 27.11% 388ms 4.92% Cell::GetMutationState 34ms 0.43% 27.54% 374ms 4.74% std::_Rb_tree::~_Rb_tree (inline) 33ms 0.42% 27.96% 366ms 4.64% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.96% 365ms 4.63% NodeLocationWriter::Visit 3ms 0.038% 27.99% 359ms 4.55% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 27.99% 359ms 4.55% MeshBasedCellPopulation::GetDampingConstant 19ms 0.24% 28.23% 350ms 4.44% std::less::operator() (inline) 22ms 0.28% 28.51% 348ms 4.41% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.51% 348ms 4.41% std::set::~set (inline) 4ms 0.051% 28.56% 339ms 4.30% std::set::set (inline) 70ms 0.89% 29.45% 338ms 4.29% std::_Rb_tree::_M_erase 5ms 0.063% 29.52% 336ms 4.26% Cell::ReadyToDivide 331ms 4.20% 33.71% 331ms 4.20% std::operator< (inline) 20ms 0.25% 33.97% 329ms 4.17% std::num_put::_M_insert_float 0 0% 33.97% 322ms 4.08% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.97% 322ms 4.08% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.97% 317ms 4.02% OutputFileHandler::OpenOutputFile 309ms 3.92% 37.89% 309ms 3.92% std::_Rb_tree::_S_right (inline) 29ms 0.37% 38.25% 303ms 3.84% std::_Rb_tree::_M_copy (inline) 9ms 0.11% 38.37% 300ms 3.81% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.076% 38.44% 292ms 3.70% Element::Element 83ms 1.05% 39.50% 272ms 3.45% std::_Rb_tree::_M_clone_node (inline) 96ms 1.22% 40.72% 269ms 3.41% __GI___libc_free 1ms 0.013% 40.73% 261ms 3.31% CellProliferativeTypesWriter::VisitCell 0 0% 40.73% 257ms 3.26% Cell::HasCellProperty (inline) 4ms 0.051% 40.78% 257ms 3.26% CellPropertyCollection::HasProperty 3ms 0.038% 40.82% 256ms 3.25% std::__cxx11::collate::do_transform 2ms 0.025% 40.84% 255ms 3.23% AbstractCellProperty::IsType (inline) 0 0% 40.84% 252ms 3.20% std::_Rb_tree::_M_drop_node (inline) 6ms 0.076% 40.92% 250ms 3.17% divconqrecurse 4ms 0.051% 40.97% 242ms 3.07% ___vsnprintf 0 0% 40.97% 238ms 3.02% __vsnprintf_internal (inline) 8ms 0.1% 41.07% 238ms 3.02% std::__new_allocator::deallocate (inline) 34ms 0.43% 41.50% 235ms 2.98% __printf_buffer 150ms 1.90% 43.40% 233ms 2.96% _int_malloc 70ms 0.89% 44.29% 232ms 2.94% mergehulls 0 0% 44.29% 231ms 2.93% std::allocator_traits::deallocate (inline) 2ms 0.025% 44.32% 223ms 2.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 16ms 0.2% 44.52% 215ms 2.73% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 44.56% 197ms 2.50% Element::RegisterWithNodes (inline) 0 0% 44.56% 197ms 2.50% std::_Rb_tree::_M_put_node (inline) 0 0% 44.56% 193ms 2.45% Node::AddElement 32ms 0.41% 44.96% 188ms 2.38% TetrahedralMesh::Clear 53ms 0.67% 45.64% 182ms 2.31% AbstractCellProperty::IsSame 9ms 0.11% 45.75% 181ms 2.30% __printf_fp_l_buffer 0 0% 45.75% 181ms 2.30% __printf_fp_spec (inline) 7ms 0.089% 45.84% 179ms 2.27% MeshBasedCellPopulation::SpringsEnd (inline) 152ms 1.93% 47.77% 172ms 2.18% _int_free 0 0% 47.77% 168ms 2.13% std::basic_ofstream::basic_ofstream (inline) 65ms 0.82% 48.59% 165ms 2.09% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 48.59% 165ms 2.09% std::basic_ofstream::open (inline) 2ms 0.025% 48.62% 164ms 2.08% std::basic_filebuf::open 79ms 1.00% 49.62% 161ms 2.04% __printf_fp_buffer_1 34ms 0.43% 50.05% 143ms 1.81% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.038% 50.09% 139ms 1.76% boost::numeric::ublas::vector_assign (inline) 59ms 0.75% 50.84% 138ms 1.75% std::__ostream_insert 7ms 0.089% 50.93% 137ms 1.74% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.93% 134ms 1.70% OutputFileHandler::CommonConstructor 0 0% 50.93% 134ms 1.70% OutputFileHandler::OutputFileHandler 5ms 0.063% 50.99% 131ms 1.66% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 51.00% 130ms 1.65% _IO_new_fopen 0 0% 51.00% 130ms 1.65% std::__basic_file::open 0 0% 51.00% 129ms 1.64% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 51.01% 129ms 1.64% _IO_new_file_fopen 0 0% 51.01% 129ms 1.64% __fopen_internal (inline) 25ms 0.32% 51.33% 129ms 1.64% std::type_info::operator== (inline) 0 0% 51.33% 128ms 1.62% TetrahedralMesh::RefreshJacobianCachedData 52ms 0.66% 51.99% 128ms 1.62% std::num_put::_M_insert_int 1ms 0.013% 52.00% 126ms 1.60% __GI__IO_file_open 14ms 0.18% 52.18% 122ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 52.19% 121ms 1.53% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.19% 121ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.038% 52.23% 121ms 1.53% alternateaxes 0 0% 52.23% 120ms 1.52% AbstractCellBasedWriter::CloseFile 0 0% 52.23% 120ms 1.52% std::basic_ofstream::close (inline) 1ms 0.013% 52.25% 120ms 1.52% std::filesystem::permissions 119ms 1.51% 53.75% 119ms 1.51% __GI_fchmodat 0 0% 53.75% 119ms 1.51% std::basic_filebuf::close 11ms 0.14% 53.89% 118ms 1.50% std::_Rb_tree_const_iterator::operator++ (inline) 11ms 0.14% 54.03% 117ms 1.48% boost::detail::shared_count::~shared_count (inline) 0 0% 54.03% 117ms 1.48% boost::shared_ptr::~shared_ptr (inline) 117ms 1.48% 55.52% 117ms 1.48% std::_Rb_tree_increment 0 0% 55.52% 115ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 8ms 0.1% 55.62% 115ms 1.46% AbstractTetrahedralElement::CalculateInverseJacobian 107ms 1.36% 56.98% 115ms 1.46% vertexmedian 112ms 1.42% 58.40% 113ms 1.43% __libc_open64 1ms 0.013% 58.41% 108ms 1.37% std::_Vector_base::_M_allocate (inline) 4ms 0.051% 58.46% 108ms 1.37% std::operator<< (inline) 40ms 0.51% 58.97% 107ms 1.36% boost::shared_ptr::shared_ptr (inline) 106ms 1.34% 60.31% 106ms 1.34% std::_Rb_tree_insert_and_rebalance 7ms 0.089% 60.40% 105ms 1.33% std::vector::push_back (inline) 16ms 0.2% 60.60% 104ms 1.32% AbstractTetrahedralElement::RefreshJacobian 18ms 0.23% 60.83% 104ms 1.32% MeshBasedCellPopulation::SpringIterator::SpringIterator 66ms 0.84% 61.67% 103ms 1.31% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 102ms 1.29% 62.96% 103ms 1.31% boost::detail::sp_counted_base::release 6ms 0.076% 63.04% 101ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 5ms 0.063% 63.10% 101ms 1.28% AbstractTetrahedralElement::AbstractTetrahedralElement 28ms 0.36% 63.46% 101ms 1.28% boost::numeric::ublas::indexing_vector_assign 101ms 1.28% 64.74% 101ms 1.28% incircle 99ms 1.26% 65.99% 99ms 1.26% [libchaste_cell_based.so] 0 0% 65.99% 96ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.11% 66.11% 94ms 1.19% std::vector::_M_realloc_insert 0 0% 66.11% 91ms 1.15% tcache_get (inline) 91ms 1.15% 67.26% 91ms 1.15% tcache_get_n (inline) 3ms 0.038% 67.30% 90ms 1.14% Node::~Node 90ms 1.14% 68.44% 90ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 68.46% 88ms 1.12% std::basic_filebuf::overflow 1ms 0.013% 68.47% 87ms 1.10% std::__basic_file::xsputn 0 0% 68.47% 87ms 1.10% std::basic_filebuf::_M_convert_to_external 0 0% 68.47% 87ms 1.10% std::basic_filebuf::_M_terminate_output 85ms 1.08% 69.55% 85ms 1.08% __GI___libc_write 9ms 0.11% 69.66% 83ms 1.05% CellPropertyCollection::AddProperty 46ms 0.58% 70.24% 78ms 0.99% std::basic_filebuf::xsputn 52ms 0.66% 70.90% 77ms 0.98% std::basic_streambuf::xsputn 63ms 0.8% 71.70% 76ms 0.96% vertexsort 0 0% 71.70% 75ms 0.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.70% 75ms 0.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 35ms 0.44% 72.15% 74ms 0.94% AbstractElement::GetNodeLocation 2ms 0.025% 72.17% 73ms 0.93% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 72.18% 68ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 4ms 0.051% 72.23% 68ms 0.86% std::filesystem::status 0 0% 72.23% 67ms 0.85% Cell::GetCellId 64ms 0.81% 73.05% 67ms 0.85% boost::detail::shared_count::shared_count (inline) 3ms 0.038% 73.08% 67ms 0.85% std::filesystem::create_directory 4ms 0.051% 73.14% 66ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeB 66ms 0.84% 73.97% 66ms 0.84% __memcpy_avx_unaligned_erms 65ms 0.82% 74.80% 65ms 0.82% __GI___fstatat64 50ms 0.63% 75.43% 65ms 0.82% std::num_put::do_put 64ms 0.81% 76.24% 64ms 0.81% Node::GetIndex 64ms 0.81% 77.05% 64ms 0.81% [libchaste_mesh.so] 50ms 0.63% 77.69% 61ms 0.77% AbstractElement::GetNodeGlobalIndex 41ms 0.52% 78.21% 61ms 0.77% malloc_consolidate 2ms 0.025% 78.23% 60ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeA 60ms 0.76% 79.00% 60ms 0.76% counterclockwise 2ms 0.025% 79.02% 59ms 0.75% Node::ConstructNodeAttributes (inline) 1ms 0.013% 79.03% 58ms 0.74% Node::ClearAppliedForce 0 0% 79.03% 58ms 0.74% boost::numeric::ublas::norm_2 (inline) 17ms 0.22% 79.25% 58ms 0.74% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 79.25% 55ms 0.7% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.25% 55ms 0.7% std::__new_allocator::destroy (inline) 0 0% 79.25% 55ms 0.7% std::allocator_traits::destroy (inline) 53ms 0.67% 79.92% 53ms 0.67% std::vector::size (inline) 25ms 0.32% 80.24% 52ms 0.66% AbstractCellCycleModel::GetAge 1ms 0.013% 80.25% 52ms 0.66% BoundaryNodeWriter::Visit 0 0% 80.25% 51ms 0.65% std::vector::vector (inline) 0 0% 80.25% 50ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 49ms 0.62% 80.87% 49ms 0.62% Node::IsDeleted 26ms 0.33% 81.20% 47ms 0.6% AbstractTetrahedralMesh::GetElement 2ms 0.025% 81.23% 47ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.23% 47ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 81.23% 46ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 6ms 0.076% 81.30% 46ms 0.58% NodeAttributes::NodeAttributes 0 0% 81.30% 46ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 45ms 0.57% 81.87% 45ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 81.87% 45ms 0.57% std::_Vector_base::_M_create_storage (inline) 16ms 0.2% 82.08% 43ms 0.55% Determinant (inline) 0 0% 82.08% 43ms 0.55% std::map::find (inline) 0 0% 82.08% 41ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline) 26ms 0.33% 82.41% 41ms 0.52% NodeAttributes::AddAppliedForceContribution 41ms 0.52% 82.93% 41ms 0.52% boost::numeric::ublas::c_vector::operator() 0 0% 82.93% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 40ms 0.51% 83.43% 40ms 0.51% [libstdc++.so.6.0.33] 25ms 0.32% 83.75% 40ms 0.51% boost::numeric::ublas::c_matrix::operator() (partial-inline) 20ms 0.25% 84.01% 40ms 0.51% hack_digit