File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6855ms, 85.67% of 8002ms total Dropped 568 nodes (cum <= 40.01ms) flat flat% sum% cum cum% 0 0% 0% 7964ms 99.53% __libc_start_call_main 0 0% 0% 7964ms 99.53% __libc_start_main_impl 0 0% 0% 7964ms 99.53% _start 0 0% 0% 7946ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7946ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7946ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7946ms 99.30% main 0 0% 0% 7901ms 98.74% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7901ms 98.74% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7901ms 98.74% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7899ms 98.71% AbstractCellBasedSimulation::Solve 0 0% 0% 3431ms 42.88% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.012% 2976ms 37.19% MeshBasedCellPopulation::Update 1ms 0.012% 0.025% 2902ms 36.27% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.037% 1556ms 19.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.062% 1471ms 18.38% MutableMesh::ReMesh 2ms 0.025% 0.087% 1463ms 18.28% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.1% 1410ms 17.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.05% 0.15% 1354ms 16.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.4% 1285ms 16.06% MeshBasedCellPopulation::SpringIterator::operator++ 130ms 1.62% 2.02% 1036ms 12.95% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 2.06% 974ms 12.17% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 425ms 5.31% 7.37% 968ms 12.10% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.40% 952ms 11.90% AbstractTwoBodyInteractionForce::AddForceContribution 236ms 2.95% 10.35% 902ms 11.27% __dynamic_cast 7ms 0.087% 10.43% 896ms 11.20% CellPopulationElementWriter::Visit 6ms 0.075% 10.51% 885ms 11.06% CellPropertyCollection::GetPropertiesType (inline) 31ms 0.39% 10.90% 826ms 10.32% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 31ms 0.39% 11.28% 806ms 10.07% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.33% 798ms 9.97% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.037% 11.37% 710ms 8.87% AbstractCellProperty::IsSubType (inline) 4ms 0.05% 11.42% 682ms 8.52% TetrahedralMesh::ImportFromMesher 1ms 0.012% 11.43% 618ms 7.72% triangulate 70ms 0.87% 12.31% 605ms 7.56% std::map::operator[] (partial-inline) 0 0% 12.31% 572ms 7.15% std::ostream::operator<< (inline) 81ms 1.01% 13.32% 571ms 7.14% std::ostream::_M_insert 0 0% 13.32% 554ms 6.92% delaunay 1ms 0.012% 13.33% 552ms 6.90% divconqdelaunay 6ms 0.075% 13.41% 531ms 6.64% LegacyCellProliferativeTypesWriter::VisitCell 32ms 0.4% 13.81% 531ms 6.64% std::_Rb_tree::find (inline) 33ms 0.41% 14.22% 529ms 6.61% operator new 8ms 0.1% 14.32% 518ms 6.47% std::set::insert (inline) 10ms 0.12% 14.45% 510ms 6.37% std::_Rb_tree::_M_insert_unique 230ms 2.87% 17.32% 508ms 6.35% __cxxabiv1::__si_class_type_info::__do_dyncast 503ms 6.29% 23.61% 503ms 6.29% __strcmp_avx2 166ms 2.07% 25.68% 499ms 6.24% __GI___libc_malloc 0 0% 25.68% 493ms 6.16% std::_Rb_tree::lower_bound (inline) 0 0% 25.68% 493ms 6.16% std::map::lower_bound (inline) 3ms 0.037% 25.72% 482ms 6.02% Cell::GetCellProliferativeType 33ms 0.41% 26.13% 479ms 5.99% std::__new_allocator::allocate (inline) 0 0% 26.13% 477ms 5.96% std::allocator_traits::allocate (inline) 0 0% 26.13% 471ms 5.89% std::set::count (inline) 45ms 0.56% 26.69% 455ms 5.69% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.037% 26.73% 440ms 5.50% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.73% 421ms 5.26% std::set::~set (inline) 70ms 0.87% 27.61% 406ms 5.07% std::_Rb_tree::_M_erase 3ms 0.037% 27.64% 390ms 4.87% Cell::GetMutationState 0 0% 27.64% 377ms 4.71% std::_Rb_tree::_M_create_node (inline) 3ms 0.037% 27.68% 367ms 4.59% NodeLocationWriter::Visit 0 0% 27.68% 356ms 4.45% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.68% 346ms 4.32% std::_Rb_tree::_M_get_node (inline) 26ms 0.32% 28.01% 344ms 4.30% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.1% 28.11% 336ms 4.20% divconqrecurse 335ms 4.19% 32.29% 335ms 4.19% std::_Rb_tree::_S_right (inline) 5ms 0.062% 32.35% 334ms 4.17% std::less::operator() (inline) 329ms 4.11% 36.47% 329ms 4.11% std::operator< (inline) 31ms 0.39% 36.85% 327ms 4.09% std::num_put::_M_insert_float 1ms 0.012% 36.87% 326ms 4.07% MeshBasedCellPopulation::GetDampingConstant 3ms 0.037% 36.90% 325ms 4.06% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.05% 36.95% 321ms 4.01% std::set::set (inline) 1ms 0.012% 36.97% 316ms 3.95% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 36.97% 316ms 3.95% std::_Rb_tree::_M_drop_node (inline) 0 0% 36.97% 314ms 3.92% AbstractCellBasedWriter::OpenOutputFileForAppend 21ms 0.26% 37.23% 313ms 3.91% std::_Rb_tree::_M_insert_ (inline) 9ms 0.11% 37.34% 309ms 3.86% AbstractCellPopulation::IsCellAttachedToLocationIndex 85ms 1.06% 38.40% 309ms 3.86% mergehulls 0 0% 38.40% 306ms 3.82% OutputFileHandler::OpenOutputFile 81ms 1.01% 39.42% 297ms 3.71% __GI___libc_free 5ms 0.062% 39.48% 291ms 3.64% Element::Element 14ms 0.17% 39.65% 288ms 3.60% std::__new_allocator::deallocate (inline) 0 0% 39.65% 284ms 3.55% std::allocator_traits::deallocate (inline) 33ms 0.41% 40.06% 282ms 3.52% std::_Rb_tree::_M_copy (inline) 8ms 0.1% 40.16% 278ms 3.47% Cell::ReadyToDivide 162ms 2.02% 42.19% 266ms 3.32% _int_malloc 0 0% 42.19% 253ms 3.16% std::_Rb_tree::_M_put_node (inline) 4ms 0.05% 42.24% 253ms 3.16% std::__cxx11::collate::do_transform 3ms 0.037% 42.28% 247ms 3.09% ___vsnprintf 0 0% 42.28% 244ms 3.05% __vsnprintf_internal (inline) 40ms 0.5% 42.78% 242ms 3.02% __printf_buffer 80ms 1% 43.78% 242ms 3.02% std::_Rb_tree::_M_clone_node (inline) 5ms 0.062% 43.84% 231ms 2.89% AbstractCellProperty::IsType (inline) 8ms 0.1% 43.94% 231ms 2.89% CellPropertyCollection::HasProperty 2ms 0.025% 43.96% 228ms 2.85% CellProliferativeTypesWriter::VisitCell 0 0% 43.96% 226ms 2.82% Cell::HasCellProperty (inline) 184ms 2.30% 46.26% 216ms 2.70% _int_free 6ms 0.075% 46.34% 192ms 2.40% MeshBasedCellPopulation::SpringsEnd (inline) 66ms 0.82% 47.16% 188ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.012% 47.18% 186ms 2.32% __printf_fp_spec (inline) 10ms 0.12% 47.30% 185ms 2.31% TetrahedralMesh::Clear 3ms 0.037% 47.34% 185ms 2.31% __printf_fp_l_buffer 2ms 0.025% 47.36% 183ms 2.29% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.025% 47.39% 181ms 2.26% Element::RegisterWithNodes (inline) 3ms 0.037% 47.43% 175ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 39ms 0.49% 47.91% 175ms 2.19% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.037% 47.95% 173ms 2.16% Node::AddElement 79ms 0.99% 48.94% 168ms 2.10% __printf_fp_buffer_1 7ms 0.087% 49.03% 163ms 2.04% AbstractTetrahedralElement::CalculateJacobian 1ms 0.012% 49.04% 159ms 1.99% std::basic_filebuf::close 1ms 0.012% 49.05% 158ms 1.97% AbstractCellBasedWriter::CloseFile 0 0% 49.05% 158ms 1.97% AbstractCellPopulation::CloseRoundRobinWritersFiles 41ms 0.51% 49.56% 158ms 1.97% AbstractCellProperty::IsSame 0 0% 49.56% 158ms 1.97% std::basic_ofstream::close (inline) 0 0% 49.56% 148ms 1.85% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.56% 145ms 1.81% std::basic_ofstream::open (inline) 0 0% 49.56% 144ms 1.80% std::basic_filebuf::open 0 0% 49.56% 143ms 1.79% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.22% 49.79% 143ms 1.79% boost::detail::shared_count::~shared_count (inline) 0 0% 49.79% 143ms 1.79% boost::shared_ptr::~shared_ptr (inline) 140ms 1.75% 51.54% 140ms 1.75% incircle 0 0% 51.54% 135ms 1.69% OutputFileHandler::CommonConstructor 0 0% 51.54% 135ms 1.69% OutputFileHandler::OutputFileHandler 15ms 0.19% 51.72% 134ms 1.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.05% 51.77% 133ms 1.66% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 51.77% 132ms 1.65% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.77% 132ms 1.65% alternateaxes 4ms 0.05% 51.82% 132ms 1.65% boost::numeric::ublas::vector_assign (inline) 0 0% 51.82% 131ms 1.64% std::_Vector_base::_M_allocate (inline) 122ms 1.52% 53.35% 131ms 1.64% vertexmedian 22ms 0.27% 53.62% 130ms 1.62% AbstractTetrahedralElement::RefreshJacobian 0 0% 53.62% 129ms 1.61% OutputFileHandler::MakeFoldersAndReturnFullPath 20ms 0.25% 53.87% 128ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 53.87% 127ms 1.59% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.012% 53.89% 127ms 1.59% std::filesystem::permissions 126ms 1.57% 55.46% 126ms 1.57% __GI_fchmodat 75ms 0.94% 56.40% 125ms 1.56% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 59ms 0.74% 57.14% 124ms 1.55% boost::shared_ptr::shared_ptr (inline) 8ms 0.1% 57.24% 121ms 1.51% Node::~Node 3ms 0.037% 57.27% 121ms 1.51% boost::numeric::ublas::c_vector::c_vector (inline) 49ms 0.61% 57.89% 120ms 1.50% std::__ostream_insert 1ms 0.012% 57.90% 119ms 1.49% std::__basic_file::open 0 0% 57.90% 118ms 1.47% _IO_new_fopen 0 0% 57.90% 118ms 1.47% __fopen_internal (inline) 34ms 0.42% 58.32% 117ms 1.46% std::type_info::operator== (inline) 2ms 0.025% 58.35% 115ms 1.44% _IO_new_file_fopen 1ms 0.012% 58.36% 113ms 1.41% __GI__IO_file_open 111ms 1.39% 59.75% 113ms 1.41% boost::detail::sp_counted_base::release 23ms 0.29% 60.03% 113ms 1.41% std::num_put::_M_insert_int 7ms 0.087% 60.12% 111ms 1.39% std::vector::push_back (inline) 1ms 0.012% 60.13% 110ms 1.37% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.13% 106ms 1.32% std::basic_filebuf::_M_terminate_output 1ms 0.012% 60.15% 104ms 1.30% std::basic_filebuf::overflow 103ms 1.29% 61.43% 103ms 1.29% [libchaste_cell_based.so] 103ms 1.29% 62.72% 103ms 1.29% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 62.75% 103ms 1.29% std::basic_filebuf::_M_convert_to_external 101ms 1.26% 64.01% 102ms 1.27% __GI___libc_write 0 0% 64.01% 101ms 1.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 64.01% 101ms 1.26% std::__basic_file::xsputn 28ms 0.35% 64.36% 100ms 1.25% boost::numeric::ublas::indexing_vector_assign 5ms 0.062% 64.42% 99ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.012% 64.43% 99ms 1.24% std::operator<< (inline) 9ms 0.11% 64.55% 99ms 1.24% std::vector::_M_realloc_insert 95ms 1.19% 65.73% 95ms 1.19% __libc_open64 56ms 0.7% 66.43% 94ms 1.17% std::basic_filebuf::xsputn 39ms 0.49% 66.92% 91ms 1.14% AbstractElement::GetNodeLocation 88ms 1.10% 68.02% 88ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 87ms 1.09% 69.11% 87ms 1.09% counterclockwise 7ms 0.087% 69.20% 85ms 1.06% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.05% 69.25% 84ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.025% 69.27% 82ms 1.02% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 82ms 1.02% 70.29% 82ms 1.02% std::_Rb_tree_increment 1ms 0.012% 70.31% 80ms 1% std::filesystem::create_directory 62ms 0.77% 71.08% 77ms 0.96% AbstractElement::GetNodeGlobalIndex 68ms 0.85% 71.93% 77ms 0.96% vertexsort 0 0% 71.93% 76ms 0.95% Cell::GetCellId 60ms 0.75% 72.68% 75ms 0.94% malloc_consolidate 73ms 0.91% 73.59% 73ms 0.91% std::vector::size (inline) 4ms 0.05% 73.64% 69ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 7ms 0.087% 73.73% 68ms 0.85% CellPropertyCollection::AddProperty 35ms 0.44% 74.17% 66ms 0.82% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.012% 74.18% 65ms 0.81% AbstractCentreBasedCellPopulation::CreateCellPair 65ms 0.81% 74.99% 65ms 0.81% Node::GetIndex 63ms 0.79% 75.78% 65ms 0.81% boost::detail::shared_count::shared_count (inline) 0 0% 75.78% 65ms 0.81% tcache_get (inline) 65ms 0.81% 76.59% 65ms 0.81% tcache_get_n (inline) 4ms 0.05% 76.64% 64ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.64% 64ms 0.8% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.64% 64ms 0.8% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 76.64% 63ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.64% 63ms 0.79% std::__new_allocator::destroy (inline) 0 0% 76.64% 63ms 0.79% std::allocator_traits::destroy (inline) 0 0% 76.64% 60ms 0.75% std::vector::vector (inline) 59ms 0.74% 77.38% 59ms 0.74% [libchaste_mesh.so] 44ms 0.55% 77.93% 58ms 0.72% hack_digit 1ms 0.012% 77.94% 58ms 0.72% std::filesystem::status 27ms 0.34% 78.28% 56ms 0.7% AbstractCellCycleModel::GetAge 56ms 0.7% 78.98% 56ms 0.7% __GI___fstatat64 0 0% 78.98% 55ms 0.69% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 55ms 0.69% 79.67% 55ms 0.69% boost::shared_ptr::operator-> (inline) 0 0% 79.67% 52ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 52ms 0.65% 80.32% 52ms 0.65% __GI___mkdir 0 0% 80.32% 52ms 0.65% std::map::find (inline) 51ms 0.64% 80.95% 51ms 0.64% __memcpy_avx_unaligned_erms 0 0% 80.95% 50ms 0.62% boost::numeric::ublas::norm_2 (inline) 14ms 0.17% 81.13% 50ms 0.62% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 81.13% 50ms 0.62% std::_Vector_base::_M_create_storage (inline) 0 0% 81.13% 50ms 0.62% std::_Vector_base::_Vector_base (inline) 1ms 0.012% 81.14% 48ms 0.6% Node::ConstructNodeAttributes (inline) 0 0% 81.14% 47ms 0.59% Node::ClearAppliedForce 44ms 0.55% 81.69% 47ms 0.59% std::num_put::do_put 46ms 0.57% 82.27% 46ms 0.57% Node::rGetLocation 2ms 0.025% 82.29% 46ms 0.57% _IO_new_fclose 32ms 0.4% 82.69% 46ms 0.57% std::basic_streambuf::xsputn 10ms 0.12% 82.82% 45ms 0.56% Inverse 0 0% 82.82% 45ms 0.56% std::__basic_file::close 44ms 0.55% 83.37% 44ms 0.55% AbstractElement::IsDeleted 44ms 0.55% 83.92% 44ms 0.55% boost::numeric::ublas::c_vector::operator() 21ms 0.26% 84.18% 43ms 0.54% AbstractTetrahedralMesh::GetElement 14ms 0.17% 84.35% 43ms 0.54% AbstractTetrahedralMesh::GetNumAllElements 43ms 0.54% 84.89% 43ms 0.54% [libstdc++.so.6.0.33] 1ms 0.012% 84.90% 42ms 0.52% _IO_new_file_close_it 1ms 0.012% 84.92% 42ms 0.52% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.12% 85.04% 42ms 0.52% std::__copy_move::__copy_m (inline) 0 0% 85.04% 42ms 0.52% std::__copy_move_a (inline) 0 0% 85.04% 42ms 0.52% std::__copy_move_a1 (inline) 0 0% 85.04% 42ms 0.52% std::__copy_move_a2 (inline) 0 0% 85.04% 42ms 0.52% std::copy (inline) 9ms 0.11% 85.15% 41ms 0.51% Determinant (inline) 41ms 0.51% 85.67% 41ms 0.51% Node::IsDeleted