File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6685ms, 84.72% of 7891ms total Dropped 584 nodes (cum <= 39.45ms) flat flat% sum% cum cum% 0 0% 0% 7855ms 99.54% __libc_start_call_main 0 0% 0% 7855ms 99.54% __libc_start_main_impl 0 0% 0% 7855ms 99.54% _start 0 0% 0% 7839ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7839ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7839ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7839ms 99.34% main 0 0% 0% 7801ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7801ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7801ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7799ms 98.83% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3393ms 43.00% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.038% 2951ms 37.40% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.063% 2907ms 36.84% MeshBasedCellPopulation::Update 2ms 0.025% 0.089% 1456ms 18.45% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.038% 0.13% 1446ms 18.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.13% 1409ms 17.86% MutableMesh::ReMesh 1ms 0.013% 0.14% 1301ms 16.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.076% 0.22% 1250ms 15.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.42% 1248ms 15.82% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.43% 1.85% 1027ms 13.01% TetrahedralMesh::EdgeIterator::operator++ 406ms 5.15% 7.00% 976ms 12.37% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.05% 921ms 11.67% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 15ms 0.19% 7.24% 914ms 11.58% CellPopulationElementWriter::Visit 15ms 0.19% 7.43% 878ms 11.13% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.013% 7.44% 845ms 10.71% AbstractTwoBodyInteractionForce::AddForceContribution 238ms 3.02% 10.45% 829ms 10.51% __dynamic_cast 4ms 0.051% 10.51% 786ms 9.96% MeshBasedCellPopulation::AcceptCellWriter 53ms 0.67% 11.18% 729ms 9.24% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.1% 11.28% 714ms 9.05% TetrahedralMesh::ImportFromMesher 33ms 0.42% 11.70% 702ms 8.90% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 11.71% 682ms 8.64% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 11.73% 612ms 7.76% std::ostream::operator<< (inline) 62ms 0.79% 12.52% 611ms 7.74% std::map::operator[] (partial-inline) 83ms 1.05% 13.57% 610ms 7.73% std::ostream::_M_insert 41ms 0.52% 14.09% 540ms 6.84% operator new 21ms 0.27% 14.36% 537ms 6.81% std::_Rb_tree::find (inline) 3ms 0.038% 14.40% 533ms 6.75% triangulate 514ms 6.51% 20.91% 514ms 6.51% __strcmp_avx2 2ms 0.025% 20.94% 513ms 6.50% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.089% 21.02% 508ms 6.44% std::set::insert (inline) 168ms 2.13% 23.15% 501ms 6.35% __GI___libc_malloc 10ms 0.13% 23.28% 501ms 6.35% std::_Rb_tree::_M_insert_unique 0 0% 23.28% 496ms 6.29% std::_Rb_tree::lower_bound (inline) 0 0% 23.28% 496ms 6.29% std::map::lower_bound (inline) 0 0% 23.28% 489ms 6.20% std::set::count (inline) 11ms 0.14% 23.42% 487ms 6.17% Cell::GetCellProliferativeType 4ms 0.051% 23.47% 476ms 6.03% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.47% 471ms 5.97% delaunay 2ms 0.025% 23.50% 471ms 5.97% divconqdelaunay 16ms 0.2% 23.70% 465ms 5.89% std::__new_allocator::allocate (inline) 0 0% 23.70% 462ms 5.85% std::allocator_traits::allocate (inline) 201ms 2.55% 26.25% 437ms 5.54% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.41% 26.65% 395ms 5.01% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.076% 26.73% 389ms 4.93% Cell::GetMutationState 0 0% 26.73% 385ms 4.88% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 26.74% 384ms 4.87% NodeLocationWriter::Visit 8ms 0.1% 26.84% 376ms 4.76% std::less::operator() (inline) 0 0% 26.84% 373ms 4.73% std::set::~set (inline) 368ms 4.66% 31.50% 368ms 4.66% std::operator< (inline) 74ms 0.94% 32.44% 361ms 4.57% std::_Rb_tree::_M_erase 0 0% 32.44% 360ms 4.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 32.44% 353ms 4.47% std::_Rb_tree::_M_get_node (inline) 117ms 1.48% 33.92% 340ms 4.31% __GI___libc_free 27ms 0.34% 34.27% 339ms 4.30% std::num_put::_M_insert_float 337ms 4.27% 38.54% 337ms 4.27% std::_Rb_tree::_S_right (inline) 25ms 0.32% 38.85% 332ms 4.21% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 38.85% 328ms 4.16% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.85% 327ms 4.14% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 38.87% 325ms 4.12% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 38.89% 323ms 4.09% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 38.89% 320ms 4.06% OutputFileHandler::OpenOutputFile 10ms 0.13% 39.02% 318ms 4.03% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.2% 39.22% 315ms 3.99% std::_Rb_tree::_M_insert_ (inline) 4ms 0.051% 39.27% 314ms 3.98% Cell::ReadyToDivide 2ms 0.025% 39.30% 310ms 3.93% std::set::set (inline) 6ms 0.076% 39.37% 296ms 3.75% std::__new_allocator::deallocate (inline) 3ms 0.038% 39.41% 293ms 3.71% Element::Element 0 0% 39.41% 292ms 3.70% std::allocator_traits::deallocate (inline) 5ms 0.063% 39.48% 270ms 3.42% divconqrecurse 1ms 0.013% 39.49% 269ms 3.41% AbstractCellProperty::IsType (inline) 0 0% 39.49% 268ms 3.40% std::_Rb_tree::_M_drop_node (inline) 27ms 0.34% 39.83% 266ms 3.37% std::_Rb_tree::_M_copy (inline) 4ms 0.051% 39.88% 264ms 3.35% std::__cxx11::collate::do_transform 75ms 0.95% 40.83% 254ms 3.22% mergehulls 4ms 0.051% 40.88% 250ms 3.17% ___vsnprintf 0 0% 40.88% 246ms 3.12% __vsnprintf_internal (inline) 166ms 2.10% 42.99% 245ms 3.10% _int_malloc 3ms 0.038% 43.02% 242ms 3.07% CellPropertyCollection::HasProperty 29ms 0.37% 43.39% 241ms 3.05% __printf_buffer 0 0% 43.39% 239ms 3.03% Cell::HasCellProperty (inline) 73ms 0.93% 44.32% 232ms 2.94% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.32% 230ms 2.91% std::_Rb_tree::_M_put_node (inline) 4ms 0.051% 44.37% 228ms 2.89% CellProliferativeTypesWriter::VisitCell 194ms 2.46% 46.83% 222ms 2.81% _int_free 5ms 0.063% 46.89% 217ms 2.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 47ms 0.6% 47.48% 214ms 2.71% AbstractCellProperty::IsSame 19ms 0.24% 47.73% 212ms 2.69% TetrahedralMesh::Clear 8ms 0.1% 47.83% 210ms 2.66% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.13% 47.95% 196ms 2.48% __printf_fp_l_buffer 0 0% 47.95% 196ms 2.48% __printf_fp_spec (inline) 3ms 0.038% 47.99% 189ms 2.40% Element::RegisterWithNodes (inline) 6ms 0.076% 48.07% 187ms 2.37% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.051% 48.12% 185ms 2.34% Node::AddElement 91ms 1.15% 49.27% 176ms 2.23% __printf_fp_buffer_1 58ms 0.74% 50.01% 176ms 2.23% std::_Rb_tree::_M_get_insert_unique_pos (inline) 29ms 0.37% 50.37% 167ms 2.12% std::type_info::operator== (inline) 13ms 0.16% 50.54% 164ms 2.08% AbstractTetrahedralElement::CalculateJacobian 33ms 0.42% 50.96% 160ms 2.03% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.96% 153ms 1.94% OutputFileHandler::OutputFileHandler 1ms 0.013% 50.97% 152ms 1.93% OutputFileHandler::CommonConstructor 0 0% 50.97% 152ms 1.93% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.97% 150ms 1.90% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 50.98% 149ms 1.89% AbstractCellBasedWriter::CloseFile 1ms 0.013% 50.99% 148ms 1.88% std::basic_ofstream::close (inline) 1ms 0.013% 51.01% 147ms 1.86% std::basic_filebuf::close 60ms 0.76% 51.77% 145ms 1.84% std::__ostream_insert 0 0% 51.77% 143ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.77% 143ms 1.81% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.77% 143ms 1.81% std::basic_filebuf::open 0 0% 51.77% 143ms 1.81% std::basic_ofstream::open (inline) 13ms 0.16% 51.93% 133ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 51.95% 132ms 1.67% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.95% 132ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 51.96% 132ms 1.67% alternateaxes 1ms 0.013% 51.97% 131ms 1.66% std::filesystem::permissions 7ms 0.089% 52.06% 130ms 1.65% AbstractTetrahedralElement::CalculateInverseJacobian 117ms 1.48% 53.54% 130ms 1.65% vertexmedian 129ms 1.63% 55.18% 129ms 1.63% __GI_fchmodat 6ms 0.076% 55.25% 128ms 1.62% boost::numeric::ublas::vector_assign (inline) 25ms 0.32% 55.57% 127ms 1.61% std::num_put::_M_insert_int 5ms 0.063% 55.63% 126ms 1.60% Node::~Node 2ms 0.025% 55.66% 121ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 121ms 1.53% 57.19% 121ms 1.53% incircle 71ms 0.9% 58.09% 118ms 1.50% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 14ms 0.18% 58.27% 117ms 1.48% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 58.28% 114ms 1.44% std::__basic_file::open 0 0% 58.28% 113ms 1.43% _IO_new_fopen 0 0% 58.28% 113ms 1.43% __fopen_internal (inline) 2ms 0.025% 58.31% 112ms 1.42% std::operator<< (inline) 1ms 0.013% 58.32% 111ms 1.41% _IO_new_file_fopen 3ms 0.038% 58.36% 110ms 1.39% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 58.37% 110ms 1.39% std::_Vector_base::_M_allocate (inline) 109ms 1.38% 59.75% 109ms 1.38% std::_Rb_tree_insert_and_rebalance 108ms 1.37% 61.12% 108ms 1.37% std::_Rb_tree_increment 0 0% 61.12% 107ms 1.36% __GI__IO_file_open 1ms 0.013% 61.13% 105ms 1.33% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.063% 61.20% 105ms 1.33% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.15% 61.35% 104ms 1.32% AbstractTetrahedralElement::RefreshJacobian 2ms 0.025% 61.37% 103ms 1.31% std::vector::push_back (inline) 3ms 0.038% 61.41% 100ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 61.41% 100ms 1.27% boost::shared_ptr::~shared_ptr (inline) 9ms 0.11% 61.53% 99ms 1.25% std::vector::_M_realloc_insert 1ms 0.013% 61.54% 98ms 1.24% std::basic_filebuf::_M_terminate_output 4ms 0.051% 61.59% 97ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.038% 61.63% 97ms 1.23% std::basic_filebuf::overflow 50ms 0.63% 62.26% 96ms 1.22% boost::shared_ptr::shared_ptr (inline) 95ms 1.20% 63.46% 95ms 1.20% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 95ms 1.20% 64.67% 95ms 1.20% boost::detail::sp_counted_base::release 93ms 1.18% 65.85% 93ms 1.18% __GI___libc_write 92ms 1.17% 67.01% 93ms 1.18% __libc_open64 0 0% 67.01% 93ms 1.18% std::__basic_file::xsputn 0 0% 67.01% 93ms 1.18% std::basic_filebuf::_M_convert_to_external 34ms 0.43% 67.44% 90ms 1.14% boost::numeric::ublas::indexing_vector_assign 0 0% 67.44% 86ms 1.09% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 60ms 0.76% 68.20% 86ms 1.09% std::basic_streambuf::xsputn 1ms 0.013% 68.22% 86ms 1.09% std::filesystem::create_directory 50ms 0.63% 68.85% 83ms 1.05% std::basic_filebuf::xsputn 2ms 0.025% 68.88% 81ms 1.03% AbstractCellPopulation::GetLocationIndexUsingCell 79ms 1.00% 69.88% 79ms 1.00% [libchaste_cell_based.so] 0 0% 69.88% 78ms 0.99% tcache_get (inline) 78ms 0.99% 70.87% 78ms 0.99% tcache_get_n (inline) 27ms 0.34% 71.21% 77ms 0.98% AbstractElement::GetNodeLocation 0 0% 71.21% 74ms 0.94% Cell::GetCellId 2ms 0.025% 71.23% 74ms 0.94% std::filesystem::status 72ms 0.91% 72.15% 72ms 0.91% __GI___fstatat64 6ms 0.076% 72.22% 70ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 56ms 0.71% 72.93% 66ms 0.84% AbstractElement::GetNodeGlobalIndex 66ms 0.84% 73.77% 66ms 0.84% Node::GetIndex 3ms 0.038% 73.81% 66ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 43ms 0.54% 74.35% 65ms 0.82% malloc_consolidate 4ms 0.051% 74.40% 64ms 0.81% std::_Vector_base::_M_deallocate (inline) 62ms 0.79% 75.19% 62ms 0.79% __memcpy_avx_unaligned_erms 7ms 0.089% 75.28% 59ms 0.75% CellPropertyCollection::AddProperty 21ms 0.27% 75.54% 58ms 0.74% Determinant (inline) 0 0% 75.54% 58ms 0.74% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 75.54% 58ms 0.74% std::vector::vector (inline) 48ms 0.61% 76.15% 57ms 0.72% std::num_put::do_put 57ms 0.72% 76.87% 57ms 0.72% std::vector::size (inline) 56ms 0.71% 77.58% 56ms 0.71% boost::shared_ptr::operator-> (inline) 41ms 0.52% 78.10% 55ms 0.7% boost::numeric::ublas::c_matrix::operator() 55ms 0.7% 78.80% 55ms 0.7% counterclockwise 51ms 0.65% 79.44% 55ms 0.7% vertexsort 35ms 0.44% 79.89% 53ms 0.67% AbstractTetrahedralMesh::GetElement 0 0% 79.89% 53ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 53ms 0.67% 80.56% 53ms 0.67% [libchaste_mesh.so] 1ms 0.013% 80.57% 53ms 0.67% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.076% 80.65% 52ms 0.66% Node::ConstructNodeAttributes (inline) 50ms 0.63% 81.28% 50ms 0.63% Node::IsDeleted 0 0% 81.28% 50ms 0.63% std::_Vector_base::_Vector_base (inline) 0 0% 81.28% 49ms 0.62% BoundaryNodeWriter::Visit 0 0% 81.28% 48ms 0.61% Node::ClearAppliedForce 0 0% 81.28% 48ms 0.61% std::_Vector_base::_M_create_storage (inline) 0 0% 81.28% 46ms 0.58% AbstractCentreBasedCellPopulation::CreateCellPair 16ms 0.2% 81.49% 46ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 45ms 0.57% 82.06% 46ms 0.58% boost::detail::shared_count::shared_count (inline) 32ms 0.41% 82.46% 45ms 0.57% hack_digit 44ms 0.56% 83.02% 44ms 0.56% Node::rGetLocation 44ms 0.56% 83.58% 44ms 0.56% __GI___mkdir 44ms 0.56% 84.13% 44ms 0.56% boost::numeric::ublas::c_vector::operator() (inline) 4ms 0.051% 84.18% 43ms 0.54% Element::~Element 0 0% 84.18% 43ms 0.54% std::map::find (inline) 1ms 0.013% 84.20% 42ms 0.53% _IO_new_fclose 0 0% 84.20% 42ms 0.53% std::__basic_file::close 0 0% 84.20% 41ms 0.52% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 41ms 0.52% 84.72% 41ms 0.52% unlink_chunk 0 0% 84.72% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline)