File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6614ms, 84.08% of 7866ms total Dropped 571 nodes (cum <= 39.33ms) flat flat% sum% cum cum% 0 0% 0% 7828ms 99.52% __libc_start_call_main 0 0% 0% 7828ms 99.52% __libc_start_main_impl 0 0% 0% 7828ms 99.52% _start 0 0% 0% 7813ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7813ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7813ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7813ms 99.33% main 0 0% 0% 7776ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7776ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7776ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7773ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0% 3347ms 42.55% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2910ms 36.99% MeshBasedCellPopulation::Update 0 0% 0% 2879ms 36.60% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.013% 1533ms 19.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.025% 1446ms 18.38% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.025% 1403ms 17.84% MutableMesh::ReMesh 2ms 0.025% 0.051% 1400ms 17.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.038% 0.089% 1343ms 17.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 39ms 0.5% 0.58% 1262ms 16.04% MeshBasedCellPopulation::SpringIterator::operator++ 101ms 1.28% 1.87% 1004ms 12.76% TetrahedralMesh::EdgeIterator::operator++ 421ms 5.35% 7.22% 965ms 12.27% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.076% 7.30% 951ms 12.09% CellPropertyCollection::GetPropertiesType (inline) 304ms 3.86% 11.16% 943ms 11.99% __dynamic_cast 4ms 0.051% 11.21% 930ms 11.82% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 11.24% 922ms 11.72% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.051% 11.29% 898ms 11.42% CellPopulationElementWriter::Visit 53ms 0.67% 11.96% 839ms 10.67% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.013% 11.98% 798ms 10.14% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.025% 12.00% 749ms 9.52% AbstractCellProperty::IsSubType (inline) 23ms 0.29% 12.29% 731ms 9.29% AbstractCellPopulation::GetCellUsingLocationIndex 18ms 0.23% 12.52% 714ms 9.08% TetrahedralMesh::ImportFromMesher 79ms 1.00% 13.53% 577ms 7.34% std::ostream::_M_insert 0 0% 13.53% 577ms 7.34% std::ostream::operator<< (inline) 32ms 0.41% 13.93% 573ms 7.28% std::map::operator[] (partial-inline) 4ms 0.051% 13.98% 559ms 7.11% Cell::GetCellProliferativeType 26ms 0.33% 14.31% 546ms 6.94% operator new 7ms 0.089% 14.40% 533ms 6.78% std::set::insert (inline) 12ms 0.15% 14.56% 526ms 6.69% std::_Rb_tree::_M_insert_unique 524ms 6.66% 21.22% 524ms 6.66% __strcmp_avx2 19ms 0.24% 21.46% 521ms 6.62% std::_Rb_tree::find (inline) 1ms 0.013% 21.47% 513ms 6.52% triangulate 174ms 2.21% 23.68% 510ms 6.48% __GI___libc_malloc 1ms 0.013% 23.70% 490ms 6.23% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.70% 489ms 6.22% std::_Rb_tree::lower_bound (inline) 28ms 0.36% 24.05% 489ms 6.22% std::__new_allocator::allocate (inline) 0 0% 24.05% 489ms 6.22% std::map::lower_bound (inline) 0 0% 24.05% 484ms 6.15% std::allocator_traits::allocate (inline) 0 0% 24.05% 472ms 6.00% std::set::count (inline) 0 0% 24.05% 454ms 5.77% delaunay 2ms 0.025% 24.08% 452ms 5.75% divconqdelaunay 195ms 2.48% 26.56% 439ms 5.58% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.038% 26.60% 424ms 5.39% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.60% 423ms 5.38% std::_Rb_tree::_M_create_node (inline) 0 0% 26.60% 400ms 5.09% std::_Rb_tree::_Alloc_node::operator() (inline) 43ms 0.55% 27.14% 393ms 5.00% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.14% 386ms 4.91% std::_Rb_tree::_M_get_node (inline) 3ms 0.038% 27.18% 380ms 4.83% Cell::GetMutationState 0 0% 27.18% 376ms 4.78% std::set::~set (inline) 2ms 0.025% 27.21% 364ms 4.63% NodeLocationWriter::Visit 13ms 0.17% 27.37% 355ms 4.51% std::less::operator() (inline) 92ms 1.17% 28.54% 348ms 4.42% std::_Rb_tree::_M_erase 27ms 0.34% 28.88% 346ms 4.40% std::_Rb_tree::_Rb_tree (partial-inline) 342ms 4.35% 33.23% 342ms 4.35% std::operator< (inline) 1ms 0.013% 33.24% 338ms 4.30% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.24% 336ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 19ms 0.24% 33.49% 333ms 4.23% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 33.52% 326ms 4.14% std::set::set (inline) 321ms 4.08% 37.60% 321ms 4.08% std::_Rb_tree::_S_right (inline) 21ms 0.27% 37.87% 316ms 4.02% std::num_put::_M_insert_float 10ms 0.13% 38.00% 311ms 3.95% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 38.00% 311ms 3.95% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.00% 310ms 3.94% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.051% 38.05% 309ms 3.93% Element::Element 2ms 0.025% 38.08% 306ms 3.89% Cell::ReadyToDivide 1ms 0.013% 38.09% 305ms 3.88% OutputFileHandler::OpenOutputFile 29ms 0.37% 38.46% 299ms 3.80% std::_Rb_tree::_M_copy (inline) 10ms 0.13% 38.58% 286ms 3.64% divconqrecurse 87ms 1.11% 39.69% 272ms 3.46% __GI___libc_free 176ms 2.24% 41.93% 272ms 3.46% _int_malloc 2ms 0.025% 41.95% 268ms 3.41% CellProliferativeTypesWriter::VisitCell 75ms 0.95% 42.91% 266ms 3.38% std::_Rb_tree::_M_clone_node (inline) 79ms 1.00% 43.91% 264ms 3.36% mergehulls 5ms 0.064% 43.97% 259ms 3.29% AbstractCellProperty::IsType (inline) 4ms 0.051% 44.02% 256ms 3.25% std::__cxx11::collate::do_transform 6ms 0.076% 44.10% 247ms 3.14% ___vsnprintf 4ms 0.051% 44.15% 242ms 3.08% CellPropertyCollection::HasProperty 0 0% 44.15% 241ms 3.06% Cell::HasCellProperty (inline) 0 0% 44.15% 241ms 3.06% __vsnprintf_internal (inline) 25ms 0.32% 44.47% 237ms 3.01% __printf_buffer 0 0% 44.47% 235ms 2.99% std::_Rb_tree::_M_drop_node (inline) 7ms 0.089% 44.56% 222ms 2.82% std::__new_allocator::deallocate (inline) 0 0% 44.56% 220ms 2.80% std::allocator_traits::deallocate (inline) 4ms 0.051% 44.61% 209ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.076% 44.69% 206ms 2.62% Element::RegisterWithNodes (inline) 11ms 0.14% 44.83% 203ms 2.58% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 63ms 0.8% 45.63% 200ms 2.54% AbstractCellProperty::IsSame 5ms 0.064% 45.69% 196ms 2.49% Node::AddElement 18ms 0.23% 45.92% 194ms 2.47% TetrahedralMesh::Clear 5ms 0.064% 45.98% 192ms 2.44% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.038% 46.02% 192ms 2.44% __printf_fp_spec (inline) 11ms 0.14% 46.16% 189ms 2.40% __printf_fp_l_buffer 160ms 2.03% 48.19% 185ms 2.35% _int_free 0 0% 48.19% 183ms 2.33% std::_Rb_tree::_M_put_node (inline) 55ms 0.7% 48.89% 182ms 2.31% TetrahedralMesh::EdgesEnd (partial-inline) 70ms 0.89% 49.78% 182ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 98ms 1.25% 51.03% 168ms 2.14% __printf_fp_buffer_1 1ms 0.013% 51.04% 167ms 2.12% OutputFileHandler::CommonConstructor 0 0% 51.04% 167ms 2.12% OutputFileHandler::OutputFileHandler 1ms 0.013% 51.06% 158ms 2.01% OutputFileHandler::MakeFoldersAndReturnFullPath 9ms 0.11% 51.17% 157ms 2.00% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.17% 154ms 1.96% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.17% 151ms 1.92% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.17% 146ms 1.86% std::basic_filebuf::open 0 0% 51.17% 146ms 1.86% std::basic_ofstream::open (inline) 10ms 0.13% 51.30% 137ms 1.74% AbstractTetrahedralElement::CalculateInverseJacobian 29ms 0.37% 51.67% 137ms 1.74% std::type_info::operator== (inline) 54ms 0.69% 52.35% 134ms 1.70% std::__ostream_insert 2ms 0.025% 52.38% 129ms 1.64% boost::numeric::ublas::vector_assign (inline) 0 0% 52.38% 128ms 1.63% FilesystemPermissions::SetFilePermissions (inline) 128ms 1.63% 54.00% 128ms 1.63% __GI_fchmodat 7ms 0.089% 54.09% 128ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 54.09% 128ms 1.63% std::filesystem::permissions 0 0% 54.09% 126ms 1.60% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 54.09% 125ms 1.59% AbstractCellBasedWriter::CloseFile 1ms 0.013% 54.11% 125ms 1.59% std::basic_ofstream::close (inline) 0 0% 54.11% 124ms 1.58% std::basic_filebuf::close 14ms 0.18% 54.28% 123ms 1.56% AbstractTetrahedralElement::RefreshJacobian 41ms 0.52% 54.81% 121ms 1.54% std::num_put::_M_insert_int 120ms 1.53% 56.33% 120ms 1.53% std::_Rb_tree_insert_and_rebalance 4ms 0.051% 56.38% 113ms 1.44% AbstractTetrahedralElement::AbstractTetrahedralElement 25ms 0.32% 56.70% 113ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 56.70% 110ms 1.40% _IO_new_fopen 1ms 0.013% 56.71% 110ms 1.40% __fopen_internal (inline) 0 0% 56.71% 110ms 1.40% std::__basic_file::open 109ms 1.39% 58.10% 109ms 1.39% incircle 5ms 0.064% 58.16% 109ms 1.39% std::operator<< (inline) 6ms 0.076% 58.24% 108ms 1.37% Node::~Node 1ms 0.013% 58.25% 108ms 1.37% _IO_new_file_fopen 0 0% 58.25% 106ms 1.35% __GI__IO_file_open 102ms 1.30% 59.55% 102ms 1.30% [libchaste_cell_based.so] 15ms 0.19% 59.74% 102ms 1.30% boost::detail::shared_count::~shared_count (inline) 0 0% 59.74% 102ms 1.30% boost::shared_ptr::~shared_ptr (inline) 69ms 0.88% 60.62% 101ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 9ms 0.11% 60.73% 100ms 1.27% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.038% 60.77% 100ms 1.27% std::vector::push_back (inline) 1ms 0.013% 60.78% 99ms 1.26% std::_Vector_base::_M_allocate (inline) 97ms 1.23% 62.01% 98ms 1.25% __libc_open64 11ms 0.14% 62.15% 97ms 1.23% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 62.15% 96ms 1.22% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.038% 62.19% 95ms 1.21% alternateaxes 51ms 0.65% 62.84% 94ms 1.20% boost::shared_ptr::shared_ptr (inline) 94ms 1.20% 64.04% 94ms 1.20% std::_Rb_tree_increment 9ms 0.11% 64.15% 94ms 1.20% std::vector::_M_realloc_insert 36ms 0.46% 64.61% 93ms 1.18% AbstractElement::GetNodeLocation 1ms 0.013% 64.62% 93ms 1.18% std::basic_filebuf::_M_convert_to_external 0 0% 64.62% 93ms 1.18% std::basic_filebuf::_M_terminate_output 0 0% 64.62% 93ms 1.18% std::basic_filebuf::overflow 5ms 0.064% 64.68% 92ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 92ms 1.17% 65.85% 92ms 1.17% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 92ms 1.17% 67.02% 92ms 1.17% __GI___libc_write 0 0% 67.02% 92ms 1.17% std::__basic_file::xsputn 83ms 1.06% 68.08% 91ms 1.16% vertexmedian 30ms 0.38% 68.46% 90ms 1.14% boost::numeric::ublas::indexing_vector_assign 89ms 1.13% 69.59% 89ms 1.13% __GI___fstatat64 0 0% 69.59% 88ms 1.12% std::filesystem::status 85ms 1.08% 70.67% 85ms 1.08% boost::detail::sp_counted_base::release 2ms 0.025% 70.70% 82ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 70.71% 80ms 1.02% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.71% 79ms 1.00% std::filesystem::create_directory 0 0% 70.71% 75ms 0.95% Cell::GetCellId 3ms 0.038% 70.75% 74ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeB 11ms 0.14% 70.89% 73ms 0.93% CellPropertyCollection::AddProperty 51ms 0.65% 71.54% 71ms 0.9% malloc_consolidate 69ms 0.88% 72.41% 69ms 0.88% counterclockwise 1ms 0.013% 72.43% 68ms 0.86% AbstractCellPopulation::GetLocationIndexUsingCell 68ms 0.86% 73.29% 68ms 0.86% [libchaste_mesh.so] 67ms 0.85% 74.14% 67ms 0.85% boost::shared_ptr::operator-> (inline) 49ms 0.62% 74.76% 67ms 0.85% std::basic_streambuf::xsputn 1ms 0.013% 74.78% 65ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeA 43ms 0.55% 75.32% 65ms 0.83% std::basic_filebuf::xsputn 52ms 0.66% 75.99% 64ms 0.81% AbstractElement::GetNodeGlobalIndex 64ms 0.81% 76.80% 64ms 0.81% Node::GetIndex 64ms 0.81% 77.61% 64ms 0.81% std::vector::size (inline) 48ms 0.61% 78.22% 63ms 0.8% std::num_put::do_put 60ms 0.76% 78.99% 63ms 0.8% vertexsort 0 0% 78.99% 61ms 0.78% tcache_get (inline) 61ms 0.78% 79.76% 61ms 0.78% tcache_get_n (inline) 28ms 0.36% 80.12% 58ms 0.74% AbstractTetrahedralMesh::GetElement 55ms 0.7% 80.82% 55ms 0.7% [libstdc++.so.6.0.33] 2ms 0.025% 80.84% 53ms 0.67% Node::ConstructNodeAttributes (inline) 53ms 0.67% 81.52% 53ms 0.67% __memcpy_avx_unaligned_erms 0 0% 81.52% 52ms 0.66% Node::ClearAppliedForce 0 0% 81.52% 52ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.52% 52ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.52% 52ms 0.66% std::__new_allocator::destroy (inline) 0 0% 81.52% 52ms 0.66% std::allocator_traits::destroy (inline) 25ms 0.32% 81.83% 51ms 0.65% boost::numeric::ublas::c_matrix::operator() (partial-inline) 49ms 0.62% 82.46% 49ms 0.62% Node::rGetLocation 47ms 0.6% 83.05% 47ms 0.6% std::ostream::sentry::sentry 0 0% 83.05% 46ms 0.58% BoundaryNodeWriter::Visit 0 0% 83.05% 46ms 0.58% std::vector::vector (inline) 17ms 0.22% 83.27% 44ms 0.56% AbstractCellCycleModel::GetAge 0 0% 83.27% 44ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.53% 83.80% 43ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 83.80% 43ms 0.55% std::_Vector_base::_Vector_base (inline) 13ms 0.17% 83.97% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 0 0% 83.97% 42ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.051% 84.02% 41ms 0.52% Element::~Element 0 0% 84.02% 41ms 0.52% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 1ms 0.013% 84.03% 41ms 0.52% std::_Vector_base::_M_create_storage (inline) 2ms 0.025% 84.06% 40ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.013% 84.07% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 1ms 0.013% 84.08% 40ms 0.51% std::__new_allocator::construct (inline) 0 0% 84.08% 40ms 0.51% std::allocator_traits::construct (inline) 0 0% 84.08% 40ms 0.51% std::map::find (inline)