File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6575ms, 83.34% of 7889ms total Dropped 576 nodes (cum <= 39.45ms) flat flat% sum% cum cum% 0 0% 0% 7851ms 99.52% __libc_start_call_main 0 0% 0% 7851ms 99.52% __libc_start_main_impl 0 0% 0% 7851ms 99.52% _start 0 0% 0% 7834ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7834ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7834ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7834ms 99.30% main 0 0% 0% 7797ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7797ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7797ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7795ms 98.81% AbstractCellBasedSimulation::Solve 2ms 0.025% 0.025% 3368ms 42.69% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.051% 2947ms 37.36% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.063% 2886ms 36.58% MeshBasedCellPopulation::Update 2ms 0.025% 0.089% 1473ms 18.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.089% 1415ms 17.94% MutableMesh::ReMesh 1ms 0.013% 0.1% 1413ms 17.91% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.11% 1332ms 16.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.076% 0.19% 1284ms 16.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 16ms 0.2% 0.39% 1224ms 15.52% MeshBasedCellPopulation::SpringIterator::operator++ 118ms 1.50% 1.89% 1014ms 12.85% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.91% 960ms 12.17% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 456ms 5.78% 7.69% 956ms 12.12% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.15% 7.85% 912ms 11.56% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.089% 7.94% 877ms 11.12% CellPopulationElementWriter::Visit 2ms 0.025% 7.96% 866ms 10.98% AbstractTwoBodyInteractionForce::AddForceContribution 252ms 3.19% 11.15% 845ms 10.71% __dynamic_cast 5ms 0.063% 11.22% 807ms 10.23% MeshBasedCellPopulation::AcceptCellWriter 49ms 0.62% 11.84% 766ms 9.71% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 26ms 0.33% 12.17% 751ms 9.52% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 12.26% 728ms 9.23% TetrahedralMesh::ImportFromMesher 0 0% 12.26% 684ms 8.67% AbstractCellProperty::IsSubType (inline) 98ms 1.24% 13.50% 665ms 8.43% std::ostream::_M_insert 0 0% 13.50% 665ms 8.43% std::ostream::operator<< (inline) 34ms 0.43% 13.93% 595ms 7.54% operator new 48ms 0.61% 14.54% 589ms 7.47% std::map::operator[] (partial-inline) 182ms 2.31% 16.85% 556ms 7.05% __GI___libc_malloc 7ms 0.089% 16.93% 538ms 6.82% std::set::insert (inline) 10ms 0.13% 17.06% 531ms 6.73% std::_Rb_tree::_M_insert_unique 4ms 0.051% 17.11% 528ms 6.69% Cell::GetCellProliferativeType 25ms 0.32% 17.43% 524ms 6.64% std::__new_allocator::allocate (inline) 1ms 0.013% 17.44% 522ms 6.62% triangulate 2ms 0.025% 17.47% 521ms 6.60% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 17.47% 521ms 6.60% std::allocator_traits::allocate (inline) 503ms 6.38% 23.84% 503ms 6.38% __strcmp_avx2 0 0% 23.84% 500ms 6.34% std::_Rb_tree::lower_bound (inline) 0 0% 23.84% 500ms 6.34% std::map::lower_bound (inline) 19ms 0.24% 24.08% 495ms 6.27% std::_Rb_tree::find (inline) 8ms 0.1% 24.19% 462ms 5.86% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.19% 457ms 5.79% std::set::count (inline) 0 0% 24.19% 451ms 5.72% delaunay 1ms 0.013% 24.20% 450ms 5.70% divconqdelaunay 0 0% 24.20% 437ms 5.54% std::_Rb_tree::_M_create_node (inline) 34ms 0.43% 24.63% 436ms 5.53% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.051% 24.68% 430ms 5.45% NodeLocationWriter::Visit 0 0% 24.68% 415ms 5.26% std::_Rb_tree::_Alloc_node::operator() (inline) 195ms 2.47% 27.15% 414ms 5.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.15% 414ms 5.25% std::set::~set (inline) 0 0% 27.15% 399ms 5.06% std::_Rb_tree::_M_get_node (inline) 79ms 1.00% 28.15% 398ms 5.04% std::_Rb_tree::_M_erase 29ms 0.37% 28.52% 390ms 4.94% std::num_put::_M_insert_float 5ms 0.063% 28.58% 385ms 4.88% Cell::GetMutationState 21ms 0.27% 28.85% 340ms 4.31% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.051% 28.90% 340ms 4.31% std::less::operator() (inline) 16ms 0.2% 29.10% 339ms 4.30% std::_Rb_tree::_M_insert_ (inline) 336ms 4.26% 33.36% 336ms 4.26% std::operator< (inline) 1ms 0.013% 33.38% 332ms 4.21% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 33.39% 331ms 4.20% AbstractCentreBasedCellPopulation::GetDampingConstant 119ms 1.51% 34.90% 331ms 4.20% __GI___libc_free 0 0% 34.90% 327ms 4.15% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 34.92% 325ms 4.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.92% 321ms 4.07% OutputFileHandler::OpenOutputFile 6ms 0.076% 35.00% 311ms 3.94% Cell::ReadyToDivide 0 0% 35.00% 301ms 3.82% std::set::set (inline) 0 0% 35.00% 300ms 3.80% std::_Rb_tree::_M_drop_node (inline) 15ms 0.19% 35.19% 297ms 3.76% std::__new_allocator::deallocate (inline) 3ms 0.038% 35.23% 296ms 3.75% Element::Element 27ms 0.34% 35.57% 293ms 3.71% std::_Rb_tree::_M_copy (inline) 7ms 0.089% 35.66% 291ms 3.69% std::__cxx11::collate::do_transform 0 0% 35.66% 291ms 3.69% std::allocator_traits::deallocate (inline) 3ms 0.038% 35.70% 287ms 3.64% AbstractCellPopulation::IsCellAttachedToLocationIndex 286ms 3.63% 39.32% 286ms 3.63% std::_Rb_tree::_S_right (inline) 176ms 2.23% 41.55% 277ms 3.51% _int_malloc 3ms 0.038% 41.59% 272ms 3.45% ___vsnprintf 0 0% 41.59% 269ms 3.41% __vsnprintf_internal (inline) 5ms 0.063% 41.65% 268ms 3.40% AbstractCellProperty::IsType (inline) 8ms 0.1% 41.75% 263ms 3.33% CellPropertyCollection::HasProperty 65ms 0.82% 42.58% 263ms 3.33% std::_Rb_tree::_M_clone_node (inline) 31ms 0.39% 42.97% 261ms 3.31% __printf_buffer 0 0% 42.97% 260ms 3.30% Cell::HasCellProperty (inline) 4ms 0.051% 43.02% 253ms 3.21% CellProliferativeTypesWriter::VisitCell 0 0% 43.02% 241ms 3.05% std::_Rb_tree::_M_put_node (inline) 11ms 0.14% 43.16% 232ms 2.94% divconqrecurse 60ms 0.76% 43.92% 213ms 2.70% mergehulls 179ms 2.27% 46.19% 211ms 2.67% _int_free 1ms 0.013% 46.20% 209ms 2.65% __printf_fp_spec (inline) 7ms 0.089% 46.29% 208ms 2.64% __printf_fp_l_buffer 49ms 0.62% 46.91% 200ms 2.54% AbstractCellProperty::IsSame 16ms 0.2% 47.12% 195ms 2.47% TetrahedralMesh::Clear 5ms 0.063% 47.18% 194ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 103ms 1.31% 48.49% 192ms 2.43% __printf_fp_buffer_1 10ms 0.13% 48.61% 189ms 2.40% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 48.65% 184ms 2.33% MeshBasedCellPopulation::SpringsEnd (inline) 71ms 0.9% 49.55% 183ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.089% 49.64% 182ms 2.31% Element::RegisterWithNodes (inline) 5ms 0.063% 49.70% 173ms 2.19% Node::AddElement 10ms 0.13% 49.83% 160ms 2.03% AbstractTetrahedralElement::CalculateJacobian 41ms 0.52% 50.35% 160ms 2.03% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.35% 153ms 1.94% std::basic_ofstream::basic_ofstream (inline) 32ms 0.41% 50.75% 151ms 1.91% std::type_info::operator== (inline) 2ms 0.025% 50.78% 149ms 1.89% alternateaxes 1ms 0.013% 50.79% 149ms 1.89% std::basic_ofstream::open (inline) 0 0% 50.79% 147ms 1.86% std::basic_filebuf::open 136ms 1.72% 52.52% 147ms 1.86% vertexmedian 0 0% 52.52% 140ms 1.77% FilesystemPermissions::SetFilePermissions (inline) 140ms 1.77% 54.29% 140ms 1.77% std::_Rb_tree_increment 139ms 1.76% 56.05% 139ms 1.76% __GI_fchmodat 0 0% 56.05% 139ms 1.76% std::filesystem::permissions 6ms 0.076% 56.13% 134ms 1.70% std::_Rb_tree_const_iterator::operator++ (inline) 41ms 0.52% 56.65% 133ms 1.69% std::num_put::_M_insert_int 0 0% 56.65% 132ms 1.67% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 56.66% 129ms 1.64% OutputFileHandler::OutputFileHandler 10ms 0.13% 56.79% 127ms 1.61% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 56.79% 126ms 1.60% OutputFileHandler::CommonConstructor 4ms 0.051% 56.84% 126ms 1.60% std::_Vector_base::_M_allocate (inline) 4ms 0.051% 56.89% 124ms 1.57% boost::numeric::ublas::vector_assign (inline) 0 0% 56.89% 124ms 1.57% std::basic_filebuf::close 0 0% 56.89% 123ms 1.56% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 56.89% 122ms 1.55% AbstractCellBasedWriter::CloseFile 0 0% 56.89% 122ms 1.55% std::basic_ofstream::close (inline) 4ms 0.051% 56.94% 121ms 1.53% AbstractTetrahedralElement::AbstractTetrahedralElement 14ms 0.18% 57.12% 121ms 1.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 57.12% 121ms 1.53% OutputFileHandler::MakeFoldersAndReturnFullPath 4ms 0.051% 57.17% 121ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 16ms 0.2% 57.37% 120ms 1.52% AbstractTetrahedralElement::RefreshJacobian 50ms 0.63% 58.00% 117ms 1.48% std::__ostream_insert 15ms 0.19% 58.19% 116ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 58.21% 115ms 1.46% std::__basic_file::open 7ms 0.089% 58.30% 114ms 1.45% std::vector::push_back (inline) 0 0% 58.30% 113ms 1.43% _IO_new_fopen 1ms 0.013% 58.31% 113ms 1.43% __fopen_internal (inline) 0 0% 58.31% 111ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 58.33% 111ms 1.41% _IO_new_file_fopen 111ms 1.41% 59.74% 111ms 1.41% incircle 109ms 1.38% 61.12% 109ms 1.38% std::_Rb_tree_insert_and_rebalance 7ms 0.089% 61.21% 108ms 1.37% Node::~Node 1ms 0.013% 61.22% 108ms 1.37% __GI__IO_file_open 66ms 0.84% 62.06% 107ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 8ms 0.1% 62.16% 104ms 1.32% boost::detail::shared_count::~shared_count (inline) 0 0% 62.16% 104ms 1.32% boost::shared_ptr::~shared_ptr (inline) 6ms 0.076% 62.24% 104ms 1.32% std::vector::_M_realloc_insert 5ms 0.063% 62.30% 102ms 1.29% std::basic_filebuf::overflow 0 0% 62.30% 99ms 1.25% std::basic_filebuf::_M_terminate_output 96ms 1.22% 63.52% 97ms 1.23% __libc_open64 3ms 0.038% 63.56% 97ms 1.23% std::basic_filebuf::_M_convert_to_external 3ms 0.038% 63.59% 96ms 1.22% std::operator<< (inline) 51ms 0.65% 64.24% 95ms 1.20% boost::shared_ptr::shared_ptr (inline) 93ms 1.18% 65.42% 94ms 1.19% __GI___libc_write 94ms 1.19% 66.61% 94ms 1.19% boost::detail::sp_counted_base::release 0 0% 66.61% 94ms 1.19% std::__basic_file::xsputn 0 0% 66.61% 91ms 1.15% tcache_get (inline) 91ms 1.15% 67.77% 91ms 1.15% tcache_get_n (inline) 0 0% 67.77% 89ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.051% 67.82% 88ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 88ms 1.12% 68.93% 88ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 61ms 0.77% 69.70% 86ms 1.09% std::basic_streambuf::xsputn 37ms 0.47% 70.17% 84ms 1.06% AbstractElement::GetNodeLocation 84ms 1.06% 71.24% 84ms 1.06% [libchaste_cell_based.so] 26ms 0.33% 71.57% 83ms 1.05% boost::numeric::ublas::indexing_vector_assign 57ms 0.72% 72.29% 79ms 1.00% malloc_consolidate 66ms 0.84% 73.13% 78ms 0.99% AbstractElement::GetNodeGlobalIndex 50ms 0.63% 73.76% 78ms 0.99% std::basic_filebuf::xsputn 9ms 0.11% 73.88% 74ms 0.94% CellPropertyCollection::AddProperty 3ms 0.038% 73.91% 71ms 0.9% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.025% 73.94% 68ms 0.86% Cell::GetCellId 4ms 0.051% 73.99% 66ms 0.84% std::filesystem::status 0 0% 73.99% 65ms 0.82% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 64ms 0.81% 74.80% 64ms 0.81% Node::GetIndex 64ms 0.81% 75.61% 64ms 0.81% [libchaste_mesh.so] 2ms 0.025% 75.64% 64ms 0.81% std::filesystem::create_directory 63ms 0.8% 76.44% 63ms 0.8% __GI___fstatat64 4ms 0.051% 76.49% 62ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.49% 60ms 0.76% std::__new_allocator::destroy (inline) 0 0% 76.49% 60ms 0.76% std::allocator_traits::destroy (inline) 60ms 0.76% 77.25% 60ms 0.76% std::vector::size (inline) 2ms 0.025% 77.27% 59ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 77.27% 59ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 49ms 0.62% 77.89% 58ms 0.74% vertexsort 26ms 0.33% 78.22% 57ms 0.72% AbstractCellCycleModel::GetAge 31ms 0.39% 78.62% 56ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 55ms 0.7% 79.31% 55ms 0.7% __memcpy_avx_unaligned_erms 55ms 0.7% 80.01% 55ms 0.7% boost::shared_ptr::operator-> (inline) 31ms 0.39% 80.40% 54ms 0.68% AbstractTetrahedralMesh::GetElement 2ms 0.025% 80.43% 54ms 0.68% Node::ConstructNodeAttributes (inline) 0 0% 80.43% 52ms 0.66% Node::ClearAppliedForce 52ms 0.66% 81.09% 52ms 0.66% boost::numeric::ublas::c_vector::operator() (inline) 0 0% 81.09% 52ms 0.66% std::vector::vector (inline) 1ms 0.013% 81.10% 51ms 0.65% std::_Vector_base::_M_deallocate (inline) 50ms 0.63% 81.73% 50ms 0.63% [libstdc++.so.6.0.33] 0 0% 81.73% 48ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 32ms 0.41% 82.14% 47ms 0.6% hack_digit 0 0% 82.14% 47ms 0.6% std::_Vector_base::_Vector_base (inline) 43ms 0.55% 82.68% 44ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 82.68% 44ms 0.56% std::_Vector_base::_M_create_storage (inline) 1ms 0.013% 82.70% 43ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 82.70% 43ms 0.55% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.70% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 82.71% 42ms 0.53% BoundaryNodeWriter::Visit 42ms 0.53% 83.24% 42ms 0.53% counterclockwise 2ms 0.025% 83.27% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 83.27% 42ms 0.53% std::allocator_traits::construct (inline) 4ms 0.051% 83.32% 41ms 0.52% NodeAttributes::NodeAttributes 2ms 0.025% 83.34% 41ms 0.52% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.34% 40ms 0.51% std::map::map (inline)