File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6538ms, 83.79% of 7803ms total Dropped 574 nodes (cum <= 39.02ms) flat flat% sum% cum cum% 0 0% 0% 7768ms 99.55% __libc_start_call_main 0 0% 0% 7768ms 99.55% __libc_start_main_impl 0 0% 0% 7768ms 99.55% _start 0 0% 0% 7753ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7753ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7753ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7753ms 99.36% main 0 0% 0% 7715ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7715ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7715ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7713ms 98.85% AbstractCellBasedSimulation::Solve 0 0% 0% 3327ms 42.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2877ms 36.87% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.051% 2867ms 36.74% MeshBasedCellPopulation::Update 3ms 0.038% 0.09% 1503ms 19.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.1% 1411ms 18.08% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.026% 0.13% 1395ms 17.88% MutableMesh::ReMesh 0 0% 0.13% 1348ms 17.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.051% 0.18% 1290ms 16.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.26% 0.44% 1247ms 15.98% MeshBasedCellPopulation::SpringIterator::operator++ 114ms 1.46% 1.90% 1008ms 12.92% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.064% 1.96% 988ms 12.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 230ms 2.95% 4.91% 930ms 11.92% __dynamic_cast 9ms 0.12% 5.02% 927ms 11.88% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.038% 5.06% 913ms 11.70% AbstractTwoBodyInteractionForce::AddForceContribution 455ms 5.83% 10.89% 892ms 11.43% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.077% 10.97% 857ms 10.98% CellPopulationElementWriter::Visit 3ms 0.038% 11.01% 846ms 10.84% MeshBasedCellPopulation::AcceptCellWriter 38ms 0.49% 11.50% 804ms 10.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.026% 11.52% 733ms 9.39% AbstractCellProperty::IsSubType (inline) 28ms 0.36% 11.88% 701ms 8.98% AbstractCellPopulation::GetCellUsingLocationIndex 13ms 0.17% 12.05% 691ms 8.86% TetrahedralMesh::ImportFromMesher 85ms 1.09% 13.14% 607ms 7.78% std::ostream::_M_insert 0 0% 13.14% 607ms 7.78% std::ostream::operator<< (inline) 577ms 7.39% 20.53% 577ms 7.39% __strcmp_avx2 33ms 0.42% 20.95% 573ms 7.34% operator new 5ms 0.064% 21.02% 569ms 7.29% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.064% 21.08% 558ms 7.15% Cell::GetCellProliferativeType 65ms 0.83% 21.91% 537ms 6.88% std::map::operator[] (partial-inline) 2ms 0.026% 21.94% 537ms 6.88% triangulate 181ms 2.32% 24.26% 528ms 6.77% __GI___libc_malloc 7ms 0.09% 24.35% 523ms 6.70% std::set::insert (inline) 21ms 0.27% 24.62% 519ms 6.65% std::_Rb_tree::find (inline) 214ms 2.74% 27.36% 516ms 6.61% __cxxabiv1::__si_class_type_info::__do_dyncast 17ms 0.22% 27.58% 516ms 6.61% std::_Rb_tree::_M_insert_unique 22ms 0.28% 27.86% 495ms 6.34% std::__new_allocator::allocate (inline) 0 0% 27.86% 491ms 6.29% std::allocator_traits::allocate (inline) 0 0% 27.86% 483ms 6.19% std::set::count (inline) 0 0% 27.86% 467ms 5.98% delaunay 2ms 0.026% 27.89% 465ms 5.96% divconqdelaunay 2ms 0.026% 27.91% 451ms 5.78% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.91% 422ms 5.41% std::_Rb_tree::lower_bound (inline) 0 0% 27.91% 422ms 5.41% std::map::lower_bound (inline) 0 0% 27.91% 418ms 5.36% std::_Rb_tree::_M_create_node (inline) 0 0% 27.91% 391ms 5.01% std::_Rb_tree::_Alloc_node::operator() (inline) 41ms 0.53% 28.44% 386ms 4.95% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 28.48% 382ms 4.90% Cell::GetMutationState 0 0% 28.48% 380ms 4.87% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 28.49% 373ms 4.78% NodeLocationWriter::Visit 0 0% 28.49% 359ms 4.60% std::set::~set (inline) 13ms 0.17% 28.66% 345ms 4.42% std::less::operator() (inline) 24ms 0.31% 28.96% 344ms 4.41% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 28.98% 343ms 4.40% Cell::ReadyToDivide 63ms 0.81% 29.78% 337ms 4.32% std::_Rb_tree::_M_erase 27ms 0.35% 30.13% 332ms 4.25% std::num_put::_M_insert_float 332ms 4.25% 34.38% 332ms 4.25% std::operator< (inline) 3ms 0.038% 34.42% 317ms 4.06% std::set::set (inline) 19ms 0.24% 34.67% 316ms 4.05% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 34.68% 303ms 3.88% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.68% 301ms 3.86% AbstractCellBasedWriter::OpenOutputFileForAppend 114ms 1.46% 36.14% 299ms 3.83% __GI___libc_free 0 0% 36.14% 296ms 3.79% OutputFileHandler::OpenOutputFile 41ms 0.53% 36.67% 292ms 3.74% std::_Rb_tree::_M_copy (inline) 4ms 0.051% 36.72% 287ms 3.68% MeshBasedCellPopulation::GetDampingConstant 6ms 0.077% 36.79% 284ms 3.64% Element::Element 3ms 0.038% 36.83% 282ms 3.61% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.09% 36.92% 275ms 3.52% AbstractCellPopulation::IsCellAttachedToLocationIndex 191ms 2.45% 39.37% 265ms 3.40% _int_malloc 9ms 0.12% 39.48% 262ms 3.36% std::__new_allocator::deallocate (inline) 0 0% 39.48% 261ms 3.34% std::_Rb_tree::_M_drop_node (inline) 0 0% 39.48% 260ms 3.33% Cell::HasCellProperty (inline) 8ms 0.1% 39.59% 259ms 3.32% CellPropertyCollection::HasProperty 2ms 0.026% 39.61% 258ms 3.31% AbstractCellProperty::IsType (inline) 0 0% 39.61% 258ms 3.31% std::allocator_traits::deallocate (inline) 7ms 0.09% 39.70% 256ms 3.28% divconqrecurse 7ms 0.09% 39.79% 249ms 3.19% std::__cxx11::collate::do_transform 68ms 0.87% 40.66% 248ms 3.18% std::_Rb_tree::_M_clone_node (inline) 75ms 0.96% 41.63% 242ms 3.10% mergehulls 5ms 0.064% 41.69% 237ms 3.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.051% 41.74% 237ms 3.04% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 41.78% 233ms 2.99% ___vsnprintf 0 0% 41.78% 231ms 2.96% __vsnprintf_internal (inline) 25ms 0.32% 42.10% 226ms 2.90% __printf_buffer 8ms 0.1% 42.20% 224ms 2.87% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 217ms 2.78% 44.98% 217ms 2.78% std::_Rb_tree::_S_right (inline) 0 0% 44.98% 205ms 2.63% std::_Rb_tree::_M_put_node (inline) 40ms 0.51% 45.50% 197ms 2.52% AbstractCellProperty::IsSame 3ms 0.038% 45.53% 189ms 2.42% Element::RegisterWithNodes (inline) 163ms 2.09% 47.62% 185ms 2.37% _int_free 3ms 0.038% 47.66% 183ms 2.35% Node::AddElement 73ms 0.94% 48.60% 183ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 16ms 0.21% 48.80% 182ms 2.33% TetrahedralMesh::Clear 1ms 0.013% 48.81% 180ms 2.31% __printf_fp_spec (inline) 9ms 0.12% 48.93% 179ms 2.29% MeshBasedCellPopulation::SpringsEnd (inline) 46ms 0.59% 49.52% 179ms 2.29% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.15% 49.67% 179ms 2.29% __printf_fp_l_buffer 95ms 1.22% 50.89% 163ms 2.09% __printf_fp_buffer_1 38ms 0.49% 51.38% 157ms 2.01% std::type_info::operator== (inline) 15ms 0.19% 51.57% 149ms 1.91% AbstractTetrahedralElement::CalculateJacobian 3ms 0.038% 51.61% 146ms 1.87% boost::numeric::ublas::vector_assign (inline) 67ms 0.86% 52.47% 146ms 1.87% std::__ostream_insert 1ms 0.013% 52.48% 144ms 1.85% OutputFileHandler::OutputFileHandler 31ms 0.4% 52.88% 144ms 1.85% std::num_put::_M_insert_int 0 0% 52.88% 143ms 1.83% OutputFileHandler::CommonConstructor 0 0% 52.88% 143ms 1.83% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.13% 53.01% 143ms 1.83% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 53.01% 142ms 1.82% std::basic_ofstream::basic_ofstream (inline) 0 0% 53.01% 140ms 1.79% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 53.01% 139ms 1.78% std::basic_ofstream::open (inline) 0 0% 53.01% 138ms 1.77% std::basic_filebuf::open 8ms 0.1% 53.11% 133ms 1.70% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 53.11% 128ms 1.64% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 53.12% 128ms 1.64% std::filesystem::permissions 126ms 1.61% 54.74% 126ms 1.61% __GI_fchmodat 82ms 1.05% 55.79% 123ms 1.58% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 6ms 0.077% 55.86% 121ms 1.55% alternateaxes 2ms 0.026% 55.89% 120ms 1.54% std::basic_filebuf::close 0 0% 55.89% 119ms 1.53% AbstractCellBasedWriter::CloseFile 0 0% 55.89% 119ms 1.53% AbstractCellPopulation::CloseRoundRobinWritersFiles 13ms 0.17% 56.06% 119ms 1.53% boost::detail::shared_count::~shared_count (inline) 0 0% 56.06% 119ms 1.53% boost::shared_ptr::~shared_ptr (inline) 17ms 0.22% 56.27% 119ms 1.53% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 56.27% 119ms 1.53% std::basic_ofstream::close (inline) 5ms 0.064% 56.34% 117ms 1.50% std::operator<< (inline) 2ms 0.026% 56.36% 116ms 1.49% std::vector::push_back (inline) 114ms 1.46% 57.82% 114ms 1.46% [libchaste_cell_based.so] 3ms 0.038% 57.86% 114ms 1.46% std::_Vector_base::_M_allocate (inline) 100ms 1.28% 59.14% 114ms 1.46% vertexmedian 21ms 0.27% 59.41% 112ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 46ms 0.59% 60.00% 112ms 1.44% boost::numeric::ublas::indexing_vector_assign 9ms 0.12% 60.12% 110ms 1.41% std::vector::_M_realloc_insert 3ms 0.038% 60.16% 108ms 1.38% Node::~Node 106ms 1.36% 61.51% 106ms 1.36% incircle 3ms 0.038% 61.55% 104ms 1.33% std::__basic_file::open 17ms 0.22% 61.77% 103ms 1.32% AbstractTetrahedralElement::RefreshJacobian 102ms 1.31% 63.08% 102ms 1.31% std::_Rb_tree_increment 0 0% 63.08% 101ms 1.29% _IO_new_fopen 0 0% 63.08% 101ms 1.29% __fopen_internal (inline) 99ms 1.27% 64.35% 100ms 1.28% boost::detail::sp_counted_base::release 1ms 0.013% 64.36% 98ms 1.26% _IO_new_file_fopen 2ms 0.026% 64.39% 97ms 1.24% __GI__IO_file_open 3ms 0.038% 64.42% 96ms 1.23% AbstractTetrahedralElement::AbstractTetrahedralElement 94ms 1.20% 65.63% 94ms 1.20% std::_Rb_tree_insert_and_rebalance 11ms 0.14% 65.77% 90ms 1.15% AbstractCellPopulation::Iterator::IsRealCell (inline) 54ms 0.69% 66.46% 87ms 1.11% std::basic_filebuf::xsputn 38ms 0.49% 66.95% 86ms 1.10% boost::shared_ptr::shared_ptr (inline) 61ms 0.78% 67.73% 85ms 1.09% std::basic_streambuf::xsputn 0 0% 67.73% 84ms 1.08% AbstractCellPopulation::Iterator::operator++ (inline) 80ms 1.03% 68.76% 80ms 1.03% __libc_open64 2ms 0.026% 68.78% 80ms 1.03% std::basic_filebuf::overflow 0 0% 68.78% 78ms 1% std::basic_filebuf::_M_terminate_output 3ms 0.038% 68.82% 77ms 0.99% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.038% 68.86% 77ms 0.99% std::basic_filebuf::_M_convert_to_external 0 0% 68.86% 76ms 0.97% tcache_get (inline) 76ms 0.97% 69.83% 76ms 0.97% tcache_get_n (inline) 71ms 0.91% 70.74% 76ms 0.97% vertexsort 34ms 0.44% 71.18% 74ms 0.95% AbstractElement::GetNodeLocation 7ms 0.09% 71.27% 74ms 0.95% CellPropertyCollection::AddProperty 74ms 0.95% 72.22% 74ms 0.95% __GI___libc_write 0 0% 72.22% 74ms 0.95% std::__basic_file::xsputn 6ms 0.077% 72.29% 71ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 3ms 0.038% 72.33% 69ms 0.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 68ms 0.87% 73.20% 68ms 0.87% std::vector::size (inline) 67ms 0.86% 74.06% 67ms 0.86% __memcpy_avx_unaligned_erms 0 0% 74.06% 66ms 0.85% Cell::GetCellId 2ms 0.026% 74.09% 65ms 0.83% AbstractCellPopulation::GetLocationIndexUsingCell 45ms 0.58% 74.66% 65ms 0.83% AbstractElement::GetNodeGlobalIndex 65ms 0.83% 75.50% 65ms 0.83% [libchaste_mesh.so] 1ms 0.013% 75.51% 62ms 0.79% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 62ms 0.79% 76.30% 62ms 0.79% Node::GetIndex 62ms 0.79% 77.10% 62ms 0.79% __GI___fstatat64 1ms 0.013% 77.11% 62ms 0.79% std::filesystem::status 0 0% 77.11% 61ms 0.78% std::filesystem::create_directory 37ms 0.47% 77.59% 60ms 0.77% malloc_consolidate 0 0% 77.59% 59ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.59% 59ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 33ms 0.42% 78.01% 58ms 0.74% boost::numeric::ublas::c_matrix::operator() (partial-inline) 45ms 0.58% 78.59% 58ms 0.74% std::num_put::do_put 57ms 0.73% 79.32% 57ms 0.73% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 57ms 0.73% 80.05% 57ms 0.73% [libstdc++.so.6.0.33] 5ms 0.064% 80.11% 56ms 0.72% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 80.11% 56ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.11% 56ms 0.72% std::__new_allocator::destroy (inline) 0 0% 80.11% 56ms 0.72% std::allocator_traits::destroy (inline) 54ms 0.69% 80.80% 54ms 0.69% counterclockwise 1ms 0.013% 80.82% 53ms 0.68% Node::ClearAppliedForce 3ms 0.038% 80.85% 53ms 0.68% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 80.87% 52ms 0.67% Node::ConstructNodeAttributes (inline) 0 0% 80.87% 50ms 0.64% BoundaryNodeWriter::Visit 1ms 0.013% 80.88% 50ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 28ms 0.36% 81.24% 48ms 0.62% AbstractCellCycleModel::GetAge 2ms 0.026% 81.26% 48ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 47ms 0.6% 81.87% 48ms 0.62% boost::detail::shared_count::shared_count (inline) 31ms 0.4% 82.26% 47ms 0.6% AbstractTetrahedralMesh::GetElement 13ms 0.17% 82.43% 42ms 0.54% AbstractTetrahedralMesh::GetNumAllElements 12ms 0.15% 82.58% 42ms 0.54% Determinant (inline) 42ms 0.54% 83.12% 42ms 0.54% boost::numeric::ublas::c_vector::operator() 0 0% 83.12% 42ms 0.54% boost::numeric::ublas::norm_2 (inline) 9ms 0.12% 83.24% 42ms 0.54% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.026% 83.26% 42ms 0.54% std::__new_allocator::construct (inline) 0 0% 83.26% 42ms 0.54% std::allocator_traits::construct (inline) 0 0% 83.26% 41ms 0.53% std::vector::vector (inline) 1ms 0.013% 83.28% 40ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 40ms 0.51% 83.79% 40ms 0.51% std::ostream::sentry::sentry