File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6203ms, 84.07% of 7378ms total Dropped 544 nodes (cum <= 36.89ms) flat flat% sum% cum cum% 0 0% 0% 7347ms 99.58% __libc_start_call_main 0 0% 0% 7347ms 99.58% __libc_start_main_impl 0 0% 0% 7347ms 99.58% _start 0 0% 0% 7333ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7333ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7333ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7333ms 99.39% main 0 0% 0% 7299ms 98.93% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7299ms 98.93% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7299ms 98.93% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.014% 0.014% 7298ms 98.92% AbstractCellBasedSimulation::Solve 0 0% 0.014% 3234ms 43.83% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.041% 0.054% 2810ms 38.09% MeshBasedCellPopulation::Update 2ms 0.027% 0.081% 2514ms 34.07% AbstractCellPopulation::WriteResultsToFiles 1ms 0.014% 0.095% 1544ms 20.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.027% 0.12% 1391ms 18.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.041% 0.16% 1389ms 18.83% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.16% 1360ms 18.43% MutableMesh::ReMesh 0 0% 0.16% 1343ms 18.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.12% 0.28% 1197ms 16.22% MeshBasedCellPopulation::SpringIterator::operator++ 111ms 1.50% 1.79% 1001ms 13.57% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.054% 1.84% 998ms 13.53% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.11% 1.95% 981ms 13.30% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 33ms 0.45% 2.40% 885ms 12.00% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 382ms 5.18% 7.58% 848ms 11.49% std::_Rb_tree::_M_lower_bound (inline) 25ms 0.34% 7.92% 830ms 11.25% AbstractCellPopulation::GetCellUsingLocationIndex 223ms 3.02% 10.94% 824ms 11.17% __dynamic_cast 14ms 0.19% 11.13% 822ms 11.14% CellPopulationElementWriter::Visit 12ms 0.16% 11.29% 763ms 10.34% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.068% 11.36% 759ms 10.29% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.12% 11.48% 709ms 9.61% TetrahedralMesh::ImportFromMesher 30ms 0.41% 11.89% 639ms 8.66% operator new 2ms 0.027% 11.91% 619ms 8.39% AbstractCellProperty::IsSubType (inline) 186ms 2.52% 14.43% 586ms 7.94% __GI___libc_malloc 8ms 0.11% 14.54% 558ms 7.56% std::set::insert (inline) 19ms 0.26% 14.80% 554ms 7.51% std::__new_allocator::allocate (inline) 9ms 0.12% 14.92% 550ms 7.45% std::_Rb_tree::_M_insert_unique 0 0% 14.92% 550ms 7.45% std::allocator_traits::allocate (inline) 65ms 0.88% 15.80% 545ms 7.39% std::_Rb_tree::~_Rb_tree (inline) 25ms 0.34% 16.14% 523ms 7.09% std::_Rb_tree::find (inline) 3ms 0.041% 16.18% 523ms 7.09% std::ostream::operator<< (inline) 95ms 1.29% 17.47% 516ms 6.99% std::ostream::_M_insert 3ms 0.041% 17.51% 505ms 6.84% Cell::GetCellProliferativeType 0 0% 17.51% 504ms 6.83% std::set::~set (inline) 1ms 0.014% 17.53% 495ms 6.71% triangulate 1ms 0.014% 17.54% 490ms 6.64% LegacyCellProliferativeTypesWriter::VisitCell 79ms 1.07% 18.61% 490ms 6.64% std::map::operator[] (partial-inline) 0 0% 18.61% 489ms 6.63% std::set::count (inline) 66ms 0.89% 19.50% 474ms 6.42% std::_Rb_tree::_M_erase 448ms 6.07% 25.58% 448ms 6.07% __strcmp_evex 0 0% 25.58% 440ms 5.96% std::_Rb_tree::_M_create_node (inline) 0 0% 25.58% 432ms 5.86% delaunay 0 0% 25.58% 432ms 5.86% divconqdelaunay 0 0% 25.58% 427ms 5.79% std::_Rb_tree::_Alloc_node::operator() (inline) 184ms 2.49% 28.07% 424ms 5.75% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.07% 419ms 5.68% std::_Rb_tree::_M_get_node (inline) 2ms 0.027% 28.10% 417ms 5.65% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.10% 401ms 5.44% std::_Rb_tree::_M_drop_node (inline) 17ms 0.23% 28.33% 396ms 5.37% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.054% 28.38% 387ms 5.25% std::set::set (inline) 0 0% 28.38% 377ms 5.11% std::_Rb_tree::lower_bound (inline) 0 0% 28.38% 377ms 5.11% std::map::lower_bound (inline) 26ms 0.35% 28.73% 371ms 5.03% std::_Rb_tree::_M_insert_ (inline) 39ms 0.53% 29.26% 346ms 4.69% std::_Rb_tree::_M_copy (inline) 2ms 0.027% 29.29% 329ms 4.46% Element::Element 2ms 0.027% 29.32% 326ms 4.42% NodeLocationWriter::Visit 63ms 0.85% 30.17% 322ms 4.36% __GI___libc_free 10ms 0.14% 30.31% 320ms 4.34% boost::detail::shared_count::~shared_count (inline) 0 0% 30.31% 320ms 4.34% boost::shared_ptr::~shared_ptr (inline) 213ms 2.89% 33.19% 310ms 4.20% _int_malloc 11ms 0.15% 33.34% 303ms 4.11% std::__new_allocator::deallocate (inline) 300ms 4.07% 37.41% 301ms 4.08% boost::detail::sp_counted_base::release 3ms 0.041% 37.45% 299ms 4.05% Cell::GetMutationState 118ms 1.60% 39.05% 296ms 4.01% std::_Rb_tree::_M_clone_node (inline) 0 0% 39.05% 292ms 3.96% std::allocator_traits::deallocate (inline) 18ms 0.24% 39.29% 278ms 3.77% std::num_put::_M_insert_float 7ms 0.095% 39.39% 275ms 3.73% std::less::operator() (inline) 5ms 0.068% 39.46% 270ms 3.66% Cell::ReadyToDivide 268ms 3.63% 43.09% 268ms 3.63% std::operator< (inline) 4ms 0.054% 43.14% 264ms 3.58% AbstractCellPopulation::IsCellAttachedToLocationIndex 262ms 3.55% 46.69% 262ms 3.55% [libchaste_cell_based.so] 0 0% 46.69% 256ms 3.47% std::_Rb_tree::_M_put_node (inline) 2ms 0.027% 46.72% 254ms 3.44% MeshBasedCellPopulation::GetDampingConstant 225ms 3.05% 49.77% 252ms 3.42% _int_free 3ms 0.041% 49.81% 250ms 3.39% AbstractCentreBasedCellPopulation::GetDampingConstant 242ms 3.28% 53.09% 242ms 3.28% std::_Rb_tree::_S_right (inline) 4ms 0.054% 53.14% 239ms 3.24% divconqrecurse 6ms 0.081% 53.23% 234ms 3.17% std::__cxx11::collate::do_transform 5ms 0.068% 53.29% 232ms 3.14% Element::RegisterWithNodes (inline) 8ms 0.11% 53.40% 225ms 3.05% Node::AddElement 64ms 0.87% 54.27% 223ms 3.02% mergehulls 0 0% 54.27% 219ms 2.97% ___vsnprintf 2ms 0.027% 54.30% 219ms 2.97% __vsnprintf_internal (inline) 28ms 0.38% 54.68% 215ms 2.91% __printf_buffer 26ms 0.35% 55.03% 214ms 2.90% AbstractCellProperty::IsType (inline) 2ms 0.027% 55.06% 210ms 2.85% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.041% 55.10% 209ms 2.83% CellProliferativeTypesWriter::VisitCell 6ms 0.081% 55.18% 205ms 2.78% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 55.18% 191ms 2.59% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 55.18% 191ms 2.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 6ms 0.081% 55.26% 189ms 2.56% CellPropertyCollection::HasProperty 0 0% 55.26% 187ms 2.53% Cell::HasCellProperty (inline) 12ms 0.16% 55.42% 187ms 2.53% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 55.42% 187ms 2.53% OutputFileHandler::OpenOutputFile 47ms 0.64% 56.06% 170ms 2.30% std::_Rb_tree::_M_get_insert_unique_pos (inline) 9ms 0.12% 56.18% 169ms 2.29% __printf_fp_l_buffer 0 0% 56.18% 169ms 2.29% __printf_fp_spec (inline) 2ms 0.027% 56.21% 162ms 2.20% TetrahedralMesh::Clear 5ms 0.068% 56.28% 157ms 2.13% boost::numeric::ublas::vector_assign (inline) 9ms 0.12% 56.40% 154ms 2.09% AbstractTetrahedralElement::CalculateJacobian 4ms 0.054% 56.45% 152ms 2.06% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 56.45% 145ms 1.97% std::_Rb_tree::_M_destroy_node (inline) 0 0% 56.45% 145ms 1.97% std::__new_allocator::destroy (inline) 0 0% 56.45% 145ms 1.97% std::allocator_traits::destroy (inline) 2ms 0.027% 56.48% 143ms 1.94% TetrahedralMesh::RefreshJacobianCachedData 77ms 1.04% 57.52% 143ms 1.94% __printf_fp_buffer_1 63ms 0.85% 58.38% 140ms 1.90% std::__ostream_insert 7ms 0.095% 58.47% 132ms 1.79% AbstractTetrahedralElement::CalculateInverseJacobian 132ms 1.79% 60.26% 132ms 1.79% [libchaste_mesh.so] 1ms 0.014% 60.27% 132ms 1.79% std::_Vector_base::_M_allocate (inline) 22ms 0.3% 60.57% 131ms 1.78% MeshBasedCellPopulation::SpringIterator::SpringIterator 27ms 0.37% 60.94% 127ms 1.72% AbstractCellProperty::IsSame 119ms 1.61% 62.55% 119ms 1.61% [libstdc++.so.6.0.33] 1ms 0.014% 62.56% 119ms 1.61% alternateaxes 115ms 1.56% 64.12% 117ms 1.59% vertexmedian 30ms 0.41% 64.53% 114ms 1.55% TetrahedralMesh::EdgesEnd (partial-inline) 33ms 0.45% 64.98% 107ms 1.45% std::num_put::_M_insert_int 0 0% 64.98% 107ms 1.45% std::operator<< (inline) 4ms 0.054% 65.03% 104ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.027% 65.06% 104ms 1.41% AbstractTetrahedralElement::AbstractTetrahedralElement 18ms 0.24% 65.30% 104ms 1.41% boost::numeric::ublas::indexing_vector_assign 0 0% 65.30% 103ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.22% 65.52% 103ms 1.40% AbstractTetrahedralElement::RefreshJacobian 0 0% 65.52% 101ms 1.37% Node::~Node 20ms 0.27% 65.79% 100ms 1.36% std::type_info::operator== (inline) 99ms 1.34% 67.13% 99ms 1.34% incircle 7ms 0.095% 67.23% 95ms 1.29% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 6ms 0.081% 67.31% 95ms 1.29% std::vector::push_back (inline) 92ms 1.25% 68.56% 92ms 1.25% std::_Rb_tree_insert_and_rebalance 0 0% 68.56% 91ms 1.23% std::basic_ofstream::basic_ofstream (inline) 89ms 1.21% 69.76% 89ms 1.21% std::_Rb_tree::_S_left (inline) 4ms 0.054% 69.82% 87ms 1.18% std::vector::_M_realloc_insert 1ms 0.014% 69.83% 85ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 69ms 0.94% 70.76% 85ms 1.15% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 70.76% 85ms 1.15% std::basic_ofstream::open (inline) 0 0% 70.76% 84ms 1.14% std::basic_filebuf::open 64ms 0.87% 71.63% 83ms 1.12% malloc_consolidate 0 0% 71.63% 79ms 1.07% tcache_get (inline) 79ms 1.07% 72.70% 79ms 1.07% tcache_get_n (inline) 0 0% 72.70% 77ms 1.04% OutputFileHandler::CommonConstructor 0 0% 72.70% 77ms 1.04% OutputFileHandler::OutputFileHandler 3ms 0.041% 72.74% 76ms 1.03% Node::ConstructNodeAttributes (inline) 0 0% 72.74% 74ms 1.00% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 72.74% 73ms 0.99% Node::ClearAppliedForce 0 0% 72.74% 71ms 0.96% Cell::GetCellId 2ms 0.027% 72.77% 69ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 45ms 0.61% 73.38% 67ms 0.91% std::basic_streambuf::xsputn 0 0% 73.38% 67ms 0.91% std::vector::vector (inline) 62ms 0.84% 74.22% 67ms 0.91% vertexsort 0 0% 74.22% 65ms 0.88% FilesystemPermissions::SetFilePermissions (inline) 5ms 0.068% 74.29% 65ms 0.88% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.014% 74.30% 65ms 0.88% std::filesystem::permissions 40ms 0.54% 74.84% 64ms 0.87% AbstractElement::GetNodeLocation 64ms 0.87% 75.71% 64ms 0.87% __GI_fchmodat 0 0% 75.71% 64ms 0.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.71% 64ms 0.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 63ms 0.85% 76.57% 63ms 0.85% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 8ms 0.11% 76.67% 62ms 0.84% CellPropertyCollection::AddProperty 0 0% 76.67% 61ms 0.83% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 76.67% 61ms 0.83% std::_Vector_base::_Vector_base (inline) 8ms 0.11% 76.78% 58ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeB 57ms 0.77% 77.55% 57ms 0.77% counterclockwise 2ms 0.027% 77.58% 57ms 0.77% std::_Vector_base::_M_create_storage (inline) 11ms 0.15% 77.73% 55ms 0.75% Determinant (inline) 2ms 0.027% 77.76% 53ms 0.72% NodeAttributes::NodeAttributes 40ms 0.54% 78.30% 53ms 0.72% boost::numeric::ublas::c_matrix::operator() 34ms 0.46% 78.76% 51ms 0.69% boost::shared_ptr::shared_ptr (inline) 50ms 0.68% 79.44% 50ms 0.68% std::_Rb_tree_increment 0 0% 79.44% 49ms 0.66% _IO_new_fopen 0 0% 79.44% 49ms 0.66% __fopen_internal (inline) 0 0% 79.44% 49ms 0.66% std::__basic_file::open 2ms 0.027% 79.47% 48ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 79.47% 46ms 0.62% AbstractCellBasedWriter::CloseFile 0 0% 79.47% 46ms 0.62% AbstractCellPopulation::CloseRoundRobinWritersFiles 29ms 0.39% 79.86% 46ms 0.62% AbstractElement::GetNodeGlobalIndex 0 0% 79.86% 46ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 79.86% 46ms 0.62% std::basic_filebuf::close 0 0% 79.86% 46ms 0.62% std::basic_ofstream::close (inline) 23ms 0.31% 80.17% 45ms 0.61% AbstractTetrahedralMesh::GetElement 0 0% 80.17% 45ms 0.61% _IO_new_file_fopen 1ms 0.014% 80.18% 45ms 0.61% __GI__IO_file_open 45ms 0.61% 80.79% 45ms 0.61% boost::numeric::ublas::c_vector::operator() 0 0% 80.79% 44ms 0.6% AbstractCentreBasedCellPopulation::IsMarkedSpring 33ms 0.45% 81.24% 44ms 0.6% std::basic_filebuf::xsputn 37ms 0.5% 81.74% 43ms 0.58% CellPropertyCollection::GetProperty 43ms 0.58% 82.33% 43ms 0.58% Node::GetIndex 0 0% 82.33% 41ms 0.56% boost::numeric::ublas::norm_2 (inline) 14ms 0.19% 82.52% 41ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 82.52% 41ms 0.56% std::map::~map (inline) 40ms 0.54% 83.06% 40ms 0.54% __libc_open64 32ms 0.43% 83.49% 40ms 0.54% std::num_put::do_put 3ms 0.041% 83.53% 39ms 0.53% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.014% 83.55% 39ms 0.53% std::basic_filebuf::_M_terminate_output 37ms 0.5% 84.05% 38ms 0.52% __GI___libc_write 0 0% 84.05% 38ms 0.52% std::__basic_file::xsputn 0 0% 84.05% 38ms 0.52% std::basic_filebuf::_M_convert_to_external 0 0% 84.05% 38ms 0.52% std::basic_filebuf::overflow 0 0% 84.05% 38ms 0.52% std::map::map (inline) 2ms 0.027% 84.07% 37ms 0.5% std::filesystem::status