File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6697ms, 85.27% of 7854ms total Dropped 568 nodes (cum <= 39.27ms) flat flat% sum% cum cum% 0 0% 0% 7819ms 99.55% __libc_start_call_main 0 0% 0% 7819ms 99.55% __libc_start_main_impl 0 0% 0% 7819ms 99.55% _start 0 0% 0% 7805ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7805ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7805ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7805ms 99.38% main 0 0% 0% 7768ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7768ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7768ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7765ms 98.87% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3352ms 42.68% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.025% 2888ms 36.77% MeshBasedCellPopulation::Update 0 0% 0.025% 2886ms 36.75% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.025% 1517ms 19.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.038% 0.064% 1488ms 18.95% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.089% 1370ms 17.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.089% 1345ms 17.13% MutableMesh::ReMesh 3ms 0.038% 0.13% 1305ms 16.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.37% 1288ms 16.40% MeshBasedCellPopulation::SpringIterator::operator++ 123ms 1.57% 1.94% 1065ms 13.56% TetrahedralMesh::EdgeIterator::operator++ 436ms 5.55% 7.49% 1000ms 12.73% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.54% 923ms 11.75% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 275ms 3.50% 11.04% 922ms 11.74% __dynamic_cast 15ms 0.19% 11.23% 911ms 11.60% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.038% 11.27% 904ms 11.51% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.17% 11.43% 903ms 11.50% CellPopulationElementWriter::Visit 49ms 0.62% 12.06% 797ms 10.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.051% 12.11% 771ms 9.82% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 12.49% 731ms 9.31% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.064% 12.55% 727ms 9.26% AbstractCellProperty::IsSubType (inline) 11ms 0.14% 12.69% 691ms 8.80% TetrahedralMesh::ImportFromMesher 51ms 0.65% 13.34% 632ms 8.05% std::map::operator[] (partial-inline) 0 0% 13.34% 612ms 7.79% std::ostream::operator<< (inline) 93ms 1.18% 14.53% 611ms 7.78% std::ostream::_M_insert 37ms 0.47% 15.00% 560ms 7.13% operator new 7ms 0.089% 15.09% 540ms 6.88% Cell::GetCellProliferativeType 7ms 0.089% 15.18% 534ms 6.80% std::set::insert (inline) 0 0% 15.18% 533ms 6.79% std::_Rb_tree::lower_bound (inline) 0 0% 15.18% 533ms 6.79% std::map::lower_bound (inline) 28ms 0.36% 15.53% 532ms 6.77% std::_Rb_tree::find (inline) 19ms 0.24% 15.78% 527ms 6.71% std::_Rb_tree::_M_insert_unique 184ms 2.34% 18.12% 521ms 6.63% __GI___libc_malloc 0 0% 18.12% 507ms 6.46% triangulate 29ms 0.37% 18.49% 504ms 6.42% std::__new_allocator::allocate (inline) 0 0% 18.49% 499ms 6.35% std::allocator_traits::allocate (inline) 0 0% 18.49% 493ms 6.28% std::set::count (inline) 475ms 6.05% 24.54% 475ms 6.05% __strcmp_avx2 8ms 0.1% 24.64% 471ms 6.00% LegacyCellProliferativeTypesWriter::VisitCell 236ms 3.00% 27.64% 464ms 5.91% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.051% 27.69% 451ms 5.74% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.69% 448ms 5.70% delaunay 1ms 0.013% 27.71% 448ms 5.70% divconqdelaunay 0 0% 27.71% 428ms 5.45% std::_Rb_tree::_M_create_node (inline) 0 0% 27.71% 405ms 5.16% std::_Rb_tree::_M_get_node (inline) 0 0% 27.71% 398ms 5.07% std::_Rb_tree::_Alloc_node::operator() (inline) 32ms 0.41% 28.11% 396ms 5.04% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 28.15% 389ms 4.95% Cell::GetMutationState 1ms 0.013% 28.16% 389ms 4.95% NodeLocationWriter::Visit 16ms 0.2% 28.37% 376ms 4.79% std::less::operator() (inline) 0 0% 28.37% 368ms 4.69% std::set::~set (inline) 94ms 1.20% 29.56% 360ms 4.58% std::_Rb_tree::_M_erase 360ms 4.58% 34.15% 360ms 4.58% std::operator< (inline) 22ms 0.28% 34.43% 350ms 4.46% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.11% 34.54% 344ms 4.38% AbstractCellPopulation::IsCellAttachedToLocationIndex 342ms 4.35% 38.90% 342ms 4.35% std::_Rb_tree::_S_right (inline) 25ms 0.32% 39.22% 339ms 4.32% std::num_put::_M_insert_float 1ms 0.013% 39.23% 326ms 4.15% MeshBasedCellPopulation::GetDampingConstant 0 0% 39.23% 325ms 4.14% AbstractCentreBasedCellPopulation::GetDampingConstant 22ms 0.28% 39.51% 321ms 4.09% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 39.55% 319ms 4.06% std::set::set (inline) 6ms 0.076% 39.62% 314ms 4.00% Cell::ReadyToDivide 0 0% 39.62% 308ms 3.92% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 39.62% 308ms 3.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 39.65% 305ms 3.88% OutputFileHandler::OpenOutputFile 35ms 0.45% 40.09% 297ms 3.78% std::_Rb_tree::_M_copy (inline) 103ms 1.31% 41.41% 286ms 3.64% __GI___libc_free 5ms 0.064% 41.47% 280ms 3.57% Element::Element 1ms 0.013% 41.48% 265ms 3.37% CellProliferativeTypesWriter::VisitCell 4ms 0.051% 41.53% 265ms 3.37% std::__cxx11::collate::do_transform 71ms 0.9% 42.44% 259ms 3.30% std::_Rb_tree::_M_clone_node (inline) 171ms 2.18% 44.61% 258ms 3.28% _int_malloc 5ms 0.064% 44.68% 253ms 3.22% ___vsnprintf 0 0% 44.68% 248ms 3.16% __vsnprintf_internal (inline) 35ms 0.45% 45.12% 244ms 3.11% __printf_buffer 0 0% 45.12% 244ms 3.11% std::_Rb_tree::_M_drop_node (inline) 6ms 0.076% 45.20% 243ms 3.09% std::__new_allocator::deallocate (inline) 0 0% 45.20% 240ms 3.06% std::allocator_traits::deallocate (inline) 10ms 0.13% 45.33% 238ms 3.03% divconqrecurse 7ms 0.089% 45.42% 222ms 2.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 62ms 0.79% 46.21% 219ms 2.79% mergehulls 0 0% 46.21% 217ms 2.76% AbstractCellProperty::IsType (inline) 9ms 0.11% 46.32% 207ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 46.36% 206ms 2.62% CellPropertyCollection::HasProperty 0 0% 46.36% 205ms 2.61% Cell::HasCellProperty (inline) 17ms 0.22% 46.57% 200ms 2.55% TetrahedralMesh::Clear 3ms 0.038% 46.61% 197ms 2.51% Element::RegisterWithNodes (inline) 12ms 0.15% 46.77% 194ms 2.47% __printf_fp_l_buffer 0 0% 46.77% 194ms 2.47% __printf_fp_spec (inline) 0 0% 46.77% 192ms 2.44% Node::AddElement 0 0% 46.77% 190ms 2.42% std::_Rb_tree::_M_put_node (inline) 6ms 0.076% 46.84% 189ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 57ms 0.73% 47.57% 187ms 2.38% TetrahedralMesh::EdgesEnd (partial-inline) 74ms 0.94% 48.51% 187ms 2.38% std::_Rb_tree::_M_get_insert_unique_pos (inline) 155ms 1.97% 50.48% 183ms 2.33% _int_free 95ms 1.21% 51.69% 168ms 2.14% __printf_fp_buffer_1 54ms 0.69% 52.38% 160ms 2.04% AbstractCellProperty::IsSame 0 0% 52.38% 158ms 2.01% std::basic_ofstream::basic_ofstream (inline) 0 0% 52.38% 152ms 1.94% std::basic_filebuf::open 0 0% 52.38% 152ms 1.94% std::basic_ofstream::open (inline) 1ms 0.013% 52.39% 147ms 1.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.39% 144ms 1.83% AbstractCellBasedWriter::CloseFile 1ms 0.013% 52.41% 144ms 1.83% std::basic_ofstream::close (inline) 0 0% 52.41% 143ms 1.82% std::basic_filebuf::close 15ms 0.19% 52.60% 142ms 1.81% AbstractTetrahedralElement::CalculateJacobian 3ms 0.038% 52.64% 141ms 1.80% boost::numeric::ublas::vector_assign (inline) 0 0% 52.64% 135ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.025% 52.66% 135ms 1.72% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 52.67% 134ms 1.71% OutputFileHandler::CommonConstructor 0 0% 52.67% 134ms 1.71% OutputFileHandler::OutputFileHandler 0 0% 52.67% 129ms 1.64% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.038% 52.71% 127ms 1.62% alternateaxes 3ms 0.038% 52.75% 124ms 1.58% AbstractTetrahedralElement::CalculateInverseJacobian 114ms 1.45% 54.20% 124ms 1.58% vertexmedian 1ms 0.013% 54.21% 123ms 1.57% _IO_new_fopen 0 0% 54.21% 122ms 1.55% __fopen_internal (inline) 0 0% 54.21% 122ms 1.55% std::__basic_file::open 52ms 0.66% 54.88% 122ms 1.55% std::__ostream_insert 0 0% 54.88% 119ms 1.52% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 54.90% 119ms 1.52% _IO_new_file_fopen 0 0% 54.90% 119ms 1.52% std::filesystem::permissions 78ms 0.99% 55.90% 118ms 1.50% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 118ms 1.50% 57.40% 118ms 1.50% __GI_fchmodat 1ms 0.013% 57.41% 117ms 1.49% __GI__IO_file_open 6ms 0.076% 57.49% 115ms 1.46% std::_Rb_tree_const_iterator::operator++ (inline) 27ms 0.34% 57.83% 114ms 1.45% std::num_put::_M_insert_int 9ms 0.11% 57.94% 112ms 1.43% MeshBasedCellPopulation::SpringIterator::SpringIterator 19ms 0.24% 58.19% 111ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 111ms 1.41% 59.60% 111ms 1.41% std::_Rb_tree_increment 0 0% 59.60% 110ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.13% 59.73% 110ms 1.40% Node::~Node 0 0% 59.73% 107ms 1.36% std::basic_filebuf::_M_terminate_output 25ms 0.32% 60.05% 106ms 1.35% std::type_info::operator== (inline) 105ms 1.34% 61.38% 105ms 1.34% incircle 1ms 0.013% 61.40% 105ms 1.34% std::basic_filebuf::overflow 36ms 0.46% 61.85% 104ms 1.32% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 61.87% 104ms 1.32% std::basic_filebuf::_M_convert_to_external 102ms 1.30% 63.17% 103ms 1.31% __libc_open64 2ms 0.025% 63.19% 103ms 1.31% std::__basic_file::xsputn 3ms 0.038% 63.23% 103ms 1.31% std::vector::push_back (inline) 102ms 1.30% 64.53% 102ms 1.30% __GI___libc_write 45ms 0.57% 65.10% 100ms 1.27% boost::shared_ptr::shared_ptr (inline) 5ms 0.064% 65.16% 99ms 1.26% std::_Vector_base::_M_allocate (inline) 5ms 0.064% 65.23% 98ms 1.25% boost::detail::shared_count::~shared_count (inline) 0 0% 65.23% 98ms 1.25% boost::shared_ptr::~shared_ptr (inline) 97ms 1.24% 66.46% 97ms 1.24% std::_Rb_tree_insert_and_rebalance 8ms 0.1% 66.56% 97ms 1.24% std::vector::_M_realloc_insert 0 0% 66.56% 96ms 1.22% std::operator<< (inline) 14ms 0.18% 66.74% 93ms 1.18% AbstractTetrahedralElement::RefreshJacobian 91ms 1.16% 67.90% 92ms 1.17% boost::detail::sp_counted_base::release 85ms 1.08% 68.98% 85ms 1.08% [libchaste_cell_based.so] 3ms 0.038% 69.02% 82ms 1.04% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 4ms 0.051% 69.07% 82ms 1.04% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 69.09% 80ms 1.02% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 46ms 0.59% 69.67% 76ms 0.97% std::basic_filebuf::xsputn 75ms 0.95% 70.63% 75ms 0.95% Node::GetIndex 4ms 0.051% 70.68% 74ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeA 57ms 0.73% 71.40% 74ms 0.94% std::basic_streambuf::xsputn 1ms 0.013% 71.42% 72ms 0.92% std::filesystem::status 71ms 0.9% 72.32% 71ms 0.9% __GI___fstatat64 63ms 0.8% 73.12% 71ms 0.9% vertexsort 29ms 0.37% 73.49% 68ms 0.87% AbstractElement::GetNodeLocation 55ms 0.7% 74.19% 67ms 0.85% AbstractElement::GetNodeGlobalIndex 67ms 0.85% 75.04% 67ms 0.85% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 75.04% 66ms 0.84% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 75.04% 66ms 0.84% std::filesystem::create_directory 0 0% 75.04% 65ms 0.83% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.04% 65ms 0.83% tcache_get (inline) 65ms 0.83% 75.87% 65ms 0.83% tcache_get_n (inline) 51ms 0.65% 76.52% 64ms 0.81% std::num_put::do_put 62ms 0.79% 77.31% 62ms 0.79% [libchaste_mesh.so] 62ms 0.79% 78.10% 62ms 0.79% std::vector::size (inline) 1ms 0.013% 78.11% 61ms 0.78% Cell::GetCellId 0 0% 78.11% 61ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.11% 61ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 36ms 0.46% 78.57% 60ms 0.76% AbstractTetrahedralMesh::GetElement 34ms 0.43% 79.00% 59ms 0.75% AbstractCellCycleModel::GetAge 42ms 0.53% 79.54% 58ms 0.74% malloc_consolidate 52ms 0.66% 80.20% 55ms 0.7% boost::detail::shared_count::shared_count (inline) 0 0% 80.20% 54ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 7ms 0.089% 80.29% 54ms 0.69% std::_Vector_base::_M_deallocate (inline) 0 0% 80.29% 54ms 0.69% std::__new_allocator::destroy (inline) 0 0% 80.29% 54ms 0.69% std::allocator_traits::destroy (inline) 0 0% 80.29% 53ms 0.67% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 53ms 0.67% 80.97% 53ms 0.67% counterclockwise 3ms 0.038% 81.00% 52ms 0.66% Node::ConstructNodeAttributes (inline) 6ms 0.076% 81.08% 50ms 0.64% CellPropertyCollection::AddProperty 0 0% 81.08% 50ms 0.64% Node::ClearAppliedForce 50ms 0.64% 81.72% 50ms 0.64% __memcpy_avx_unaligned_erms 0 0% 81.72% 49ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 48ms 0.61% 82.33% 48ms 0.61% boost::shared_ptr::operator-> (inline) 1ms 0.013% 82.34% 48ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.34% 47ms 0.6% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 82.52% 47ms 0.6% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 82.52% 46ms 0.59% TetrahedralMesh::EdgeIterator::GetNodeB 26ms 0.33% 82.85% 46ms 0.59% boost::numeric::ublas::c_matrix::operator() (partial-inline) 45ms 0.57% 83.42% 45ms 0.57% [libstdc++.so.6.0.33] 19ms 0.24% 83.66% 44ms 0.56% Determinant (inline) 0 0% 83.66% 44ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 17ms 0.22% 83.88% 43ms 0.55% AbstractTetrahedralMesh::GetNumAllElements 26ms 0.33% 84.21% 42ms 0.53% hack_digit 0 0% 84.21% 42ms 0.53% std::vector::vector (inline) 2ms 0.025% 84.24% 41ms 0.52% BoundaryNodeWriter::Visit 41ms 0.52% 84.76% 41ms 0.52% boost::numeric::ublas::c_vector::operator() 0 0% 84.76% 40ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 40ms 0.51% 85.27% 40ms 0.51% std::ostream::sentry::sentry