File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6791ms, 85.08% of 7982ms total Dropped 597 nodes (cum <= 39.91ms) flat flat% sum% cum cum% 0 0% 0% 7942ms 99.50% __libc_start_call_main 0 0% 0% 7942ms 99.50% __libc_start_main_impl 0 0% 0% 7942ms 99.50% _start 0 0% 0% 7928ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7928ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7928ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7928ms 99.32% main 0 0% 0% 7885ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7885ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7885ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7881ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3367ms 42.18% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2960ms 37.08% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 2903ms 36.37% MeshBasedCellPopulation::Update 0 0% 0.038% 1544ms 19.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.05% 1445ms 18.10% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.063% 1395ms 17.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.063% 1393ms 17.45% MutableMesh::ReMesh 5ms 0.063% 0.13% 1344ms 16.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 18ms 0.23% 0.35% 1266ms 15.86% MeshBasedCellPopulation::SpringIterator::operator++ 118ms 1.48% 1.83% 1044ms 13.08% TetrahedralMesh::EdgeIterator::operator++ 428ms 5.36% 7.19% 973ms 12.19% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.22% 967ms 12.11% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 14ms 0.18% 7.39% 928ms 11.63% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.075% 7.47% 911ms 11.41% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.075% 7.54% 911ms 11.41% CellPopulationElementWriter::Visit 240ms 3.01% 10.55% 904ms 11.33% __dynamic_cast 42ms 0.53% 11.07% 796ms 9.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 10ms 0.13% 11.20% 790ms 9.90% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 11.54% 743ms 9.31% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.59% 738ms 9.25% AbstractCellProperty::IsSubType (inline) 10ms 0.13% 11.71% 720ms 9.02% TetrahedralMesh::ImportFromMesher 0 0% 11.71% 634ms 7.94% std::ostream::operator<< (inline) 99ms 1.24% 12.95% 632ms 7.92% std::ostream::_M_insert 48ms 0.6% 13.56% 572ms 7.17% std::map::operator[] (partial-inline) 20ms 0.25% 13.81% 557ms 6.98% std::_Rb_tree::find (inline) 532ms 6.66% 20.47% 532ms 6.66% __strcmp_avx2 28ms 0.35% 20.82% 532ms 6.66% operator new 7ms 0.088% 20.91% 526ms 6.59% Cell::GetCellProliferativeType 7ms 0.088% 21.00% 517ms 6.48% std::set::insert (inline) 15ms 0.19% 21.19% 511ms 6.40% std::_Rb_tree::_M_insert_unique 2ms 0.025% 21.21% 510ms 6.39% triangulate 0 0% 21.21% 505ms 6.33% std::set::count (inline) 198ms 2.48% 23.69% 500ms 6.26% __cxxabiv1::__si_class_type_info::__do_dyncast 153ms 1.92% 25.61% 498ms 6.24% __GI___libc_malloc 2ms 0.025% 25.63% 496ms 6.21% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 25.63% 464ms 5.81% std::_Rb_tree::lower_bound (inline) 24ms 0.3% 25.93% 464ms 5.81% std::__new_allocator::allocate (inline) 0 0% 25.93% 464ms 5.81% std::map::lower_bound (inline) 0 0% 25.93% 460ms 5.76% std::allocator_traits::allocate (inline) 4ms 0.05% 25.98% 446ms 5.59% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 26.00% 441ms 5.52% delaunay 0 0% 26.00% 440ms 5.51% divconqdelaunay 3ms 0.038% 26.03% 411ms 5.15% Cell::GetMutationState 26ms 0.33% 26.36% 397ms 4.97% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.15% 26.51% 387ms 4.85% std::less::operator() (inline) 375ms 4.70% 31.21% 375ms 4.70% std::operator< (inline) 4ms 0.05% 31.26% 369ms 4.62% NodeLocationWriter::Visit 0 0% 31.26% 367ms 4.60% std::_Rb_tree::_M_create_node (inline) 0 0% 31.26% 367ms 4.60% std::set::~set (inline) 79ms 0.99% 32.25% 361ms 4.52% std::_Rb_tree::_M_erase 24ms 0.3% 32.55% 356ms 4.46% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 32.55% 340ms 4.26% std::_Rb_tree::_Alloc_node::operator() (inline) 21ms 0.26% 32.81% 338ms 4.23% std::num_put::_M_insert_float 0 0% 32.81% 335ms 4.20% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 32.84% 332ms 4.16% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 32.86% 330ms 4.13% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.013% 32.87% 324ms 4.06% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.063% 32.94% 322ms 4.03% std::set::set (inline) 0 0% 32.94% 321ms 4.02% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 32.94% 317ms 3.97% OutputFileHandler::OpenOutputFile 31ms 0.39% 33.32% 310ms 3.88% std::_Rb_tree::_M_insert_ (inline) 49ms 0.61% 33.94% 301ms 3.77% std::_Rb_tree::_M_copy (inline) 301ms 3.77% 37.71% 301ms 3.77% std::_Rb_tree::_S_right (inline) 9ms 0.11% 37.82% 300ms 3.76% Cell::ReadyToDivide 5ms 0.063% 37.89% 297ms 3.72% Element::Element 106ms 1.33% 39.21% 293ms 3.67% __GI___libc_free 6ms 0.075% 39.29% 284ms 3.56% AbstractCellPopulation::IsCellAttachedToLocationIndex 173ms 2.17% 41.46% 274ms 3.43% _int_malloc 7ms 0.088% 41.54% 263ms 3.29% std::__cxx11::collate::do_transform 0 0% 41.54% 262ms 3.28% std::_Rb_tree::_M_drop_node (inline) 16ms 0.2% 41.74% 261ms 3.27% divconqrecurse 9ms 0.11% 41.86% 261ms 3.27% std::__new_allocator::deallocate (inline) 0 0% 41.86% 255ms 3.19% std::allocator_traits::deallocate (inline) 4ms 0.05% 41.91% 253ms 3.17% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 41.94% 251ms 3.14% ___vsnprintf 0 0% 41.94% 248ms 3.11% __vsnprintf_internal (inline) 96ms 1.20% 43.15% 248ms 3.11% std::_Rb_tree::_M_clone_node (inline) 64ms 0.8% 43.95% 238ms 2.98% mergehulls 22ms 0.28% 44.22% 237ms 2.97% __printf_buffer 3ms 0.038% 44.26% 220ms 2.76% AbstractCellProperty::IsType (inline) 5ms 0.063% 44.32% 219ms 2.74% CellPropertyCollection::HasProperty 0 0% 44.32% 215ms 2.69% Cell::HasCellProperty (inline) 0 0% 44.32% 207ms 2.59% std::_Rb_tree::_M_put_node (inline) 8ms 0.1% 44.42% 205ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.025% 44.45% 203ms 2.54% __printf_fp_spec (inline) 5ms 0.063% 44.51% 201ms 2.52% __printf_fp_l_buffer 9ms 0.11% 44.63% 194ms 2.43% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.063% 44.69% 190ms 2.38% Element::RegisterWithNodes (inline) 63ms 0.79% 45.48% 187ms 2.34% std::_Rb_tree::_M_get_insert_unique_pos (inline) 152ms 1.90% 47.38% 186ms 2.33% _int_free 6ms 0.075% 47.46% 185ms 2.32% MeshBasedCellPopulation::SpringsEnd (inline) 112ms 1.40% 48.86% 185ms 2.32% __printf_fp_buffer_1 5ms 0.063% 48.92% 183ms 2.29% Node::AddElement 23ms 0.29% 49.21% 183ms 2.29% TetrahedralMesh::Clear 0 0% 49.21% 166ms 2.08% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.21% 160ms 2.00% std::basic_ofstream::open (inline) 3ms 0.038% 49.25% 159ms 1.99% std::basic_filebuf::open 12ms 0.15% 49.40% 157ms 1.97% AbstractTetrahedralElement::CalculateJacobian 3ms 0.038% 49.44% 156ms 1.95% boost::numeric::ublas::vector_assign (inline) 42ms 0.53% 49.96% 154ms 1.93% AbstractCellProperty::IsSame 41ms 0.51% 50.48% 151ms 1.89% std::__ostream_insert 5ms 0.063% 50.54% 149ms 1.87% boost::numeric::ublas::c_vector::c_vector (inline) 40ms 0.5% 51.04% 148ms 1.85% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.04% 144ms 1.80% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 51.05% 144ms 1.80% std::basic_filebuf::close 0 0% 51.05% 144ms 1.80% std::basic_ofstream::close (inline) 0 0% 51.05% 143ms 1.79% AbstractCellBasedWriter::CloseFile 0 0% 51.05% 135ms 1.69% OutputFileHandler::CommonConstructor 0 0% 51.05% 135ms 1.69% OutputFileHandler::OutputFileHandler 0 0% 51.05% 135ms 1.69% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.23% 51.28% 130ms 1.63% AbstractTetrahedralElement::RefreshJacobian 0 0% 51.28% 130ms 1.63% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.038% 51.32% 128ms 1.60% std::_Vector_base::_M_allocate (inline) 29ms 0.36% 51.68% 128ms 1.60% std::num_put::_M_insert_int 3ms 0.038% 51.72% 128ms 1.60% std::operator<< (inline) 16ms 0.2% 51.92% 127ms 1.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.075% 51.99% 124ms 1.55% std::vector::push_back (inline) 0 0% 51.99% 123ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 0 0% 51.99% 123ms 1.54% std::__basic_file::open 2ms 0.025% 52.02% 123ms 1.54% std::filesystem::permissions 0 0% 52.02% 122ms 1.53% _IO_new_fopen 0 0% 52.02% 122ms 1.53% __fopen_internal (inline) 2ms 0.025% 52.04% 121ms 1.52% AbstractTetrahedralElement::CalculateInverseJacobian 121ms 1.52% 53.56% 121ms 1.52% __GI_fchmodat 1ms 0.013% 53.57% 121ms 1.52% alternateaxes 6ms 0.075% 53.65% 121ms 1.52% boost::detail::shared_count::~shared_count (inline) 0 0% 53.65% 121ms 1.52% boost::shared_ptr::~shared_ptr (inline) 108ms 1.35% 55.00% 120ms 1.50% vertexmedian 20ms 0.25% 55.25% 119ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 119ms 1.49% 56.74% 119ms 1.49% incircle 0 0% 56.74% 117ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 56.75% 117ms 1.47% _IO_new_file_fopen 1ms 0.013% 56.77% 116ms 1.45% __GI__IO_file_open 38ms 0.48% 57.24% 116ms 1.45% boost::numeric::ublas::indexing_vector_assign 79ms 0.99% 58.23% 114ms 1.43% std::basic_filebuf::xsputn 22ms 0.28% 58.51% 112ms 1.40% std::type_info::operator== (inline) 110ms 1.38% 59.88% 111ms 1.39% boost::detail::sp_counted_base::release 3ms 0.038% 59.92% 111ms 1.39% std::basic_filebuf::overflow 1ms 0.013% 59.93% 110ms 1.38% std::basic_filebuf::_M_terminate_output 9ms 0.11% 60.05% 110ms 1.38% std::vector::_M_realloc_insert 1ms 0.013% 60.06% 109ms 1.37% AbstractTetrahedralElement::AbstractTetrahedralElement 51ms 0.64% 60.70% 109ms 1.37% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 60.71% 108ms 1.35% std::basic_filebuf::_M_convert_to_external 107ms 1.34% 62.05% 107ms 1.34% std::_Rb_tree_insert_and_rebalance 0 0% 62.05% 107ms 1.34% std::__basic_file::xsputn 106ms 1.33% 63.38% 106ms 1.33% __GI___libc_write 44ms 0.55% 63.93% 104ms 1.30% AbstractElement::GetNodeLocation 4ms 0.05% 63.98% 100ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 99ms 1.24% 65.22% 99ms 1.24% __libc_open64 10ms 0.13% 65.35% 96ms 1.20% Node::~Node 96ms 1.20% 66.55% 96ms 1.20% std::_Rb_tree_increment 94ms 1.18% 67.73% 94ms 1.18% [libchaste_cell_based.so] 7ms 0.088% 67.82% 94ms 1.18% std::_Rb_tree_const_iterator::operator++ (inline) 65ms 0.81% 68.63% 92ms 1.15% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.038% 68.67% 91ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 58ms 0.73% 69.39% 83ms 1.04% std::basic_streambuf::xsputn 78ms 0.98% 70.37% 78ms 0.98% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 51ms 0.64% 71.01% 78ms 0.98% malloc_consolidate 3ms 0.038% 71.05% 75ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 71.06% 74ms 0.93% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 71.07% 73ms 0.91% std::filesystem::create_directory 57ms 0.71% 71.79% 70ms 0.88% AbstractElement::GetNodeGlobalIndex 9ms 0.11% 71.90% 69ms 0.86% CellPropertyCollection::AddProperty 2ms 0.025% 71.92% 68ms 0.85% Cell::GetCellId 2ms 0.025% 71.95% 68ms 0.85% std::filesystem::status 66ms 0.83% 72.78% 66ms 0.83% __GI___fstatat64 51ms 0.64% 73.42% 64ms 0.8% std::num_put::do_put 1ms 0.013% 73.43% 63ms 0.79% BoundaryNodeWriter::Visit 0 0% 73.43% 62ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.43% 62ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 61ms 0.76% 74.19% 61ms 0.76% Node::GetIndex 61ms 0.76% 74.96% 61ms 0.76% [libchaste_mesh.so] 40ms 0.5% 75.46% 60ms 0.75% AbstractTetrahedralMesh::GetElement 60ms 0.75% 76.21% 60ms 0.75% __memcpy_avx_unaligned_erms 2ms 0.025% 76.23% 60ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.05% 76.28% 58ms 0.73% TetrahedralMesh::EdgeIterator::GetNodeA 56ms 0.7% 76.99% 58ms 0.73% boost::detail::shared_count::shared_count (inline) 58ms 0.73% 77.71% 58ms 0.73% std::vector::size (inline) 1ms 0.013% 77.72% 57ms 0.71% Node::ClearAppliedForce 1ms 0.013% 77.74% 57ms 0.71% Node::ConstructNodeAttributes (inline) 0 0% 77.74% 57ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 57ms 0.71% 78.45% 57ms 0.71% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 78.45% 57ms 0.71% tcache_get (inline) 57ms 0.71% 79.17% 57ms 0.71% tcache_get_n (inline) 0 0% 79.17% 55ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.17% 55ms 0.69% std::__new_allocator::destroy (inline) 0 0% 79.17% 55ms 0.69% std::allocator_traits::destroy (inline) 5ms 0.063% 79.23% 54ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 79.23% 52ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 47ms 0.59% 79.82% 52ms 0.65% vertexsort 50ms 0.63% 80.44% 50ms 0.63% counterclockwise 5ms 0.063% 80.51% 50ms 0.63% std::_Vector_base::_M_deallocate (inline) 48ms 0.6% 81.11% 48ms 0.6% Node::rGetLocation 46ms 0.58% 81.68% 46ms 0.58% [libstdc++.so.6.0.33] 0 0% 81.68% 46ms 0.58% std::vector::vector (inline) 0 0% 81.68% 45ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 45ms 0.56% 82.25% 45ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 82.25% 44ms 0.55% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 27ms 0.34% 82.59% 44ms 0.55% boost::numeric::ublas::c_matrix::operator() 0 0% 82.59% 44ms 0.55% boost::numeric::ublas::norm_2 (inline) 12ms 0.15% 82.74% 44ms 0.55% boost::numeric::ublas::vector_norm_2::apply (inline) 44ms 0.55% 83.29% 44ms 0.55% std::ostream::sentry::sentry 4ms 0.05% 83.34% 42ms 0.53% Element::~Element 42ms 0.53% 83.86% 42ms 0.53% Node::IsDeleted 6ms 0.075% 83.94% 42ms 0.53% NodeAttributes::NodeAttributes 20ms 0.25% 84.19% 41ms 0.51% AbstractCellCycleModel::GetAge 26ms 0.33% 84.52% 41ms 0.51% hack_digit 3ms 0.038% 84.55% 41ms 0.51% std::__new_allocator::construct (inline) 0 0% 84.55% 41ms 0.51% std::allocator_traits::construct (inline) 0 0% 84.55% 41ms 0.51% std::map::find (inline) 0 0% 84.55% 41ms 0.51% std::map::map (inline) 41ms 0.51% 85.07% 41ms 0.51% unlink_chunk 1ms 0.013% 85.08% 40ms 0.5% std::_Vector_base::_M_create_storage (inline) 0 0% 85.08% 40ms 0.5% std::_Vector_base::_Vector_base (inline)