File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6681ms, 83.39% of 8012ms total Dropped 600 nodes (cum <= 40.06ms) flat flat% sum% cum cum% 0 0% 0% 7976ms 99.55% __libc_start_call_main 0 0% 0% 7976ms 99.55% __libc_start_main_impl 0 0% 0% 7976ms 99.55% _start 0 0% 0% 7962ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7962ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7962ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7962ms 99.38% main 0 0% 0% 7916ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7916ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7916ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 2ms 0.025% 0.025% 7912ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0.025% 3411ms 42.57% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.025% 2921ms 36.46% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.037% 2912ms 36.35% MeshBasedCellPopulation::Update 4ms 0.05% 0.087% 1568ms 19.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.087% 1438ms 17.95% MutableMesh::ReMesh 2ms 0.025% 0.11% 1432ms 17.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.14% 1418ms 17.70% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.062% 0.2% 1386ms 17.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 22ms 0.27% 0.47% 1249ms 15.59% MeshBasedCellPopulation::SpringIterator::operator++ 115ms 1.44% 1.91% 1022ms 12.76% TetrahedralMesh::EdgeIterator::operator++ 474ms 5.92% 7.83% 1013ms 12.64% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.037% 7.86% 945ms 11.79% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 7.89% 940ms 11.73% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.11% 8.00% 930ms 11.61% CellPropertyCollection::GetPropertiesType (inline) 268ms 3.34% 11.35% 908ms 11.33% __dynamic_cast 8ms 0.1% 11.45% 900ms 11.23% CellPopulationElementWriter::Visit 34ms 0.42% 11.87% 844ms 10.53% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.062% 11.93% 795ms 9.92% MeshBasedCellPopulation::AcceptCellWriter 32ms 0.4% 12.33% 773ms 9.65% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.12% 12.46% 752ms 9.39% TetrahedralMesh::ImportFromMesher 2ms 0.025% 12.48% 708ms 8.84% AbstractCellProperty::IsSubType (inline) 1ms 0.012% 12.49% 613ms 7.65% std::ostream::operator<< (inline) 85ms 1.06% 13.55% 611ms 7.63% std::ostream::_M_insert 66ms 0.82% 14.38% 603ms 7.53% std::map::operator[] (partial-inline) 31ms 0.39% 14.77% 576ms 7.19% operator new 20ms 0.25% 15.01% 559ms 6.98% std::_Rb_tree::find (inline) 191ms 2.38% 17.40% 546ms 6.81% __GI___libc_malloc 3ms 0.037% 17.44% 535ms 6.68% triangulate 524ms 6.54% 23.98% 524ms 6.54% __strcmp_avx2 8ms 0.1% 24.08% 521ms 6.50% LegacyCellProliferativeTypesWriter::VisitCell 40ms 0.5% 24.58% 519ms 6.48% std::__new_allocator::allocate (inline) 0 0% 24.58% 514ms 6.42% std::allocator_traits::allocate (inline) 0 0% 24.58% 507ms 6.33% std::set::count (inline) 8ms 0.1% 24.68% 498ms 6.22% std::set::insert (inline) 0 0% 24.68% 496ms 6.19% std::_Rb_tree::lower_bound (inline) 0 0% 24.68% 496ms 6.19% std::map::lower_bound (inline) 1ms 0.012% 24.69% 493ms 6.15% Cell::GetCellProliferativeType 6ms 0.075% 24.76% 491ms 6.13% std::_Rb_tree::_M_insert_unique 4ms 0.05% 24.81% 478ms 5.97% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.81% 467ms 5.83% delaunay 2ms 0.025% 24.84% 466ms 5.82% divconqdelaunay 200ms 2.50% 27.33% 459ms 5.73% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.025% 27.36% 437ms 5.45% Cell::GetMutationState 0 0% 27.36% 431ms 5.38% std::_Rb_tree::_M_create_node (inline) 0 0% 27.36% 406ms 5.07% std::_Rb_tree::_Alloc_node::operator() (inline) 27ms 0.34% 27.70% 406ms 5.07% std::_Rb_tree::_Rb_tree (partial-inline) 28ms 0.35% 28.05% 400ms 4.99% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.05% 388ms 4.84% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 28.07% 381ms 4.76% std::set::set (inline) 0 0% 28.07% 377ms 4.71% std::set::~set (inline) 1ms 0.012% 28.08% 375ms 4.68% NodeLocationWriter::Visit 61ms 0.76% 28.84% 369ms 4.61% std::_Rb_tree::_M_erase 19ms 0.24% 29.08% 365ms 4.56% std::less::operator() (inline) 2ms 0.025% 29.11% 361ms 4.51% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 29.11% 361ms 4.51% MeshBasedCellPopulation::GetDampingConstant 42ms 0.52% 29.63% 346ms 4.32% std::_Rb_tree::_M_copy (inline) 346ms 4.32% 33.95% 346ms 4.32% std::operator< (inline) 27ms 0.34% 34.29% 342ms 4.27% std::num_put::_M_insert_float 3ms 0.037% 34.32% 319ms 3.98% Cell::ReadyToDivide 319ms 3.98% 38.31% 319ms 3.98% std::_Rb_tree::_S_right (inline) 1ms 0.012% 38.32% 316ms 3.94% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.32% 316ms 3.94% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 116ms 1.45% 39.77% 314ms 3.92% __GI___libc_free 0 0% 39.77% 311ms 3.88% OutputFileHandler::OpenOutputFile 11ms 0.14% 39.90% 310ms 3.87% AbstractCellPopulation::IsCellAttachedToLocationIndex 19ms 0.24% 40.14% 306ms 3.82% std::_Rb_tree::_M_insert_ (inline) 91ms 1.14% 41.28% 298ms 3.72% std::_Rb_tree::_M_clone_node (inline) 6ms 0.075% 41.35% 295ms 3.68% Element::Element 14ms 0.17% 41.53% 289ms 3.61% std::__new_allocator::deallocate (inline) 0 0% 41.53% 288ms 3.59% std::allocator_traits::deallocate (inline) 0 0% 41.53% 286ms 3.57% std::_Rb_tree::_M_drop_node (inline) 175ms 2.18% 43.71% 269ms 3.36% _int_malloc 9ms 0.11% 43.82% 258ms 3.22% std::__cxx11::collate::do_transform 11ms 0.14% 43.96% 254ms 3.17% divconqrecurse 1ms 0.012% 43.97% 252ms 3.15% AbstractCellProperty::IsType (inline) 0 0% 43.97% 244ms 3.05% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 44.00% 241ms 3.01% ___vsnprintf 0 0% 44.00% 240ms 3.00% Cell::HasCellProperty (inline) 3ms 0.037% 44.03% 239ms 2.98% CellPropertyCollection::HasProperty 0 0% 44.03% 239ms 2.98% __vsnprintf_internal (inline) 0 0% 44.03% 238ms 2.97% CellProliferativeTypesWriter::VisitCell 74ms 0.92% 44.96% 238ms 2.97% mergehulls 24ms 0.3% 45.26% 234ms 2.92% __printf_buffer 25ms 0.31% 45.57% 211ms 2.63% TetrahedralMesh::Clear 2ms 0.025% 45.59% 205ms 2.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.062% 45.66% 198ms 2.47% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 164ms 2.05% 47.70% 198ms 2.47% _int_free 12ms 0.15% 47.85% 194ms 2.42% __printf_fp_l_buffer 0 0% 47.85% 194ms 2.42% __printf_fp_spec (inline) 52ms 0.65% 48.50% 191ms 2.38% AbstractCellProperty::IsSame 7ms 0.087% 48.59% 181ms 2.26% Element::RegisterWithNodes (inline) 53ms 0.66% 49.25% 179ms 2.23% std::_Rb_tree::_M_get_insert_unique_pos (inline) 98ms 1.22% 50.47% 173ms 2.16% __printf_fp_buffer_1 4ms 0.05% 50.52% 171ms 2.13% Node::AddElement 7ms 0.087% 50.61% 169ms 2.11% MeshBasedCellPopulation::SpringsEnd (inline) 14ms 0.17% 50.79% 162ms 2.02% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.79% 154ms 1.92% OutputFileHandler::OutputFileHandler 0 0% 50.79% 152ms 1.90% OutputFileHandler::CommonConstructor 65ms 0.81% 51.60% 151ms 1.88% std::__ostream_insert 32ms 0.4% 52.00% 150ms 1.87% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.012% 52.01% 145ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 52.01% 144ms 1.80% std::basic_ofstream::basic_ofstream (inline) 0 0% 52.01% 142ms 1.77% std::basic_filebuf::close 0 0% 52.01% 142ms 1.77% std::basic_ofstream::close (inline) 0 0% 52.01% 141ms 1.76% AbstractCellBasedWriter::CloseFile 0 0% 52.01% 141ms 1.76% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.01% 140ms 1.75% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.037% 52.05% 140ms 1.75% std::basic_filebuf::open 0 0% 52.05% 140ms 1.75% std::basic_ofstream::open (inline) 0 0% 52.05% 140ms 1.75% std::filesystem::permissions 139ms 1.73% 53.78% 139ms 1.73% __GI_fchmodat 38ms 0.47% 54.26% 139ms 1.73% std::type_info::operator== (inline) 2ms 0.025% 54.28% 132ms 1.65% boost::numeric::ublas::vector_assign (inline) 16ms 0.2% 54.48% 131ms 1.64% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.012% 54.49% 131ms 1.64% TetrahedralMesh::RefreshJacobianCachedData 40ms 0.5% 54.99% 130ms 1.62% std::num_put::_M_insert_int 0 0% 54.99% 129ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.062% 55.05% 129ms 1.61% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.037% 55.09% 128ms 1.60% std::vector::push_back (inline) 1ms 0.012% 55.10% 127ms 1.59% std::_Vector_base::_M_allocate (inline) 4ms 0.05% 55.15% 124ms 1.55% std::operator<< (inline) 4ms 0.05% 55.20% 122ms 1.52% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 55.20% 122ms 1.52% alternateaxes 117ms 1.46% 56.67% 122ms 1.52% vertexmedian 7ms 0.087% 56.75% 121ms 1.51% Node::~Node 20ms 0.25% 57.00% 120ms 1.50% AbstractTetrahedralElement::RefreshJacobian 119ms 1.49% 58.49% 119ms 1.49% std::_Rb_tree_increment 1ms 0.012% 58.50% 116ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.062% 58.56% 115ms 1.44% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.087% 58.65% 114ms 1.42% std::vector::_M_realloc_insert 46ms 0.57% 59.22% 110ms 1.37% boost::shared_ptr::shared_ptr (inline) 71ms 0.89% 60.11% 107ms 1.34% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 14ms 0.17% 60.28% 107ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 60.28% 107ms 1.34% boost::shared_ptr::~shared_ptr (inline) 35ms 0.44% 60.72% 105ms 1.31% boost::numeric::ublas::indexing_vector_assign 105ms 1.31% 62.03% 105ms 1.31% incircle 1ms 0.012% 62.04% 105ms 1.31% std::__basic_file::open 1ms 0.012% 62.06% 104ms 1.30% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 62.06% 104ms 1.30% _IO_new_fopen 2ms 0.025% 62.08% 104ms 1.30% __fopen_internal (inline) 2ms 0.025% 62.11% 103ms 1.29% std::basic_filebuf::overflow 1ms 0.012% 62.12% 102ms 1.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 62.14% 101ms 1.26% _IO_new_file_fopen 2ms 0.025% 62.17% 101ms 1.26% std::__basic_file::xsputn 0 0% 62.17% 101ms 1.26% std::basic_filebuf::_M_convert_to_external 1ms 0.012% 62.18% 101ms 1.26% std::basic_filebuf::_M_terminate_output 0 0% 62.18% 97ms 1.21% __GI__IO_file_open 97ms 1.21% 63.39% 97ms 1.21% __GI___libc_write 12ms 0.15% 63.54% 96ms 1.20% MeshBasedCellPopulation::SpringIterator::SpringIterator 94ms 1.17% 64.72% 94ms 1.17% std::_Rb_tree_insert_and_rebalance 90ms 1.12% 65.84% 91ms 1.14% boost::detail::sp_counted_base::release 2ms 0.025% 65.86% 90ms 1.12% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.19% 66.05% 87ms 1.09% CellPropertyCollection::AddProperty 35ms 0.44% 66.49% 84ms 1.05% AbstractElement::GetNodeLocation 51ms 0.64% 67.12% 84ms 1.05% std::basic_filebuf::xsputn 82ms 1.02% 68.15% 83ms 1.04% __libc_open64 81ms 1.01% 69.16% 81ms 1.01% [libchaste_cell_based.so] 2ms 0.025% 69.18% 77ms 0.96% Cell::GetCellId 73ms 0.91% 70.09% 75ms 0.94% vertexsort 48ms 0.6% 70.69% 74ms 0.92% std::basic_streambuf::xsputn 0 0% 70.69% 73ms 0.91% tcache_get (inline) 73ms 0.91% 71.61% 73ms 0.91% tcache_get_n (inline) 56ms 0.7% 72.30% 72ms 0.9% AbstractElement::GetNodeGlobalIndex 0 0% 72.30% 72ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 72.30% 72ms 0.9% std::filesystem::create_directory 54ms 0.67% 72.98% 71ms 0.89% malloc_consolidate 69ms 0.86% 73.84% 69ms 0.86% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 69ms 0.86% 74.70% 69ms 0.86% __memcpy_avx_unaligned_erms 53ms 0.66% 75.36% 66ms 0.82% std::num_put::do_put 1ms 0.012% 75.37% 65ms 0.81% std::filesystem::status 64ms 0.8% 76.17% 64ms 0.8% Node::GetIndex 3ms 0.037% 76.21% 64ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeB 64ms 0.8% 77.01% 64ms 0.8% __GI___fstatat64 61ms 0.76% 77.77% 64ms 0.8% boost::detail::shared_count::shared_count (inline) 60ms 0.75% 78.52% 60ms 0.75% std::vector::size (inline) 35ms 0.44% 78.96% 58ms 0.72% AbstractTetrahedralMesh::GetElement 57ms 0.71% 79.67% 57ms 0.71% [libchaste_mesh.so] 3ms 0.037% 79.71% 55ms 0.69% TetrahedralMesh::EdgeIterator::GetNodeA 54ms 0.67% 80.38% 54ms 0.67% boost::shared_ptr::operator-> (inline) 0 0% 80.38% 53ms 0.66% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 53ms 0.66% 81.04% 53ms 0.66% counterclockwise 0 0% 81.04% 52ms 0.65% BoundaryNodeWriter::Visit 0 0% 81.04% 52ms 0.65% std::vector::vector (inline) 0 0% 81.04% 51ms 0.64% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.04% 51ms 0.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 50ms 0.62% 81.67% 50ms 0.62% boost::numeric::ublas::c_vector::operator() (partial-inline) 3ms 0.037% 81.70% 50ms 0.62% std::__new_allocator::construct (inline) 0 0% 81.70% 50ms 0.62% std::allocator_traits::construct (inline) 0 0% 81.70% 49ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 7ms 0.087% 81.79% 49ms 0.61% std::_Vector_base::_M_deallocate (inline) 31ms 0.39% 82.18% 48ms 0.6% boost::numeric::ublas::c_matrix::operator() 17ms 0.21% 82.39% 46ms 0.57% Determinant (inline) 0 0% 82.39% 46ms 0.57% std::_Vector_base::_Vector_base (inline) 0 0% 82.39% 45ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 45ms 0.56% 82.95% 45ms 0.56% [libstdc++.so.6.0.33] 0 0% 82.95% 44ms 0.55% std::_Vector_base::_M_create_storage (inline) 2ms 0.025% 82.98% 43ms 0.54% Node::ConstructNodeAttributes (inline) 0 0% 82.98% 43ms 0.54% std::_Rb_tree::_M_construct_node (inline) 0 0% 82.98% 43ms 0.54% std::map::find (inline) 18ms 0.22% 83.20% 42ms 0.52% AbstractCellCycleModel::GetAge 1ms 0.012% 83.21% 42ms 0.52% Node::ClearAppliedForce 0 0% 83.21% 42ms 0.52% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.21% 42ms 0.52% std::__new_allocator::destroy (inline) 0 0% 83.21% 42ms 0.52% std::allocator_traits::destroy (inline) 0 0% 83.21% 41ms 0.51% CxxTest::RealWorldDescription::setUp 0 0% 83.21% 41ms 0.51% PetscInitialize 0 0% 83.21% 41ms 0.51% PetscSetup::setUpWorld 0 0% 83.21% 41ms 0.51% PetscSetupUtils::CommonSetup 0 0% 83.21% 41ms 0.51% PetscSetupUtils::InitialisePetsc 0 0% 83.21% 41ms 0.51% boost::numeric::ublas::norm_2 (inline) 12ms 0.15% 83.36% 41ms 0.51% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.025% 83.39% 41ms 0.51% std::_Rb_tree::_M_emplace_hint_unique