File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6945ms, 85.04% of 8167ms total Dropped 577 nodes (cum <= 40.84ms) flat flat% sum% cum cum% 0 0% 0% 8131ms 99.56% __libc_start_call_main 0 0% 0% 8131ms 99.56% __libc_start_main_impl 0 0% 0% 8131ms 99.56% _start 0 0% 0% 8113ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8113ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8113ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8113ms 99.34% main 0 0% 0% 8072ms 98.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 8072ms 98.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 8072ms 98.84% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 8069ms 98.80% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3452ms 42.27% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.037% 0.049% 2999ms 36.72% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.049% 2979ms 36.48% MeshBasedCellPopulation::Update 0 0% 0.049% 1607ms 19.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.049% 1476ms 18.07% MutableMesh::ReMesh 0 0% 0.049% 1438ms 17.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.024% 0.073% 1437ms 17.60% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.086% 0.16% 1398ms 17.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.23% 0.39% 1245ms 15.24% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.049% 0.44% 1006ms 12.32% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 104ms 1.27% 1.71% 1000ms 12.24% TetrahedralMesh::EdgeIterator::operator++ 270ms 3.31% 5.02% 965ms 11.82% __dynamic_cast 4ms 0.049% 5.07% 957ms 11.72% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.13% 5.20% 946ms 11.58% CellPropertyCollection::GetPropertiesType (inline) 417ms 5.11% 10.31% 935ms 11.45% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.073% 10.38% 879ms 10.76% CellPopulationElementWriter::Visit 3ms 0.037% 10.42% 865ms 10.59% MeshBasedCellPopulation::AcceptCellWriter 37ms 0.45% 10.87% 859ms 10.52% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 25ms 0.31% 11.18% 769ms 9.42% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.012% 11.19% 753ms 9.22% AbstractCellProperty::IsSubType (inline) 15ms 0.18% 11.38% 728ms 8.91% TetrahedralMesh::ImportFromMesher 60ms 0.73% 12.11% 610ms 7.47% std::map::operator[] (partial-inline) 32ms 0.39% 12.50% 601ms 7.36% operator new 1ms 0.012% 12.51% 594ms 7.27% std::ostream::operator<< (inline) 100ms 1.22% 13.74% 590ms 7.22% std::ostream::_M_insert 1ms 0.012% 13.75% 582ms 7.13% triangulate 3ms 0.037% 13.79% 569ms 6.97% LegacyCellProliferativeTypesWriter::VisitCell 565ms 6.92% 20.71% 565ms 6.92% __strcmp_avx2 217ms 2.66% 23.36% 562ms 6.88% __GI___libc_malloc 40ms 0.49% 23.85% 553ms 6.77% std::__new_allocator::allocate (inline) 2ms 0.024% 23.88% 552ms 6.76% Cell::GetCellProliferativeType 0 0% 23.88% 550ms 6.73% std::allocator_traits::allocate (inline) 8ms 0.098% 23.97% 540ms 6.61% std::set::insert (inline) 9ms 0.11% 24.08% 532ms 6.51% std::_Rb_tree::_M_insert_unique 0 0% 24.08% 520ms 6.37% delaunay 2ms 0.024% 24.11% 520ms 6.37% divconqdelaunay 240ms 2.94% 27.05% 498ms 6.10% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.26% 27.31% 496ms 6.07% std::_Rb_tree::find (inline) 0 0% 27.31% 492ms 6.02% std::_Rb_tree::lower_bound (inline) 0 0% 27.31% 492ms 6.02% std::map::lower_bound (inline) 0 0% 27.31% 470ms 5.75% std::_Rb_tree::_M_create_node (inline) 2ms 0.024% 27.33% 461ms 5.64% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.33% 448ms 5.49% std::set::count (inline) 0 0% 27.33% 442ms 5.41% std::_Rb_tree::_M_get_node (inline) 0 0% 27.33% 438ms 5.36% std::_Rb_tree::_Alloc_node::operator() (inline) 44ms 0.54% 27.87% 438ms 5.36% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.87% 409ms 5.01% std::set::~set (inline) 85ms 1.04% 28.91% 390ms 4.78% std::_Rb_tree::_M_erase 3ms 0.037% 28.95% 383ms 4.69% Cell::GetMutationState 17ms 0.21% 29.15% 376ms 4.60% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.15% 362ms 4.43% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.012% 29.17% 362ms 4.43% NodeLocationWriter::Visit 0 0% 29.17% 361ms 4.42% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.024% 29.19% 360ms 4.41% OutputFileHandler::OpenOutputFile 1ms 0.012% 29.20% 350ms 4.29% MeshBasedCellPopulation::GetDampingConstant 1ms 0.012% 29.22% 349ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 10ms 0.12% 29.34% 348ms 4.26% std::less::operator() (inline) 338ms 4.14% 33.48% 338ms 4.14% std::operator< (inline) 4ms 0.049% 33.53% 336ms 4.11% std::set::set (inline) 7ms 0.086% 33.61% 334ms 4.09% Cell::ReadyToDivide 23ms 0.28% 33.89% 329ms 4.03% std::_Rb_tree::_M_insert_ (inline) 5ms 0.061% 33.95% 319ms 3.91% AbstractCellProperty::IsType (inline) 2ms 0.024% 33.98% 319ms 3.91% CellPropertyCollection::HasProperty 0 0% 33.98% 318ms 3.89% Cell::HasCellProperty (inline) 30ms 0.37% 34.35% 316ms 3.87% std::_Rb_tree::_M_copy (inline) 311ms 3.81% 38.15% 311ms 3.81% std::_Rb_tree::_S_right (inline) 21ms 0.26% 38.41% 311ms 3.81% std::num_put::_M_insert_float 7ms 0.086% 38.50% 308ms 3.77% AbstractCellPopulation::IsCellAttachedToLocationIndex 78ms 0.96% 39.45% 308ms 3.77% __GI___libc_free 5ms 0.061% 39.51% 301ms 3.69% Element::Element 12ms 0.15% 39.66% 301ms 3.69% divconqrecurse 10ms 0.12% 39.78% 285ms 3.49% std::__new_allocator::deallocate (inline) 0 0% 39.78% 282ms 3.45% std::_Rb_tree::_M_drop_node (inline) 0 0% 39.78% 281ms 3.44% std::allocator_traits::deallocate (inline) 62ms 0.76% 40.54% 278ms 3.40% std::_Rb_tree::_M_clone_node (inline) 85ms 1.04% 41.58% 275ms 3.37% mergehulls 178ms 2.18% 43.76% 273ms 3.34% _int_malloc 2ms 0.024% 43.79% 259ms 3.17% CellProliferativeTypesWriter::VisitCell 3ms 0.037% 43.82% 258ms 3.16% std::__cxx11::collate::do_transform 54ms 0.66% 44.48% 248ms 3.04% AbstractCellProperty::IsSame 1ms 0.012% 44.50% 245ms 3.00% ___vsnprintf 0 0% 44.50% 244ms 2.99% __vsnprintf_internal (inline) 37ms 0.45% 44.95% 239ms 2.93% __printf_buffer 199ms 2.44% 47.39% 228ms 2.79% _int_free 0 0% 47.39% 228ms 2.79% std::_Rb_tree::_M_put_node (inline) 2ms 0.024% 47.41% 210ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.049% 47.46% 205ms 2.51% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.086% 47.54% 201ms 2.46% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.061% 47.61% 196ms 2.40% Element::RegisterWithNodes (inline) 12ms 0.15% 47.75% 196ms 2.40% TetrahedralMesh::Clear 72ms 0.88% 48.63% 194ms 2.38% std::_Rb_tree::_M_get_insert_unique_pos (inline) 38ms 0.47% 49.10% 194ms 2.38% std::type_info::operator== (inline) 12ms 0.15% 49.25% 186ms 2.28% __printf_fp_l_buffer 0 0% 49.25% 186ms 2.28% __printf_fp_spec (inline) 5ms 0.061% 49.31% 185ms 2.27% Node::AddElement 49ms 0.6% 49.91% 176ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 100ms 1.22% 51.13% 170ms 2.08% __printf_fp_buffer_1 0 0% 51.13% 166ms 2.03% std::basic_ofstream::basic_ofstream (inline) 1ms 0.012% 51.14% 164ms 2.01% OutputFileHandler::OutputFileHandler 0 0% 51.14% 163ms 2.00% OutputFileHandler::CommonConstructor 0 0% 51.14% 160ms 1.96% std::basic_ofstream::open (inline) 0 0% 51.14% 159ms 1.95% std::basic_filebuf::open 12ms 0.15% 51.29% 157ms 1.92% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.29% 155ms 1.90% FilesystemPermissions::SetFilePermissions (inline) 0 0% 51.29% 155ms 1.90% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.024% 51.32% 155ms 1.90% std::filesystem::permissions 153ms 1.87% 53.19% 153ms 1.87% __GI_fchmodat 4ms 0.049% 53.24% 151ms 1.85% boost::numeric::ublas::vector_assign (inline) 4ms 0.049% 53.29% 147ms 1.80% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.024% 53.31% 145ms 1.78% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.024% 53.34% 145ms 1.78% alternateaxes 17ms 0.21% 53.54% 143ms 1.75% MeshBasedCellPopulation::SpringIterator::SpringIterator 132ms 1.62% 55.16% 143ms 1.75% vertexmedian 52ms 0.64% 55.80% 137ms 1.68% std::__ostream_insert 0 0% 55.80% 134ms 1.64% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 55.80% 132ms 1.62% AbstractCellBasedWriter::CloseFile 1ms 0.012% 55.81% 132ms 1.62% _IO_new_fopen 0 0% 55.81% 132ms 1.62% std::__basic_file::open 1ms 0.012% 55.82% 132ms 1.62% std::basic_filebuf::close 0 0% 55.82% 132ms 1.62% std::basic_ofstream::close (inline) 1ms 0.012% 55.83% 131ms 1.60% __fopen_internal (inline) 130ms 1.59% 57.43% 130ms 1.59% incircle 0 0% 57.43% 128ms 1.57% _IO_new_file_fopen 1ms 0.012% 57.44% 128ms 1.57% __GI__IO_file_open 7ms 0.086% 57.52% 127ms 1.56% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.086% 57.61% 123ms 1.51% Node::~Node 9ms 0.11% 57.72% 123ms 1.51% std::_Rb_tree_const_iterator::operator++ (inline) 122ms 1.49% 59.21% 122ms 1.49% std::_Rb_tree_increment 0 0% 59.21% 117ms 1.43% std::operator<< (inline) 75ms 0.92% 60.13% 113ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 28ms 0.34% 60.48% 113ms 1.38% std::num_put::_M_insert_int 22ms 0.27% 60.74% 109ms 1.33% AbstractTetrahedralElement::RefreshJacobian 13ms 0.16% 60.90% 108ms 1.32% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.037% 60.94% 108ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.13% 61.08% 108ms 1.32% boost::detail::shared_count::~shared_count (inline) 0 0% 61.08% 108ms 1.32% boost::shared_ptr::~shared_ptr (inline) 0 0% 61.08% 108ms 1.32% std::_Vector_base::_M_allocate (inline) 107ms 1.31% 62.39% 107ms 1.31% __libc_open64 38ms 0.47% 62.85% 106ms 1.30% boost::numeric::ublas::indexing_vector_assign 5ms 0.061% 62.91% 105ms 1.29% std::vector::push_back (inline) 0 0% 62.91% 104ms 1.27% AbstractCellPopulation::Iterator::operator++ (inline) 104ms 1.27% 64.19% 104ms 1.27% [libchaste_cell_based.so] 2ms 0.024% 64.21% 103ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 52ms 0.64% 64.85% 96ms 1.18% boost::shared_ptr::shared_ptr (inline) 11ms 0.13% 64.98% 96ms 1.18% std::vector::_M_realloc_insert 95ms 1.16% 66.14% 95ms 1.16% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.024% 66.17% 94ms 1.15% std::basic_filebuf::overflow 0 0% 66.17% 93ms 1.14% std::basic_filebuf::_M_terminate_output 92ms 1.13% 67.30% 92ms 1.13% std::_Rb_tree_insert_and_rebalance 0 0% 67.30% 92ms 1.13% std::__basic_file::xsputn 0 0% 67.30% 92ms 1.13% std::basic_filebuf::_M_convert_to_external 3ms 0.037% 67.33% 91ms 1.11% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.33% 91ms 1.11% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 90ms 1.10% 68.43% 91ms 1.11% __GI___libc_write 0 0% 68.43% 91ms 1.11% std::filesystem::create_directory 81ms 0.99% 69.43% 88ms 1.08% boost::detail::sp_counted_base::release 3ms 0.037% 69.46% 87ms 1.07% std::filesystem::status 86ms 1.05% 70.52% 86ms 1.05% __GI___fstatat64 1ms 0.012% 70.53% 84ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 47ms 0.58% 71.10% 82ms 1.00% std::basic_filebuf::xsputn 0 0% 71.10% 78ms 0.96% Cell::GetCellId 6ms 0.073% 71.18% 78ms 0.96% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 71.18% 77ms 0.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.18% 77ms 0.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 33ms 0.4% 71.58% 75ms 0.92% AbstractElement::GetNodeLocation 48ms 0.59% 72.17% 71ms 0.87% malloc_consolidate 70ms 0.86% 73.03% 70ms 0.86% [libstdc++.so.6.0.33] 60ms 0.73% 73.76% 69ms 0.84% AbstractElement::GetNodeGlobalIndex 5ms 0.061% 73.82% 67ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 66ms 0.81% 74.63% 66ms 0.81% std::vector::size (inline) 64ms 0.78% 75.41% 64ms 0.78% counterclockwise 46ms 0.56% 75.98% 63ms 0.77% std::num_put::do_put 0 0% 75.98% 63ms 0.77% tcache_get (inline) 63ms 0.77% 76.75% 63ms 0.77% tcache_get_n (inline) 55ms 0.67% 77.42% 63ms 0.77% vertexsort 18ms 0.22% 77.64% 61ms 0.75% AbstractTetrahedralMesh::GetElement 40ms 0.49% 78.13% 60ms 0.73% std::basic_streambuf::xsputn 59ms 0.72% 78.85% 59ms 0.72% Node::GetIndex 2ms 0.024% 78.88% 58ms 0.71% Node::ConstructNodeAttributes (inline) 39ms 0.48% 79.36% 58ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 58ms 0.71% 80.07% 58ms 0.71% boost::shared_ptr::operator-> (inline) 4ms 0.049% 80.12% 58ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.12% 57ms 0.7% Node::ClearAppliedForce 0 0% 80.12% 57ms 0.7% boost::numeric::ublas::norm_2 (inline) 22ms 0.27% 80.38% 57ms 0.7% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.38% 56ms 0.69% BoundaryNodeWriter::Visit 5ms 0.061% 80.45% 56ms 0.69% CellPropertyCollection::AddProperty 55ms 0.67% 81.12% 55ms 0.67% __memcpy_avx_unaligned_erms 0 0% 81.12% 55ms 0.67% std::vector::vector (inline) 0 0% 81.12% 54ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 4ms 0.049% 81.17% 54ms 0.66% std::_Vector_base::_M_deallocate (inline) 0 0% 81.17% 54ms 0.66% std::__new_allocator::destroy (inline) 0 0% 81.17% 54ms 0.66% std::allocator_traits::destroy (inline) 52ms 0.64% 81.80% 52ms 0.64% [libchaste_mesh.so] 0 0% 81.80% 51ms 0.62% AbstractCentreBasedCellPopulation::CreateCellPair 11ms 0.13% 81.94% 51ms 0.62% Determinant (inline) 2ms 0.024% 81.96% 50ms 0.61% NodeAttributes::NodeAttributes 48ms 0.59% 82.55% 48ms 0.59% std::ostream::sentry::sentry 0 0% 82.55% 46ms 0.56% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.55% 46ms 0.56% std::_Vector_base::_Vector_base (inline) 0 0% 82.55% 46ms 0.56% std::map::map (inline) 44ms 0.54% 83.09% 44ms 0.54% __GI___mkdir 43ms 0.53% 83.62% 44ms 0.54% boost::detail::shared_count::shared_count (inline) 44ms 0.54% 84.16% 44ms 0.54% boost::numeric::ublas::c_vector::operator() 29ms 0.36% 84.51% 44ms 0.54% hack_digit 0 0% 84.51% 43ms 0.53% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 84.51% 43ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 29ms 0.36% 84.87% 43ms 0.53% TetrahedralMesh::SolveElementMapping 1ms 0.012% 84.88% 43ms 0.53% std::_Vector_base::_M_create_storage (inline) 0 0% 84.88% 42ms 0.51% std::map::find (inline) 13ms 0.16% 85.04% 41ms 0.5% AbstractCellCycleModel::GetAge