File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6870ms, 85.54% of 8031ms total Dropped 572 nodes (cum <= 40.16ms) flat flat% sum% cum cum% 0 0% 0% 7990ms 99.49% __libc_start_call_main 0 0% 0% 7990ms 99.49% __libc_start_main_impl 0 0% 0% 7990ms 99.49% _start 0 0% 0% 7971ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7971ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7971ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7971ms 99.25% main 0 0% 0% 7931ms 98.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7931ms 98.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7931ms 98.75% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7926ms 98.69% AbstractCellBasedSimulation::Solve 0 0% 0% 3385ms 42.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2953ms 36.77% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 2898ms 36.09% MeshBasedCellPopulation::Update 1ms 0.012% 0.012% 1578ms 19.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 1467ms 18.27% MutableMesh::ReMesh 0 0% 0.012% 1409ms 17.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.075% 0.087% 1377ms 17.15% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.05% 0.14% 1361ms 16.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 10ms 0.12% 0.26% 1186ms 14.77% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.062% 0.32% 988ms 12.30% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 0.35% 988ms 12.30% AbstractTwoBodyInteractionForce::AddForceContribution 101ms 1.26% 1.61% 986ms 12.28% TetrahedralMesh::EdgeIterator::operator++ 428ms 5.33% 6.94% 974ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 278ms 3.46% 10.40% 939ms 11.69% __dynamic_cast 10ms 0.12% 10.52% 914ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.14% 10.66% 879ms 10.95% CellPopulationElementWriter::Visit 50ms 0.62% 11.28% 877ms 10.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 7ms 0.087% 11.37% 838ms 10.43% MeshBasedCellPopulation::AcceptCellWriter 18ms 0.22% 11.59% 782ms 9.74% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.062% 11.65% 725ms 9.03% AbstractCellProperty::IsSubType (inline) 12ms 0.15% 11.80% 710ms 8.84% TetrahedralMesh::ImportFromMesher 50ms 0.62% 12.43% 594ms 7.40% std::map::operator[] (partial-inline) 0 0% 12.43% 579ms 7.21% std::ostream::operator<< (inline) 94ms 1.17% 13.60% 576ms 7.17% std::ostream::_M_insert 1ms 0.012% 13.61% 570ms 7.10% triangulate 34ms 0.42% 14.03% 567ms 7.06% operator new 2ms 0.025% 14.06% 559ms 6.96% Cell::GetCellProliferativeType 8ms 0.1% 14.16% 548ms 6.82% LegacyCellProliferativeTypesWriter::VisitCell 166ms 2.07% 16.22% 530ms 6.60% __GI___libc_malloc 530ms 6.60% 22.82% 530ms 6.60% __strcmp_avx2 17ms 0.21% 23.04% 529ms 6.59% std::_Rb_tree::find (inline) 5ms 0.062% 23.10% 516ms 6.43% std::set::insert (inline) 10ms 0.12% 23.22% 511ms 6.36% std::_Rb_tree::_M_insert_unique 36ms 0.45% 23.67% 507ms 6.31% std::__new_allocator::allocate (inline) 0 0% 23.67% 504ms 6.28% std::allocator_traits::allocate (inline) 0 0% 23.67% 499ms 6.21% delaunay 7ms 0.087% 23.76% 498ms 6.20% divconqdelaunay 0 0% 23.76% 486ms 6.05% std::_Rb_tree::lower_bound (inline) 0 0% 23.76% 486ms 6.05% std::map::lower_bound (inline) 4ms 0.05% 23.81% 478ms 5.95% AbstractCellBasedSimulation::DoCellBirth 225ms 2.80% 26.61% 478ms 5.95% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.61% 478ms 5.95% std::set::count (inline) 40ms 0.5% 27.11% 446ms 5.55% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.11% 422ms 5.25% std::_Rb_tree::_M_create_node (inline) 0 0% 27.11% 416ms 5.18% std::set::~set (inline) 84ms 1.05% 28.15% 406ms 5.06% std::_Rb_tree::_M_erase 0 0% 28.15% 395ms 4.92% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.15% 394ms 4.91% std::_Rb_tree::_M_get_node (inline) 15ms 0.19% 28.34% 358ms 4.46% std::less::operator() (inline) 4ms 0.05% 28.39% 353ms 4.40% Cell::GetMutationState 33ms 0.41% 28.80% 351ms 4.37% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.012% 28.81% 349ms 4.35% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 28.84% 348ms 4.33% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.84% 343ms 4.27% OutputFileHandler::OpenOutputFile 343ms 4.27% 33.11% 343ms 4.27% std::operator< (inline) 2ms 0.025% 33.13% 340ms 4.23% NodeLocationWriter::Visit 5ms 0.062% 33.20% 339ms 4.22% Cell::ReadyToDivide 324ms 4.03% 37.23% 324ms 4.03% std::_Rb_tree::_S_right (inline) 3ms 0.037% 37.27% 315ms 3.92% std::set::set (inline) 88ms 1.10% 38.36% 312ms 3.88% __GI___libc_free 25ms 0.31% 38.68% 311ms 3.87% std::_Rb_tree::_M_insert_ (inline) 4ms 0.05% 38.72% 306ms 3.81% Element::Element 0 0% 38.72% 302ms 3.76% std::_Rb_tree::_M_drop_node (inline) 31ms 0.39% 39.11% 298ms 3.71% std::num_put::_M_insert_float 8ms 0.1% 39.21% 288ms 3.59% divconqrecurse 181ms 2.25% 41.46% 286ms 3.56% _int_malloc 2ms 0.025% 41.49% 284ms 3.54% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 41.49% 284ms 3.54% MeshBasedCellPopulation::GetDampingConstant 5ms 0.062% 41.55% 283ms 3.52% std::__new_allocator::deallocate (inline) 27ms 0.34% 41.89% 282ms 3.51% std::_Rb_tree::_M_copy (inline) 0 0% 41.89% 280ms 3.49% std::allocator_traits::deallocate (inline) 4ms 0.05% 41.94% 272ms 3.39% AbstractCellProperty::IsType (inline) 80ms 1% 42.93% 271ms 3.37% mergehulls 5ms 0.062% 43.00% 267ms 3.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 43.00% 267ms 3.32% Cell::HasCellProperty (inline) 4ms 0.05% 43.05% 267ms 3.32% CellPropertyCollection::HasProperty 64ms 0.8% 43.84% 249ms 3.10% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.84% 245ms 3.05% std::_Rb_tree::_M_put_node (inline) 7ms 0.087% 43.93% 244ms 3.04% std::__cxx11::collate::do_transform 1ms 0.012% 43.94% 240ms 2.99% CellProliferativeTypesWriter::VisitCell 0 0% 43.94% 228ms 2.84% ___vsnprintf 1ms 0.012% 43.95% 228ms 2.84% __vsnprintf_internal (inline) 30ms 0.37% 44.33% 225ms 2.80% __printf_buffer 192ms 2.39% 46.72% 223ms 2.78% _int_free 4ms 0.05% 46.77% 222ms 2.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.05% 46.82% 215ms 2.68% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 55ms 0.68% 47.50% 210ms 2.61% AbstractCellProperty::IsSame 12ms 0.15% 47.65% 210ms 2.61% TetrahedralMesh::Clear 1ms 0.012% 47.67% 203ms 2.53% Element::RegisterWithNodes (inline) 5ms 0.062% 47.73% 197ms 2.45% Node::AddElement 64ms 0.8% 48.52% 190ms 2.37% std::_Rb_tree::_M_get_insert_unique_pos (inline) 8ms 0.1% 48.62% 188ms 2.34% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.1% 48.72% 182ms 2.27% __printf_fp_l_buffer 0 0% 48.72% 182ms 2.27% __printf_fp_spec (inline) 0 0% 48.72% 174ms 2.17% std::basic_ofstream::basic_ofstream (inline) 1ms 0.012% 48.74% 172ms 2.14% TetrahedralMesh::RefreshJacobianCachedData 0 0% 48.74% 171ms 2.13% std::basic_ofstream::open (inline) 1ms 0.012% 48.75% 170ms 2.12% std::basic_filebuf::open 16ms 0.2% 48.95% 165ms 2.05% AbstractTetrahedralElement::CalculateJacobian 10ms 0.12% 49.07% 162ms 2.02% AbstractTetrahedralElement::CalculateInverseJacobian 87ms 1.08% 50.16% 161ms 2.00% __printf_fp_buffer_1 0 0% 50.16% 155ms 1.93% OutputFileHandler::CommonConstructor 0 0% 50.16% 155ms 1.93% OutputFileHandler::OutputFileHandler 37ms 0.46% 50.62% 155ms 1.93% std::type_info::operator== (inline) 0 0% 50.62% 152ms 1.89% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.62% 151ms 1.88% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 50.64% 151ms 1.88% std::filesystem::permissions 149ms 1.86% 52.50% 149ms 1.86% __GI_fchmodat 0 0% 52.50% 148ms 1.84% AbstractCellBasedWriter::CloseFile 0 0% 52.50% 148ms 1.84% std::basic_filebuf::close 0 0% 52.50% 148ms 1.84% std::basic_ofstream::close (inline) 0 0% 52.50% 145ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.062% 52.56% 138ms 1.72% Node::~Node 56ms 0.7% 53.26% 137ms 1.71% std::__ostream_insert 19ms 0.24% 53.49% 133ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 53.49% 133ms 1.66% boost::shared_ptr::~shared_ptr (inline) 17ms 0.21% 53.70% 131ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.012% 53.72% 131ms 1.63% alternateaxes 4ms 0.05% 53.77% 130ms 1.62% boost::numeric::ublas::vector_assign (inline) 113ms 1.41% 55.17% 129ms 1.61% vertexmedian 0 0% 55.17% 126ms 1.57% _IO_new_fopen 0 0% 55.17% 126ms 1.57% __fopen_internal (inline) 0 0% 55.17% 126ms 1.57% std::__basic_file::open 20ms 0.25% 55.42% 124ms 1.54% AbstractTetrahedralElement::RefreshJacobian 1ms 0.012% 55.44% 121ms 1.51% _IO_new_file_fopen 4ms 0.05% 55.48% 121ms 1.51% boost::numeric::ublas::c_vector::c_vector (inline) 121ms 1.51% 56.99% 121ms 1.51% incircle 14ms 0.17% 57.17% 119ms 1.48% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 57.17% 119ms 1.48% __GI__IO_file_open 29ms 0.36% 57.53% 117ms 1.46% std::num_put::_M_insert_int 5ms 0.062% 57.59% 115ms 1.43% std::_Vector_base::_M_allocate (inline) 6ms 0.075% 57.66% 113ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 57.66% 113ms 1.41% std::operator<< (inline) 110ms 1.37% 59.03% 110ms 1.37% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 10ms 0.12% 59.16% 108ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 107ms 1.33% 60.49% 107ms 1.33% std::_Rb_tree_increment 3ms 0.037% 60.53% 106ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.53% 105ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 99ms 1.23% 61.76% 104ms 1.29% boost::detail::sp_counted_base::release 50ms 0.62% 62.38% 103ms 1.28% boost::shared_ptr::shared_ptr (inline) 102ms 1.27% 63.65% 102ms 1.27% __libc_open64 0 0% 63.65% 102ms 1.27% std::basic_filebuf::_M_terminate_output 1ms 0.012% 63.67% 102ms 1.27% std::basic_filebuf::overflow 1ms 0.012% 63.68% 101ms 1.26% std::basic_filebuf::_M_convert_to_external 100ms 1.25% 64.92% 100ms 1.25% __GI___libc_write 0 0% 64.92% 100ms 1.25% std::__basic_file::xsputn 2ms 0.025% 64.95% 100ms 1.25% std::vector::push_back (inline) 99ms 1.23% 66.18% 99ms 1.23% [libchaste_cell_based.so] 71ms 0.88% 67.07% 98ms 1.22% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 6ms 0.075% 67.14% 97ms 1.21% std::vector::_M_realloc_insert 32ms 0.4% 67.54% 93ms 1.16% boost::numeric::ublas::indexing_vector_assign 38ms 0.47% 68.01% 92ms 1.15% AbstractElement::GetNodeLocation 65ms 0.81% 68.82% 90ms 1.12% malloc_consolidate 90ms 1.12% 69.94% 90ms 1.12% std::_Rb_tree_insert_and_rebalance 0 0% 69.94% 85ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 69.95% 85ms 1.06% std::filesystem::create_directory 3ms 0.037% 69.99% 84ms 1.05% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 69.99% 80ms 1% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 47ms 0.59% 70.58% 80ms 1% std::basic_filebuf::xsputn 1ms 0.012% 70.59% 79ms 0.98% Cell::GetCellId 77ms 0.96% 71.55% 77ms 0.96% __GI___fstatat64 1ms 0.012% 71.56% 77ms 0.96% std::filesystem::status 11ms 0.14% 71.70% 75ms 0.93% TetrahedralMesh::EdgeIterator::GetNodeB 73ms 0.91% 72.61% 73ms 0.91% counterclockwise 72ms 0.9% 73.50% 72ms 0.9% std::vector::size (inline) 3ms 0.037% 73.54% 70ms 0.87% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.6% 74.14% 70ms 0.87% AbstractElement::GetNodeGlobalIndex 0 0% 74.14% 70ms 0.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.14% 70ms 0.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 56ms 0.7% 74.84% 68ms 0.85% std::num_put::do_put 63ms 0.78% 75.62% 67ms 0.83% vertexsort 66ms 0.82% 76.44% 66ms 0.82% Node::GetIndex 41ms 0.51% 76.95% 66ms 0.82% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 76.95% 66ms 0.82% tcache_get (inline) 66ms 0.82% 77.77% 66ms 0.82% tcache_get_n (inline) 7ms 0.087% 77.86% 65ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 65ms 0.81% 78.67% 65ms 0.81% __memcpy_avx_unaligned_erms 9ms 0.11% 78.78% 64ms 0.8% CellPropertyCollection::AddProperty 1ms 0.012% 78.79% 59ms 0.73% Node::ClearAppliedForce 3ms 0.037% 78.83% 59ms 0.73% Node::ConstructNodeAttributes (inline) 31ms 0.39% 79.22% 58ms 0.72% AbstractTetrahedralMesh::GetElement 4ms 0.05% 79.27% 58ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.27% 57ms 0.71% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 79.52% 57ms 0.71% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 79.52% 57ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.52% 57ms 0.71% std::__new_allocator::destroy (inline) 0 0% 79.52% 57ms 0.71% std::allocator_traits::destroy (inline) 0 0% 79.52% 57ms 0.71% std::vector::vector (inline) 52ms 0.65% 80.16% 53ms 0.66% boost::detail::shared_count::shared_count (inline) 0 0% 80.16% 53ms 0.66% std::_Vector_base::_Vector_base (inline) 52ms 0.65% 80.81% 52ms 0.65% [libchaste_mesh.so] 36ms 0.45% 81.26% 52ms 0.65% std::basic_streambuf::xsputn 1ms 0.012% 81.27% 51ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.27% 50ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 11ms 0.14% 81.41% 50ms 0.62% Determinant (inline) 50ms 0.62% 82.03% 50ms 0.62% boost::shared_ptr::operator-> (inline) 2ms 0.025% 82.06% 49ms 0.61% BoundaryNodeWriter::Visit 0 0% 82.06% 49ms 0.61% std::_Vector_base::_M_create_storage (inline) 6ms 0.075% 82.13% 47ms 0.59% Inverse 46ms 0.57% 82.70% 46ms 0.57% [libstdc++.so.6.0.33] 5ms 0.062% 82.77% 46ms 0.57% std::__copy_move::__copy_m (inline) 0 0% 82.77% 46ms 0.57% std::__copy_move_a (inline) 0 0% 82.77% 46ms 0.57% std::__copy_move_a1 (inline) 0 0% 82.77% 46ms 0.57% std::__copy_move_a2 (inline) 0 0% 82.77% 46ms 0.57% std::copy (inline) 0 0% 82.77% 44ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 44ms 0.55% 83.31% 44ms 0.55% Node::IsDeleted 0 0% 83.31% 44ms 0.55% std::map::find (inline) 25ms 0.31% 83.63% 43ms 0.54% AbstractCellCycleModel::GetAge 43ms 0.54% 84.16% 43ms 0.54% Node::rGetLocation 0 0% 84.16% 42ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 42ms 0.52% 84.68% 42ms 0.52% __GI___mkdir 28ms 0.35% 85.03% 42ms 0.52% hack_digit 0 0% 85.03% 42ms 0.52% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 85.03% 41ms 0.51% _IO_new_fclose 0 0% 85.03% 41ms 0.51% _dl_init 41ms 0.51% 85.54% 41ms 0.51% boost::numeric::ublas::c_vector::operator() 0 0% 85.54% 41ms 0.51% call_init (inline) 0 0% 85.54% 41ms 0.51% std::__basic_file::close 0 0% 85.54% 41ms 0.51% std::map::map (inline)