File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5248ms, 85.44% of 6142ms total Dropped 509 nodes (cum <= 30.71ms) flat flat% sum% cum cum% 0 0% 0% 6112ms 99.51% __libc_start_call_main 0 0% 0% 6112ms 99.51% __libc_start_main_impl 0 0% 0% 6112ms 99.51% _start 0 0% 0% 6099ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6099ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6099ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6099ms 99.30% main 0 0% 0% 6061ms 98.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6061ms 98.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6061ms 98.68% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6059ms 98.65% AbstractCellBasedSimulation::Solve 0 0% 0% 2580ms 42.01% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.016% 0.016% 2260ms 36.80% AbstractCellPopulation::WriteResultsToFiles 2ms 0.033% 0.049% 2232ms 36.34% MeshBasedCellPopulation::Update 1ms 0.016% 0.065% 1213ms 19.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.065% 1098ms 17.88% MutableMesh::ReMesh 2ms 0.033% 0.098% 1089ms 17.73% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.11% 1078ms 17.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.098% 0.21% 1032ms 16.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 18ms 0.29% 0.5% 946ms 15.40% MeshBasedCellPopulation::SpringIterator::operator++ 86ms 1.40% 1.90% 787ms 12.81% TetrahedralMesh::EdgeIterator::operator++ 337ms 5.49% 7.39% 745ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.081% 7.47% 726ms 11.82% CellPopulationElementWriter::Visit 3ms 0.049% 7.52% 724ms 11.79% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.049% 7.57% 663ms 10.79% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 174ms 2.83% 10.40% 653ms 10.63% __dynamic_cast 8ms 0.13% 10.53% 637ms 10.37% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.42% 10.96% 631ms 10.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 20ms 0.33% 11.28% 585ms 9.52% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.13% 11.41% 547ms 8.91% TetrahedralMesh::ImportFromMesher 8ms 0.13% 11.54% 544ms 8.86% MeshBasedCellPopulation::AcceptCellWriter 0 0% 11.54% 521ms 8.48% AbstractCellProperty::IsSubType (inline) 0 0% 11.54% 499ms 8.12% std::ostream::operator<< (inline) 42ms 0.68% 12.23% 498ms 8.11% std::map::operator[] (partial-inline) 74ms 1.20% 13.43% 498ms 8.11% std::ostream::_M_insert 24ms 0.39% 13.82% 458ms 7.46% operator new 6ms 0.098% 13.92% 427ms 6.95% std::set::insert (inline) 5ms 0.081% 14.00% 422ms 6.87% std::_Rb_tree::_M_insert_unique 136ms 2.21% 16.22% 421ms 6.85% __GI___libc_malloc 1ms 0.016% 16.23% 411ms 6.69% triangulate 0 0% 16.23% 403ms 6.56% std::_Rb_tree::lower_bound (inline) 0 0% 16.23% 403ms 6.56% std::map::lower_bound (inline) 24ms 0.39% 16.62% 402ms 6.55% std::__new_allocator::allocate (inline) 0 0% 16.62% 398ms 6.48% std::allocator_traits::allocate (inline) 19ms 0.31% 16.93% 381ms 6.20% std::_Rb_tree::find (inline) 380ms 6.19% 23.12% 380ms 6.19% __strcmp_evex 0 0% 23.12% 365ms 5.94% delaunay 3ms 0.049% 23.17% 365ms 5.94% divconqdelaunay 3ms 0.049% 23.22% 346ms 5.63% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.065% 23.28% 342ms 5.57% Cell::GetCellProliferativeType 0 0% 23.28% 342ms 5.57% std::set::count (inline) 4ms 0.065% 23.35% 337ms 5.49% AbstractCellBasedSimulation::DoCellBirth 28ms 0.46% 23.80% 325ms 5.29% std::_Rb_tree::~_Rb_tree (inline) 0 0% 23.80% 319ms 5.19% std::_Rb_tree::_M_create_node (inline) 154ms 2.51% 26.31% 312ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.31% 310ms 5.05% std::set::~set (inline) 3ms 0.049% 26.36% 304ms 4.95% NodeLocationWriter::Visit 0 0% 26.36% 300ms 4.88% std::_Rb_tree::_M_get_node (inline) 0 0% 26.36% 296ms 4.82% std::_Rb_tree::_Alloc_node::operator() (inline) 57ms 0.93% 27.29% 295ms 4.80% std::_Rb_tree::_M_erase 4ms 0.065% 27.35% 290ms 4.72% Cell::GetMutationState 0 0% 27.35% 268ms 4.36% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 27.35% 268ms 4.36% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 27.35% 267ms 4.35% OutputFileHandler::OpenOutputFile 18ms 0.29% 27.65% 267ms 4.35% std::_Rb_tree::_Rb_tree (partial-inline) 265ms 4.31% 31.96% 265ms 4.31% std::_Rb_tree::_S_right (inline) 8ms 0.13% 32.09% 265ms 4.31% std::less::operator() (inline) 27ms 0.44% 32.53% 257ms 4.18% std::num_put::_M_insert_float 257ms 4.18% 36.71% 257ms 4.18% std::operator< (inline) 13ms 0.21% 36.93% 248ms 4.04% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.081% 37.01% 243ms 3.96% std::set::set (inline) 1ms 0.016% 37.02% 241ms 3.92% MeshBasedCellPopulation::GetDampingConstant 1ms 0.016% 37.04% 240ms 3.91% AbstractCentreBasedCellPopulation::GetDampingConstant 15ms 0.24% 37.28% 238ms 3.87% std::_Rb_tree::_M_insert_ (inline) 4ms 0.065% 37.35% 234ms 3.81% Element::Element 70ms 1.14% 38.49% 234ms 3.81% __GI___libc_free 136ms 2.21% 40.70% 229ms 3.73% _int_malloc 0 0% 40.70% 227ms 3.70% std::_Rb_tree::_M_drop_node (inline) 3ms 0.049% 40.75% 221ms 3.60% Cell::ReadyToDivide 27ms 0.44% 41.19% 217ms 3.53% std::_Rb_tree::_M_copy (inline) 6ms 0.098% 41.29% 212ms 3.45% std::__new_allocator::deallocate (inline) 0 0% 41.29% 212ms 3.45% std::allocator_traits::deallocate (inline) 6ms 0.098% 41.39% 208ms 3.39% divconqrecurse 10ms 0.16% 41.55% 204ms 3.32% std::__cxx11::collate::do_transform 53ms 0.86% 42.41% 198ms 3.22% mergehulls 1ms 0.016% 42.43% 192ms 3.13% ___vsnprintf 1ms 0.016% 42.45% 191ms 3.11% __vsnprintf_internal (inline) 33ms 0.54% 42.98% 189ms 3.08% __printf_buffer 53ms 0.86% 43.85% 185ms 3.01% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.85% 184ms 3.00% std::_Rb_tree::_M_put_node (inline) 64ms 1.04% 44.89% 179ms 2.91% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.049% 44.94% 175ms 2.85% CellPropertyCollection::HasProperty 0 0% 44.94% 174ms 2.83% Cell::HasCellProperty (inline) 2ms 0.033% 44.97% 173ms 2.82% AbstractCellProperty::IsType (inline) 145ms 2.36% 47.33% 164ms 2.67% _int_free 1ms 0.016% 47.35% 156ms 2.54% CellProliferativeTypesWriter::VisitCell 4ms 0.065% 47.41% 149ms 2.43% Element::RegisterWithNodes (inline) 11ms 0.18% 47.59% 149ms 2.43% TetrahedralMesh::Clear 1ms 0.016% 47.61% 145ms 2.36% Node::AddElement 3ms 0.049% 47.66% 144ms 2.34% __printf_fp_l_buffer 0 0% 47.66% 144ms 2.34% __printf_fp_spec (inline) 71ms 1.16% 48.81% 140ms 2.28% __printf_fp_buffer_1 5ms 0.081% 48.89% 139ms 2.26% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 48.89% 138ms 2.25% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.016% 48.91% 136ms 2.21% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 48.91% 135ms 2.20% std::basic_ofstream::basic_ofstream (inline) 40ms 0.65% 49.56% 133ms 2.17% AbstractCellProperty::IsSame 1ms 0.016% 49.58% 132ms 2.15% std::basic_ofstream::open (inline) 2ms 0.033% 49.61% 131ms 2.13% std::basic_filebuf::open 13ms 0.21% 49.82% 127ms 2.07% AbstractTetrahedralElement::CalculateJacobian 1ms 0.016% 49.84% 124ms 2.02% OutputFileHandler::CommonConstructor 0 0% 49.84% 124ms 2.02% OutputFileHandler::OutputFileHandler 0 0% 49.84% 123ms 2.00% TetrahedralMesh::RefreshJacobianCachedData 0 0% 49.84% 118ms 1.92% OutputFileHandler::MakeFoldersAndReturnFullPath 48ms 0.78% 50.62% 115ms 1.87% std::__ostream_insert 34ms 0.55% 51.17% 112ms 1.82% std::num_put::_M_insert_int 4ms 0.065% 51.24% 111ms 1.81% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 51.24% 111ms 1.81% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.049% 51.29% 111ms 1.81% boost::numeric::ublas::vector_assign (inline) 1ms 0.016% 51.30% 111ms 1.81% std::filesystem::permissions 110ms 1.79% 53.09% 110ms 1.79% __GI_fchmodat 4ms 0.065% 53.16% 110ms 1.79% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 53.16% 108ms 1.76% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 53.16% 107ms 1.74% AbstractCellBasedWriter::CloseFile 9ms 0.15% 53.31% 107ms 1.74% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.016% 53.32% 107ms 1.74% std::basic_ofstream::close (inline) 0 0% 53.32% 106ms 1.73% std::basic_filebuf::close 17ms 0.28% 53.60% 103ms 1.68% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.016% 53.61% 101ms 1.64% alternateaxes 89ms 1.45% 55.06% 100ms 1.63% vertexmedian 0 0% 55.06% 98ms 1.60% std::_Vector_base::_M_allocate (inline) 0 0% 55.06% 97ms 1.58% _IO_new_fopen 0 0% 55.06% 97ms 1.58% __fopen_internal (inline) 4ms 0.065% 55.13% 97ms 1.58% boost::detail::shared_count::~shared_count (inline) 0 0% 55.13% 97ms 1.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 55.13% 97ms 1.58% std::__basic_file::open 12ms 0.2% 55.32% 96ms 1.56% AbstractCellPopulation::Iterator::IsRealCell (inline) 69ms 1.12% 56.45% 96ms 1.56% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 56.45% 96ms 1.56% _IO_new_file_fopen 0 0% 56.45% 95ms 1.55% __GI__IO_file_open 0 0% 56.45% 94ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.42% 56.87% 93ms 1.51% std::type_info::operator== (inline) 12ms 0.2% 57.07% 92ms 1.50% AbstractTetrahedralElement::RefreshJacobian 1ms 0.016% 57.08% 91ms 1.48% std::operator<< (inline) 88ms 1.43% 58.52% 88ms 1.43% incircle 5ms 0.081% 58.60% 87ms 1.42% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 58.60% 86ms 1.40% std::basic_filebuf::_M_terminate_output 3ms 0.049% 58.65% 85ms 1.38% Node::~Node 28ms 0.46% 59.10% 85ms 1.38% boost::numeric::ublas::indexing_vector_assign 4ms 0.065% 59.17% 85ms 1.38% std::basic_filebuf::overflow 83ms 1.35% 60.52% 83ms 1.35% __libc_open64 81ms 1.32% 61.84% 82ms 1.34% boost::detail::sp_counted_base::release 6ms 0.098% 61.93% 82ms 1.34% std::vector::push_back (inline) 1ms 0.016% 61.95% 81ms 1.32% std::__basic_file::xsputn 0 0% 61.95% 81ms 1.32% std::basic_filebuf::_M_convert_to_external 80ms 1.30% 63.25% 80ms 1.30% __GI___libc_write 78ms 1.27% 64.52% 78ms 1.27% [libchaste_cell_based.so] 7ms 0.11% 64.64% 75ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 39ms 0.63% 65.27% 75ms 1.22% boost::shared_ptr::shared_ptr (inline) 51ms 0.83% 66.10% 74ms 1.20% malloc_consolidate 42ms 0.68% 66.79% 73ms 1.19% std::basic_filebuf::xsputn 5ms 0.081% 66.87% 73ms 1.19% std::vector::_M_realloc_insert 72ms 1.17% 68.04% 72ms 1.17% std::_Rb_tree_insert_and_rebalance 0 0% 68.04% 70ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.46% 68.50% 70ms 1.14% AbstractElement::GetNodeLocation 0 0% 68.50% 68ms 1.11% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.016% 68.51% 68ms 1.11% std::filesystem::create_directory 1ms 0.016% 68.53% 64ms 1.04% std::filesystem::status 63ms 1.03% 69.55% 63ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 63ms 1.03% 70.58% 63ms 1.03% __GI___fstatat64 3ms 0.049% 70.63% 62ms 1.01% std::_Rb_tree_const_iterator::operator++ (inline) 60ms 0.98% 71.61% 60ms 0.98% std::_Rb_tree_increment 48ms 0.78% 72.39% 60ms 0.98% std::num_put::do_put 0 0% 72.39% 59ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.39% 58ms 0.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.39% 58ms 0.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.39% 56ms 0.91% Cell::GetCellId 55ms 0.9% 73.28% 55ms 0.9% counterclockwise 0 0% 73.28% 53ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 52ms 0.85% 74.13% 52ms 0.85% Node::GetIndex 44ms 0.72% 74.85% 51ms 0.83% vertexsort 5ms 0.081% 74.93% 47ms 0.77% TetrahedralMesh::EdgeIterator::GetNodeA 29ms 0.47% 75.40% 47ms 0.77% hack_digit 0 0% 75.40% 47ms 0.77% tcache_get (inline) 47ms 0.77% 76.16% 47ms 0.77% tcache_get_n (inline) 34ms 0.55% 76.72% 46ms 0.75% AbstractElement::GetNodeGlobalIndex 0 0% 76.72% 46ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 46ms 0.75% 77.47% 46ms 0.75% [libstdc++.so.6.0.33] 0 0% 77.47% 45ms 0.73% boost::numeric::ublas::norm_2 (inline) 13ms 0.21% 77.68% 45ms 0.73% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 77.68% 45ms 0.73% std::vector::vector (inline) 32ms 0.52% 78.20% 44ms 0.72% std::basic_streambuf::xsputn 44ms 0.72% 78.92% 44ms 0.72% std::vector::size (inline) 0 0% 78.92% 43ms 0.7% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.92% 43ms 0.7% std::__new_allocator::destroy (inline) 0 0% 78.92% 43ms 0.7% std::allocator_traits::destroy (inline) 0 0% 78.92% 42ms 0.68% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 42ms 0.68% 79.60% 42ms 0.68% [libchaste_mesh.so] 0 0% 79.60% 42ms 0.68% std::_Vector_base::_Vector_base (inline) 1ms 0.016% 79.62% 41ms 0.67% Node::ClearAppliedForce 8ms 0.13% 79.75% 41ms 0.67% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.016% 79.76% 40ms 0.65% Node::ConstructNodeAttributes (inline) 0 0% 79.76% 40ms 0.65% std::_Vector_base::_M_create_storage (inline) 20ms 0.33% 80.09% 39ms 0.63% AbstractTetrahedralMesh::GetElement 9ms 0.15% 80.23% 39ms 0.63% CellPropertyCollection::AddProperty 39ms 0.63% 80.87% 39ms 0.63% boost::shared_ptr::operator-> (inline) 38ms 0.62% 81.49% 38ms 0.62% __memcpy_avx512_unaligned_erms 0 0% 81.49% 36ms 0.59% AbstractCentreBasedCellPopulation::CreateCellPair 23ms 0.37% 81.86% 36ms 0.59% boost::numeric::ublas::c_matrix::operator() 36ms 0.59% 82.45% 36ms 0.59% boost::numeric::ublas::same_impl_ex 0 0% 82.45% 35ms 0.57% BoundaryNodeWriter::Visit 0 0% 82.45% 35ms 0.57% CxxTest::RealWorldDescription::setUp 35ms 0.57% 83.02% 35ms 0.57% Node::rGetLocation 0 0% 83.02% 35ms 0.57% PMPI_Init_thread 0 0% 83.02% 35ms 0.57% PetscInitialize 0 0% 83.02% 35ms 0.57% PetscSetup::setUpWorld 0 0% 83.02% 35ms 0.57% PetscSetupUtils::CommonSetup 0 0% 83.02% 35ms 0.57% PetscSetupUtils::InitialisePetsc 33ms 0.54% 83.56% 35ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 83.56% 35ms 0.57% ompi_mpi_init 6ms 0.098% 83.65% 34ms 0.55% AbstractMesh::GetVectorFromAtoB 0 0% 83.65% 34ms 0.55% _dl_init 34ms 0.55% 84.21% 34ms 0.55% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 84.21% 34ms 0.55% call_init (inline) 7ms 0.11% 84.32% 34ms 0.55% std::_Vector_base::_M_deallocate (inline) 12ms 0.2% 84.52% 33ms 0.54% Inverse 33ms 0.54% 85.05% 33ms 0.54% __GI___mkdir 21ms 0.34% 85.40% 32ms 0.52% AbstractCellCycleModel::GetAge 3ms 0.049% 85.44% 31ms 0.5% Element::~Element 0 0% 85.44% 31ms 0.5% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 85.44% 31ms 0.5% std::map::find (inline)