File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4446ms, 85.17% of 5220ms total Dropped 488 nodes (cum <= 26.10ms) flat flat% sum% cum cum% 0 0% 0% 5194ms 99.50% __libc_start_call_main 0 0% 0% 5194ms 99.50% __libc_start_main_impl 0 0% 0% 5194ms 99.50% _start 0 0% 0% 5181ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5181ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5181ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5181ms 99.25% main 0 0% 0% 5146ms 98.58% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5146ms 98.58% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5146ms 98.58% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.019% 0.019% 5143ms 98.52% AbstractCellBasedSimulation::Solve 0 0% 0.019% 2412ms 46.21% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.019% 2098ms 40.19% MeshBasedCellPopulation::Update 0 0% 0.019% 1752ms 33.56% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.019% 1110ms 21.26% MeshBasedCellPopulation::UpdateNodePairs 16ms 0.31% 0.33% 979ms 18.75% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.33% 978ms 18.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.33% 949ms 18.18% MutableMesh::ReMesh 2ms 0.038% 0.36% 859ms 16.46% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.36% 818ms 15.67% AbstractNumericalMethod::ComputeForcesIncludingDamping 96ms 1.84% 2.20% 801ms 15.34% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.11% 2.32% 656ms 12.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 290ms 5.56% 7.87% 608ms 11.65% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.038% 7.91% 603ms 11.55% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.077% 7.99% 595ms 11.40% CellPopulationElementWriter::Visit 24ms 0.46% 8.45% 569ms 10.90% AbstractCellPopulation::GetCellUsingLocationIndex 139ms 2.66% 11.11% 557ms 10.67% __dynamic_cast 18ms 0.34% 11.46% 538ms 10.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.096% 11.55% 535ms 10.25% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.17% 11.72% 524ms 10.04% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.11% 11.84% 499ms 9.56% TetrahedralMesh::ImportFromMesher 30ms 0.57% 12.41% 476ms 9.12% operator new 178ms 3.41% 15.82% 442ms 8.47% __GI___libc_malloc 4ms 0.077% 15.90% 439ms 8.41% AbstractCellProperty::IsSubType (inline) 10ms 0.19% 16.09% 429ms 8.22% std::set::insert (inline) 13ms 0.25% 16.34% 426ms 8.16% std::__new_allocator::allocate (inline) 0 0% 16.34% 423ms 8.10% std::allocator_traits::allocate (inline) 7ms 0.13% 16.48% 419ms 8.03% std::_Rb_tree::_M_insert_unique 0 0% 16.48% 410ms 7.85% std::ostream::operator<< (inline) 57ms 1.09% 17.57% 409ms 7.84% std::ostream::_M_insert 72ms 1.38% 18.95% 380ms 7.28% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.096% 19.04% 368ms 7.05% std::_Rb_tree::find (inline) 0 0% 19.04% 363ms 6.95% std::set::~set (inline) 3ms 0.057% 19.10% 362ms 6.93% Cell::GetCellProliferativeType 2ms 0.038% 19.14% 352ms 6.74% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 19.14% 351ms 6.72% std::set::count (inline) 34ms 0.65% 19.79% 349ms 6.69% std::map::operator[] (partial-inline) 0 0% 19.79% 339ms 6.49% triangulate 0 0% 19.79% 330ms 6.32% std::_Rb_tree::_M_create_node (inline) 0 0% 19.79% 323ms 6.19% std::_Rb_tree::_M_get_node (inline) 315ms 6.03% 25.82% 315ms 6.03% __strcmp_evex 0 0% 25.82% 310ms 5.94% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.82% 308ms 5.90% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.82% 306ms 5.86% delaunay 0 0% 25.82% 305ms 5.84% divconqdelaunay 37ms 0.71% 26.53% 305ms 5.84% std::_Rb_tree::_M_erase 2ms 0.038% 26.57% 271ms 5.19% NodeLocationWriter::Visit 12ms 0.23% 26.80% 269ms 5.15% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 26.80% 269ms 5.15% std::_Rb_tree::lower_bound (inline) 0 0% 26.80% 269ms 5.15% std::map::lower_bound (inline) 131ms 2.51% 29.31% 265ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 29.31% 261ms 5.00% std::_Rb_tree::_M_drop_node (inline) 23ms 0.44% 29.75% 260ms 4.98% std::_Rb_tree::_M_insert_ (inline) 1ms 0.019% 29.77% 256ms 4.90% std::set::set (inline) 19ms 0.36% 30.13% 241ms 4.62% std::num_put::_M_insert_float 19ms 0.36% 30.50% 238ms 4.56% std::_Rb_tree::_M_copy (inline) 4ms 0.077% 30.57% 237ms 4.54% boost::detail::shared_count::~shared_count (inline) 0 0% 30.57% 237ms 4.54% boost::shared_ptr::~shared_ptr (inline) 228ms 4.37% 34.94% 229ms 4.39% boost::detail::sp_counted_base::release 2ms 0.038% 34.98% 220ms 4.21% Element::Element 51ms 0.98% 35.96% 215ms 4.12% __GI___libc_free 2ms 0.038% 36.00% 210ms 4.02% Cell::GetMutationState 75ms 1.44% 37.43% 208ms 3.98% std::_Rb_tree::_M_clone_node (inline) 146ms 2.80% 40.23% 197ms 3.77% _int_malloc 196ms 3.75% 43.98% 196ms 3.75% std::_Rb_tree::_S_right (inline) 8ms 0.15% 44.14% 196ms 3.75% std::__cxx11::collate::do_transform 4ms 0.077% 44.21% 192ms 3.68% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.019% 44.23% 188ms 3.60% Cell::ReadyToDivide 7ms 0.13% 44.37% 186ms 3.56% std::less::operator() (inline) 3ms 0.057% 44.43% 183ms 3.51% ___vsnprintf 1ms 0.019% 44.44% 180ms 3.45% __vsnprintf_internal (inline) 179ms 3.43% 47.87% 179ms 3.43% std::operator< (inline) 3ms 0.057% 47.93% 178ms 3.41% divconqrecurse 9ms 0.17% 48.10% 173ms 3.31% __printf_buffer 6ms 0.11% 48.22% 171ms 3.28% std::__new_allocator::deallocate (inline) 0 0% 48.22% 169ms 3.24% std::allocator_traits::deallocate (inline) 46ms 0.88% 49.10% 168ms 3.22% mergehulls 166ms 3.18% 52.28% 166ms 3.18% [libchaste_cell_based.so] 0 0% 52.28% 163ms 3.12% MeshBasedCellPopulation::GetDampingConstant 146ms 2.80% 55.08% 163ms 3.12% _int_free 1ms 0.019% 55.10% 162ms 3.10% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.019% 55.11% 154ms 2.95% __printf_fp_spec (inline) 4ms 0.077% 55.19% 153ms 2.93% __printf_fp_l_buffer 58ms 1.11% 56.30% 152ms 2.91% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.077% 56.38% 147ms 2.82% CellPropertyCollection::HasProperty 0 0% 56.38% 146ms 2.80% Cell::HasCellProperty (inline) 1ms 0.019% 56.40% 145ms 2.78% Element::RegisterWithNodes (inline) 0 0% 56.40% 145ms 2.78% std::_Rb_tree::_M_put_node (inline) 3ms 0.057% 56.46% 143ms 2.74% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.096% 56.55% 141ms 2.70% Node::AddElement 2ms 0.038% 56.59% 140ms 2.68% AbstractCellProperty::IsType (inline) 1ms 0.019% 56.61% 138ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 80ms 1.53% 58.14% 137ms 2.62% __printf_fp_buffer_1 1ms 0.019% 58.16% 135ms 2.59% CellProliferativeTypesWriter::VisitCell 5ms 0.096% 58.26% 132ms 2.53% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.038% 58.30% 118ms 2.26% TetrahedralMesh::Clear 6ms 0.11% 58.41% 116ms 2.22% AbstractTetrahedralElement::CalculateJacobian 0 0% 58.41% 116ms 2.22% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.41% 116ms 2.22% std::__new_allocator::destroy (inline) 0 0% 58.41% 116ms 2.22% std::allocator_traits::destroy (inline) 0 0% 58.41% 110ms 2.11% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 58.41% 110ms 2.11% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 58.41% 108ms 2.07% OutputFileHandler::OpenOutputFile 20ms 0.38% 58.79% 103ms 1.97% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 58.79% 100ms 1.92% TetrahedralMesh::RefreshJacobianCachedData 0 0% 58.79% 100ms 1.92% std::_Vector_base::_M_allocate (inline) 2ms 0.038% 58.83% 97ms 1.86% std::vector::push_back (inline) 8ms 0.15% 58.98% 96ms 1.84% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 58.98% 91ms 1.74% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.057% 59.04% 91ms 1.74% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.36% 59.41% 90ms 1.72% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 59.41% 88ms 1.69% boost::numeric::ublas::vector_assign (inline) 4ms 0.077% 59.48% 88ms 1.69% std::vector::_M_realloc_insert 14ms 0.27% 59.75% 87ms 1.67% AbstractCellProperty::IsSame 86ms 1.65% 61.40% 86ms 1.65% [libchaste_mesh.so] 3ms 0.057% 61.46% 85ms 1.63% alternateaxes 42ms 0.8% 62.26% 84ms 1.61% std::__ostream_insert 66ms 1.26% 63.52% 82ms 1.57% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.038% 63.56% 82ms 1.57% boost::numeric::ublas::c_vector::c_vector (inline) 69ms 1.32% 64.89% 81ms 1.55% vertexmedian 8ms 0.15% 65.04% 79ms 1.51% AbstractTetrahedralElement::RefreshJacobian 3ms 0.057% 65.10% 77ms 1.48% AbstractTetrahedralElement::AbstractTetrahedralElement 19ms 0.36% 65.46% 75ms 1.44% std::num_put::_M_insert_int 73ms 1.40% 66.86% 73ms 1.40% incircle 6ms 0.11% 66.97% 73ms 1.40% std::type_info::operator== (inline) 8ms 0.15% 67.13% 71ms 1.36% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 70ms 1.34% 68.47% 70ms 1.34% std::_Rb_tree_insert_and_rebalance 1ms 0.019% 68.49% 68ms 1.30% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.48% 68.97% 66ms 1.26% AbstractElement::GetNodeLocation 2ms 0.038% 69.00% 65ms 1.25% std::operator<< (inline) 15ms 0.29% 69.29% 61ms 1.17% boost::numeric::ublas::indexing_vector_assign 60ms 1.15% 70.44% 60ms 1.15% [libstdc++.so.6.0.33] 4ms 0.077% 70.52% 57ms 1.09% Node::~Node 0 0% 70.52% 56ms 1.07% std::basic_ofstream::basic_ofstream (inline) 0 0% 70.52% 55ms 1.05% tcache_get (inline) 55ms 1.05% 71.57% 55ms 1.05% tcache_get_n (inline) 1ms 0.019% 71.59% 54ms 1.03% std::basic_ofstream::open (inline) 2ms 0.038% 71.63% 53ms 1.02% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.63% 53ms 1.02% std::basic_filebuf::open 2ms 0.038% 71.67% 52ms 1% CellPropertyCollection::AddProperty 3ms 0.057% 71.72% 51ms 0.98% AbstractCellPopulation::GetLocationIndexUsingCell 50ms 0.96% 72.68% 50ms 0.96% std::_Rb_tree::_S_left (inline) 50ms 0.96% 73.64% 50ms 0.96% std::vector::size (inline) 0 0% 73.64% 49ms 0.94% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 73.64% 48ms 0.92% Cell::GetCellId 12ms 0.23% 73.87% 48ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeB 47ms 0.9% 74.77% 47ms 0.9% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.019% 74.79% 46ms 0.88% std::_Rb_tree::_M_emplace_hint_unique 45ms 0.86% 75.65% 45ms 0.86% std::_Rb_tree_increment 0 0% 75.65% 44ms 0.84% OutputFileHandler::CommonConstructor 0 0% 75.65% 44ms 0.84% OutputFileHandler::OutputFileHandler 5ms 0.096% 75.75% 44ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 21ms 0.4% 76.15% 43ms 0.82% AbstractElement::GetNodeGlobalIndex 0 0% 76.15% 43ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.15% 43ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 43ms 0.82% 76.97% 43ms 0.82% counterclockwise 33ms 0.63% 77.61% 43ms 0.82% malloc_consolidate 29ms 0.56% 78.16% 42ms 0.8% std::basic_filebuf::xsputn 32ms 0.61% 78.77% 42ms 0.8% std::basic_streambuf::xsputn 0 0% 78.77% 41ms 0.79% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 78.77% 39ms 0.75% AbstractCellBasedWriter::CloseFile 0 0% 78.77% 39ms 0.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.019% 78.79% 39ms 0.75% Node::ConstructNodeAttributes (inline) 2ms 0.038% 78.83% 39ms 0.75% std::basic_filebuf::close 0 0% 78.83% 39ms 0.75% std::basic_ofstream::close (inline) 0 0% 78.83% 39ms 0.75% std::vector::vector (inline) 35ms 0.67% 79.50% 39ms 0.75% vertexsort 16ms 0.31% 79.81% 38ms 0.73% Determinant (inline) 0 0% 79.81% 38ms 0.73% Node::ClearAppliedForce 0 0% 79.81% 36ms 0.69% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 36ms 0.69% 80.50% 36ms 0.69% __memcpy_avx512_unaligned_erms 0 0% 80.50% 36ms 0.69% std::_Vector_base::_Vector_base (inline) 24ms 0.46% 80.96% 34ms 0.65% AbstractTetrahedralMesh::GetElement 34ms 0.65% 81.61% 34ms 0.65% Node::GetIndex 1ms 0.019% 81.63% 34ms 0.65% std::_Vector_base::_M_create_storage (inline) 26ms 0.5% 82.13% 32ms 0.61% CellPropertyCollection::GetProperty 0 0% 82.13% 32ms 0.61% CxxTest::RealWorldDescription::setUp 0 0% 82.13% 32ms 0.61% PetscSetup::setUpWorld 0 0% 82.13% 32ms 0.61% PetscSetupUtils::CommonSetup 0 0% 82.13% 31ms 0.59% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 82.13% 31ms 0.59% PMPI_Init_thread 0 0% 82.13% 31ms 0.59% PetscInitialize 0 0% 82.13% 31ms 0.59% PetscSetupUtils::InitialisePetsc 0 0% 82.13% 31ms 0.59% ompi_mpi_init 1ms 0.019% 82.15% 31ms 0.59% std::__basic_file::open 0 0% 82.15% 30ms 0.57% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.038% 82.18% 30ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.18% 30ms 0.57% _IO_new_fopen 30ms 0.57% 82.76% 30ms 0.57% __GI_fchmodat 0 0% 82.76% 30ms 0.57% __fopen_internal (inline) 17ms 0.33% 83.08% 30ms 0.57% boost::shared_ptr::shared_ptr (inline) 16ms 0.31% 83.39% 30ms 0.57% hack_digit 0 0% 83.39% 30ms 0.57% std::filesystem::permissions 27ms 0.52% 83.91% 29ms 0.56% std::num_put::do_put 0 0% 83.91% 28ms 0.54% 28ms 0.54% 84.44% 28ms 0.54% Node::rGetLocation 0 0% 84.44% 28ms 0.54% _IO_new_file_fopen 0 0% 84.44% 28ms 0.54% __GI__IO_file_open 0 0% 84.44% 28ms 0.54% boost::numeric::ublas::norm_2 (inline) 28ms 0.54% 84.98% 28ms 0.54% boost::numeric::ublas::same_impl_ex 10ms 0.19% 85.17% 28ms 0.54% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 85.17% 27ms 0.52% NodeAttributes::NodeAttributes 0 0% 85.17% 27ms 0.52% _dl_init 0 0% 85.17% 27ms 0.52% call_init (inline) 0 0% 85.17% 27ms 0.52% std::map::map (inline)