File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5244ms, 86.01% of 6097ms total Dropped 514 nodes (cum <= 30.48ms) flat flat% sum% cum cum% 0 0% 0% 6070ms 99.56% __libc_start_call_main 0 0% 0% 6070ms 99.56% __libc_start_main_impl 0 0% 0% 6070ms 99.56% _start 0 0% 0% 6057ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6057ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6057ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6057ms 99.34% main 0 0% 0% 6019ms 98.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6019ms 98.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6019ms 98.72% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6014ms 98.64% AbstractCellBasedSimulation::Solve 0 0% 0% 2638ms 43.27% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.033% 0.033% 2334ms 38.28% MeshBasedCellPopulation::Update 0 0% 0.033% 2166ms 35.53% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.033% 1204ms 19.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.033% 1177ms 19.30% MutableMesh::ReMesh 0 0% 0.033% 1119ms 18.35% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.049% 1073ms 17.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.033% 0.082% 1040ms 17.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 12ms 0.2% 0.28% 958ms 15.71% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.033% 0.31% 770ms 12.63% AbstractTwoBodyInteractionForce::AddForceContribution 91ms 1.49% 1.80% 770ms 12.63% TetrahedralMesh::EdgeIterator::operator++ 343ms 5.63% 7.43% 764ms 12.53% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.082% 7.51% 696ms 11.42% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 20ms 0.33% 7.84% 678ms 11.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.13% 7.97% 674ms 11.05% CellPopulationElementWriter::Visit 201ms 3.30% 11.27% 661ms 10.84% __dynamic_cast 8ms 0.13% 11.40% 612ms 10.04% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.31% 11.71% 598ms 9.81% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.098% 11.81% 595ms 9.76% TetrahedralMesh::ImportFromMesher 7ms 0.11% 11.92% 567ms 9.30% MeshBasedCellPopulation::AcceptCellWriter 44ms 0.72% 12.65% 506ms 8.30% std::map::operator[] (partial-inline) 3ms 0.049% 12.69% 496ms 8.14% AbstractCellProperty::IsSubType (inline) 36ms 0.59% 13.29% 478ms 7.84% operator new 3ms 0.049% 13.33% 447ms 7.33% triangulate 160ms 2.62% 15.96% 440ms 7.22% __GI___libc_malloc 23ms 0.38% 16.34% 428ms 7.02% std::__new_allocator::allocate (inline) 0 0% 16.34% 422ms 6.92% std::allocator_traits::allocate (inline) 0 0% 16.34% 420ms 6.89% std::ostream::operator<< (inline) 78ms 1.28% 17.62% 415ms 6.81% std::ostream::_M_insert 0 0% 17.62% 412ms 6.76% std::_Rb_tree::lower_bound (inline) 0 0% 17.62% 412ms 6.76% std::map::lower_bound (inline) 17ms 0.28% 17.89% 394ms 6.46% std::_Rb_tree::find (inline) 0 0% 17.89% 384ms 6.30% delaunay 2ms 0.033% 17.93% 384ms 6.30% divconqdelaunay 4ms 0.066% 17.99% 383ms 6.28% std::set::insert (inline) 3ms 0.049% 18.04% 379ms 6.22% std::_Rb_tree::_M_insert_unique 362ms 5.94% 23.98% 362ms 5.94% __strcmp_evex 0 0% 23.98% 361ms 5.92% std::set::count (inline) 4ms 0.066% 24.04% 359ms 5.89% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.066% 24.11% 347ms 5.69% Cell::GetCellProliferativeType 30ms 0.49% 24.60% 342ms 5.61% std::_Rb_tree::~_Rb_tree (inline) 156ms 2.56% 27.16% 333ms 5.46% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.16% 333ms 5.46% std::_Rb_tree::_M_create_node (inline) 0 0% 27.16% 326ms 5.35% std::set::~set (inline) 0 0% 27.16% 312ms 5.12% std::_Rb_tree::_M_get_node (inline) 0 0% 27.16% 309ms 5.07% std::_Rb_tree::_Alloc_node::operator() (inline) 63ms 1.03% 28.19% 304ms 4.99% std::_Rb_tree::_M_erase 2ms 0.033% 28.23% 292ms 4.79% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.23% 278ms 4.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.23% 274ms 4.49% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.016% 28.24% 272ms 4.46% OutputFileHandler::OpenOutputFile 5ms 0.082% 28.33% 264ms 4.33% std::less::operator() (inline) 23ms 0.38% 28.70% 262ms 4.30% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.049% 28.75% 261ms 4.28% Cell::GetMutationState 259ms 4.25% 33.00% 259ms 4.25% std::_Rb_tree::_S_right (inline) 259ms 4.25% 37.25% 259ms 4.25% std::operator< (inline) 57ms 0.93% 38.18% 252ms 4.13% __GI___libc_free 15ms 0.25% 38.43% 250ms 4.10% std::_Rb_tree::_M_insert_ (inline) 0 0% 38.43% 249ms 4.08% NodeLocationWriter::Visit 3ms 0.049% 38.48% 248ms 4.07% Element::Element 3ms 0.049% 38.53% 237ms 3.89% std::set::set (inline) 6ms 0.098% 38.63% 228ms 3.74% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 38.63% 228ms 3.74% std::_Rb_tree::_M_drop_node (inline) 147ms 2.41% 41.04% 223ms 3.66% _int_malloc 7ms 0.11% 41.15% 217ms 3.56% std::__new_allocator::deallocate (inline) 0 0% 41.15% 217ms 3.56% std::allocator_traits::deallocate (inline) 9ms 0.15% 41.30% 216ms 3.54% divconqrecurse 27ms 0.44% 41.74% 214ms 3.51% std::_Rb_tree::_M_copy (inline) 1ms 0.016% 41.76% 213ms 3.49% MeshBasedCellPopulation::GetDampingConstant 3ms 0.049% 41.81% 212ms 3.48% AbstractCentreBasedCellPopulation::GetDampingConstant 23ms 0.38% 42.18% 211ms 3.46% std::num_put::_M_insert_float 49ms 0.8% 42.99% 203ms 3.33% mergehulls 4ms 0.066% 43.05% 198ms 3.25% Cell::ReadyToDivide 154ms 2.53% 45.58% 194ms 3.18% _int_free 0 0% 45.58% 191ms 3.13% std::_Rb_tree::_M_put_node (inline) 45ms 0.74% 46.32% 182ms 2.99% std::_Rb_tree::_M_clone_node (inline) 0 0% 46.32% 176ms 2.89% CellProliferativeTypesWriter::VisitCell 2ms 0.033% 46.35% 172ms 2.82% AbstractCellProperty::IsType (inline) 6ms 0.098% 46.45% 171ms 2.80% std::__cxx11::collate::do_transform 0 0% 46.45% 170ms 2.79% Cell::HasCellProperty (inline) 2ms 0.033% 46.48% 170ms 2.79% CellPropertyCollection::HasProperty 9ms 0.15% 46.63% 168ms 2.76% TetrahedralMesh::Clear 0 0% 46.63% 161ms 2.64% ___vsnprintf 29ms 0.48% 47.11% 161ms 2.64% __printf_buffer 0 0% 47.11% 161ms 2.64% __vsnprintf_internal (inline) 7ms 0.11% 47.22% 159ms 2.61% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.066% 47.29% 152ms 2.49% Element::RegisterWithNodes (inline) 7ms 0.11% 47.40% 145ms 2.38% Node::AddElement 26ms 0.43% 47.83% 143ms 2.35% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.18% 48.01% 139ms 2.28% AbstractTetrahedralElement::CalculateJacobian 2ms 0.033% 48.04% 134ms 2.20% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 48.04% 131ms 2.15% std::basic_ofstream::basic_ofstream (inline) 8ms 0.13% 48.17% 130ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.049% 48.22% 127ms 2.08% std::basic_filebuf::open 0 0% 48.22% 127ms 2.08% std::basic_ofstream::open (inline) 51ms 0.84% 49.06% 126ms 2.07% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.016% 49.07% 125ms 2.05% __printf_fp_l_buffer 0 0% 49.07% 125ms 2.05% __printf_fp_spec (inline) 0 0% 49.07% 122ms 2.00% FilesystemPermissions::SetFilePermissions (inline) 60ms 0.98% 50.06% 122ms 2.00% __printf_fp_buffer_1 1ms 0.016% 50.07% 122ms 2.00% std::filesystem::permissions 21ms 0.34% 50.42% 121ms 1.98% AbstractCellProperty::IsSame 121ms 1.98% 52.40% 121ms 1.98% __GI_fchmodat 0 0% 52.40% 116ms 1.90% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.033% 52.44% 112ms 1.84% std::_Vector_base::_M_allocate (inline) 4ms 0.066% 52.50% 111ms 1.82% Node::~Node 0 0% 52.50% 110ms 1.80% AbstractCellBasedWriter::CloseFile 0 0% 52.50% 110ms 1.80% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.016% 52.52% 110ms 1.80% std::basic_ofstream::close (inline) 0 0% 52.52% 109ms 1.79% std::basic_filebuf::close 7ms 0.11% 52.63% 108ms 1.77% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.016% 52.65% 108ms 1.77% alternateaxes 99ms 1.62% 54.27% 107ms 1.75% vertexmedian 1ms 0.016% 54.29% 106ms 1.74% std::__basic_file::open 0 0% 54.29% 105ms 1.72% _IO_new_file_fopen 0 0% 54.29% 105ms 1.72% _IO_new_fopen 0 0% 54.29% 105ms 1.72% __fopen_internal (inline) 1ms 0.016% 54.31% 104ms 1.71% __GI__IO_file_open 64ms 1.05% 55.36% 103ms 1.69% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.033% 55.39% 103ms 1.69% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 55.39% 102ms 1.67% OutputFileHandler::CommonConstructor 0 0% 55.39% 102ms 1.67% OutputFileHandler::OutputFileHandler 2ms 0.033% 55.42% 102ms 1.67% boost::numeric::ublas::vector_assign (inline) 13ms 0.21% 55.63% 100ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 28ms 0.46% 56.09% 100ms 1.64% std::type_info::operator== (inline) 0 0% 56.09% 99ms 1.62% OutputFileHandler::MakeFoldersAndReturnFullPath 4ms 0.066% 56.16% 98ms 1.61% AbstractTetrahedralElement::AbstractTetrahedralElement 17ms 0.28% 56.44% 97ms 1.59% AbstractTetrahedralElement::RefreshJacobian 30ms 0.49% 56.93% 97ms 1.59% std::__ostream_insert 96ms 1.57% 58.50% 96ms 1.57% incircle 93ms 1.53% 60.03% 93ms 1.53% __libc_open64 27ms 0.44% 60.47% 92ms 1.51% std::num_put::_M_insert_int 6ms 0.098% 60.57% 91ms 1.49% boost::detail::shared_count::~shared_count (inline) 0 0% 60.57% 91ms 1.49% boost::shared_ptr::~shared_ptr (inline) 1ms 0.016% 60.59% 81ms 1.33% std::basic_filebuf::_M_terminate_output 2ms 0.033% 60.62% 81ms 1.33% std::basic_filebuf::overflow 2ms 0.033% 60.65% 81ms 1.33% std::vector::push_back (inline) 77ms 1.26% 61.92% 80ms 1.31% boost::detail::sp_counted_base::release 1ms 0.016% 61.93% 79ms 1.30% std::basic_filebuf::_M_convert_to_external 0 0% 61.93% 78ms 1.28% std::__basic_file::xsputn 1ms 0.016% 61.95% 78ms 1.28% std::operator<< (inline) 3ms 0.049% 62.00% 78ms 1.28% std::vector::_M_realloc_insert 77ms 1.26% 63.26% 77ms 1.26% __GI___libc_write 9ms 0.15% 63.41% 75ms 1.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.41% 75ms 1.23% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.33% 63.74% 74ms 1.21% boost::numeric::ublas::indexing_vector_assign 33ms 0.54% 64.28% 73ms 1.20% boost::shared_ptr::shared_ptr (inline) 73ms 1.20% 65.47% 73ms 1.20% std::_Rb_tree_insert_and_rebalance 72ms 1.18% 66.66% 72ms 1.18% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 70ms 1.15% 67.80% 70ms 1.15% [libchaste_cell_based.so] 22ms 0.36% 68.16% 68ms 1.12% AbstractElement::GetNodeLocation 39ms 0.64% 68.80% 67ms 1.10% std::basic_filebuf::xsputn 1ms 0.016% 68.82% 63ms 1.03% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 44ms 0.72% 69.54% 63ms 1.03% malloc_consolidate 7ms 0.11% 69.66% 62ms 1.02% TetrahedralMesh::EdgeIterator::GetNodeA 49ms 0.8% 70.46% 61ms 1.00% AbstractElement::GetNodeGlobalIndex 61ms 1.00% 71.46% 61ms 1.00% std::vector::size (inline) 1ms 0.016% 71.48% 60ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.93% 72.41% 57ms 0.93% [libchaste_mesh.so] 1ms 0.016% 72.43% 56ms 0.92% Cell::GetCellId 2ms 0.033% 72.46% 55ms 0.9% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.46% 55ms 0.9% std::filesystem::status 0 0% 72.46% 55ms 0.9% std::vector::vector (inline) 54ms 0.89% 73.35% 54ms 0.89% __GI___fstatat64 5ms 0.082% 73.43% 54ms 0.89% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 73.43% 54ms 0.89% tcache_get (inline) 54ms 0.89% 74.32% 54ms 0.89% tcache_get_n (inline) 3ms 0.049% 74.36% 53ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 0.87% 75.23% 53ms 0.87% std::_Rb_tree_increment 52ms 0.85% 76.09% 52ms 0.85% counterclockwise 47ms 0.77% 76.86% 52ms 0.85% vertexsort 36ms 0.59% 77.45% 51ms 0.84% boost::numeric::ublas::c_matrix::operator() (partial-inline) 3ms 0.049% 77.50% 50ms 0.82% std::_Rb_tree::_M_emplace_hint_unique 48ms 0.79% 78.28% 48ms 0.79% Node::GetIndex 0 0% 78.28% 47ms 0.77% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 78.28% 47ms 0.77% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 78.28% 47ms 0.77% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 78.28% 47ms 0.77% std::filesystem::create_directory 5ms 0.082% 78.37% 46ms 0.75% CellPropertyCollection::AddProperty 46ms 0.75% 79.12% 46ms 0.75% __memcpy_avx512_unaligned_erms 8ms 0.13% 79.25% 45ms 0.74% Determinant (inline) 0 0% 79.25% 44ms 0.72% std::_Vector_base::_Vector_base (inline) 35ms 0.57% 79.83% 43ms 0.71% std::num_put::do_put 0 0% 79.83% 41ms 0.67% std::_Vector_base::_M_create_storage (inline) 20ms 0.33% 80.15% 40ms 0.66% AbstractTetrahedralMesh::GetElement 37ms 0.61% 80.76% 40ms 0.66% boost::detail::shared_count::shared_count (inline) 0 0% 80.76% 40ms 0.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 80.76% 40ms 0.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 39ms 0.64% 81.40% 39ms 0.64% boost::shared_ptr::operator-> (inline) 26ms 0.43% 81.83% 39ms 0.64% std::basic_streambuf::xsputn 0 0% 81.83% 37ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.83% 37ms 0.61% std::__new_allocator::destroy (inline) 0 0% 81.83% 37ms 0.61% std::allocator_traits::destroy (inline) 18ms 0.3% 82.12% 36ms 0.59% AbstractCellCycleModel::GetAge 36ms 0.59% 82.71% 36ms 0.59% Node::IsDeleted 36ms 0.59% 83.30% 36ms 0.59% [libstdc++.so.6.0.33] 20ms 0.33% 83.63% 36ms 0.59% hack_digit 0 0% 83.63% 35ms 0.57% CxxTest::RealWorldDescription::setUp 35ms 0.57% 84.21% 35ms 0.57% Node::rGetLocation 0 0% 84.21% 35ms 0.57% PMPI_Init_thread 0 0% 84.21% 35ms 0.57% PetscInitialize 0 0% 84.21% 35ms 0.57% PetscSetup::setUpWorld 0 0% 84.21% 35ms 0.57% PetscSetupUtils::CommonSetup 0 0% 84.21% 35ms 0.57% PetscSetupUtils::InitialisePetsc 35ms 0.57% 84.78% 35ms 0.57% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 84.78% 35ms 0.57% ompi_mpi_init 2ms 0.033% 84.81% 34ms 0.56% Node::ClearAppliedForce 2ms 0.033% 84.85% 34ms 0.56% Node::ConstructNodeAttributes (inline) 1ms 0.016% 84.86% 33ms 0.54% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 84.86% 33ms 0.54% _dl_init 0 0% 84.86% 33ms 0.54% call_init (inline) 33ms 0.54% 85.40% 33ms 0.54% unlink_chunk 1ms 0.016% 85.42% 32ms 0.52% 6ms 0.098% 85.52% 32ms 0.52% Inverse 22ms 0.36% 85.88% 32ms 0.52% writeedges 8ms 0.13% 86.01% 31ms 0.51% AbstractTetrahedralMesh::GetNumAllElements 0 0% 86.01% 31ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline)