File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 3922ms, 85.90% of 4566ms total Dropped 464 nodes (cum <= 22.83ms) flat flat% sum% cum cum% 0 0% 0% 4541ms 99.45% __libc_start_call_main 0 0% 0% 4541ms 99.45% __libc_start_main_impl 0 0% 0% 4541ms 99.45% _start 0 0% 0% 4529ms 99.19% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4529ms 99.19% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4529ms 99.19% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4529ms 99.19% main 0 0% 0% 4497ms 98.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4497ms 98.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4497ms 98.49% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4495ms 98.45% AbstractCellBasedSimulation::Solve 0 0% 0% 1964ms 43.01% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 1733ms 37.95% MeshBasedCellPopulation::Update 0 0% 0% 1715ms 37.56% AbstractCellPopulation::WriteResultsToFiles 2ms 0.044% 0.044% 903ms 19.78% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.044% 810ms 17.74% MutableMesh::ReMesh 1ms 0.022% 0.066% 810ms 17.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.28% 0.35% 773ms 16.93% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.044% 0.39% 704ms 15.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.39% 672ms 14.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 69ms 1.51% 1.91% 648ms 14.19% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.066% 1.97% 550ms 12.05% CellPopulationElementWriter::Visit 3ms 0.066% 2.04% 523ms 11.45% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.088% 2.12% 472ms 10.34% AbstractTwoBodyInteractionForce::AddForceContribution 240ms 5.26% 7.38% 470ms 10.29% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.18% 7.56% 453ms 9.92% MeshBasedCellPopulation::AcceptCellWriter 14ms 0.31% 7.86% 437ms 9.57% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.31% 8.17% 436ms 9.55% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.15% 8.32% 436ms 9.55% CellPropertyCollection::GetPropertiesType (inline) 97ms 2.12% 10.45% 430ms 9.42% __dynamic_cast 5ms 0.11% 10.56% 413ms 9.05% TetrahedralMesh::ImportFromMesher 73ms 1.60% 12.16% 355ms 7.77% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.066% 12.22% 352ms 7.71% AbstractCellProperty::IsSubType (inline) 6ms 0.13% 12.35% 347ms 7.60% std::set::insert (inline) 19ms 0.42% 12.77% 344ms 7.53% operator new 0 0% 12.77% 341ms 7.47% std::_Rb_tree::_M_insert_unique 0 0% 12.77% 331ms 7.25% std::set::~set (inline) 0 0% 12.77% 326ms 7.14% std::ostream::operator<< (inline) 42ms 0.92% 13.69% 325ms 7.12% std::ostream::_M_insert 146ms 3.20% 16.89% 320ms 7.01% __GI___libc_malloc 3ms 0.066% 16.95% 319ms 6.99% LegacyCellProliferativeTypesWriter::VisitCell 16ms 0.35% 17.30% 313ms 6.86% std::_Rb_tree::find (inline) 0 0% 17.30% 313ms 6.86% triangulate 7ms 0.15% 17.46% 306ms 6.70% std::__new_allocator::allocate (inline) 0 0% 17.46% 301ms 6.59% std::allocator_traits::allocate (inline) 0 0% 17.46% 300ms 6.57% std::set::count (inline) 0 0% 17.46% 281ms 6.15% delaunay 0 0% 17.46% 281ms 6.15% divconqdelaunay 24ms 0.53% 17.98% 279ms 6.11% std::_Rb_tree::_M_erase 3ms 0.066% 18.05% 274ms 6.00% Cell::GetCellProliferativeType 0 0% 18.05% 253ms 5.54% std::_Rb_tree::_M_drop_node (inline) 132ms 2.89% 20.94% 246ms 5.39% __cxxabiv1::__si_class_type_info::__do_dyncast 238ms 5.21% 26.15% 238ms 5.21% __strcmp_evex 0 0% 26.15% 238ms 5.21% std::_Rb_tree::_M_create_node (inline) 13ms 0.28% 26.43% 237ms 5.19% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 26.43% 234ms 5.12% std::_Rb_tree::_M_get_node (inline) 7ms 0.15% 26.59% 232ms 5.08% boost::detail::shared_count::~shared_count (inline) 0 0% 26.59% 232ms 5.08% boost::shared_ptr::~shared_ptr (inline) 17ms 0.37% 26.96% 230ms 5.04% std::map::operator[] (partial-inline) 0 0% 26.96% 227ms 4.97% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 26.96% 226ms 4.95% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.022% 26.98% 225ms 4.93% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.98% 225ms 4.93% OutputFileHandler::OpenOutputFile 0 0% 26.98% 220ms 4.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.98% 220ms 4.82% std::set::set (inline) 217ms 4.75% 31.73% 219ms 4.80% boost::detail::sp_counted_base::release 13ms 0.28% 32.02% 219ms 4.80% std::less::operator() (inline) 26ms 0.57% 32.59% 217ms 4.75% std::_Rb_tree::_M_insert_ (inline) 25ms 0.55% 33.14% 212ms 4.64% std::_Rb_tree::_M_copy (inline) 206ms 4.51% 37.65% 206ms 4.51% std::operator< (inline) 0 0% 37.65% 205ms 4.49% NodeLocationWriter::Visit 33ms 0.72% 38.37% 205ms 4.49% __GI___libc_free 3ms 0.066% 38.44% 204ms 4.47% Cell::GetMutationState 104ms 2.28% 40.71% 187ms 4.10% std::_Rb_tree::_M_clone_node (inline) 13ms 0.28% 41.00% 186ms 4.07% std::num_put::_M_insert_float 3ms 0.066% 41.06% 185ms 4.05% Element::Element 0 0% 41.06% 180ms 3.94% std::_Rb_tree::lower_bound (inline) 0 0% 41.06% 180ms 3.94% std::map::lower_bound (inline) 5ms 0.11% 41.17% 173ms 3.79% std::__new_allocator::deallocate (inline) 159ms 3.48% 44.66% 172ms 3.77% _int_free 0 0% 44.66% 171ms 3.75% std::allocator_traits::deallocate (inline) 1ms 0.022% 44.68% 165ms 3.61% MeshBasedCellPopulation::GetDampingConstant 1ms 0.022% 44.70% 164ms 3.59% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.11% 44.81% 159ms 3.48% divconqrecurse 4ms 0.088% 44.90% 157ms 3.44% AbstractCellPopulation::IsCellAttachedToLocationIndex 41ms 0.9% 45.80% 151ms 3.31% mergehulls 3ms 0.066% 45.86% 149ms 3.26% std::__cxx11::collate::do_transform 5ms 0.11% 45.97% 146ms 3.20% Cell::ReadyToDivide 0 0% 45.97% 143ms 3.13% std::_Rb_tree::_M_put_node (inline) 2ms 0.044% 46.01% 140ms 3.07% ___vsnprintf 0 0% 46.01% 138ms 3.02% __vsnprintf_internal (inline) 5ms 0.11% 46.12% 137ms 3.00% Element::RegisterWithNodes (inline) 32ms 0.7% 46.82% 135ms 2.96% __printf_buffer 86ms 1.88% 48.71% 135ms 2.96% _int_malloc 5ms 0.11% 48.82% 128ms 2.80% CellPropertyCollection::HasProperty 3ms 0.066% 48.88% 128ms 2.80% Node::AddElement 0 0% 48.88% 125ms 2.74% Cell::HasCellProperty (inline) 2ms 0.044% 48.93% 124ms 2.72% AbstractCellProperty::IsType (inline) 47ms 1.03% 49.96% 124ms 2.72% std::_Rb_tree::_M_get_insert_unique_pos (inline) 6ms 0.13% 50.09% 117ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 50.09% 113ms 2.47% CellProliferativeTypesWriter::VisitCell 0 0% 50.09% 110ms 2.41% std::_Rb_tree::_M_destroy_node (inline) 0 0% 50.09% 110ms 2.41% std::__new_allocator::destroy (inline) 0 0% 50.09% 110ms 2.41% std::allocator_traits::destroy (inline) 0 0% 50.09% 106ms 2.32% FilesystemPermissions::SetFilePermissions (inline) 106ms 2.32% 52.41% 106ms 2.32% __GI_fchmodat 0 0% 52.41% 106ms 2.32% std::filesystem::permissions 0 0% 52.41% 104ms 2.28% TetrahedralMesh::Clear 2ms 0.044% 52.45% 102ms 2.23% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 52.45% 102ms 2.23% std::basic_ofstream::basic_ofstream (inline) 16ms 0.35% 52.80% 100ms 2.19% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.022% 52.83% 100ms 2.19% std::basic_filebuf::open 0 0% 52.83% 100ms 2.19% std::basic_ofstream::open (inline) 2ms 0.044% 52.87% 98ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.11% 52.98% 95ms 2.08% __printf_fp_l_buffer 0 0% 52.98% 95ms 2.08% __printf_fp_spec (inline) 0 0% 52.98% 93ms 2.04% OutputFileHandler::CommonConstructor 0 0% 52.98% 93ms 2.04% OutputFileHandler::OutputFileHandler 0 0% 52.98% 92ms 2.01% OutputFileHandler::MakeFoldersAndReturnFullPath 36ms 0.79% 53.77% 90ms 1.97% std::__ostream_insert 12ms 0.26% 54.03% 89ms 1.95% AbstractTetrahedralElement::CalculateJacobian 45ms 0.99% 55.02% 89ms 1.95% __printf_fp_buffer_1 1ms 0.022% 55.04% 87ms 1.91% std::operator<< (inline) 0 0% 55.04% 86ms 1.88% _IO_new_file_fopen 0 0% 55.04% 86ms 1.88% _IO_new_fopen 0 0% 55.04% 86ms 1.88% __GI__IO_file_open 0 0% 55.04% 86ms 1.88% __fopen_internal (inline) 0 0% 55.04% 86ms 1.88% std::__basic_file::open 24ms 0.53% 55.56% 83ms 1.82% AbstractCellProperty::IsSame 2ms 0.044% 55.61% 83ms 1.82% alternateaxes 79ms 1.73% 57.34% 81ms 1.77% __libc_open64 77ms 1.69% 59.02% 81ms 1.77% vertexmedian 0 0% 59.02% 80ms 1.75% TetrahedralMesh::RefreshJacobianCachedData 79ms 1.73% 60.75% 79ms 1.73% std::_Rb_tree::_S_right (inline) 0 0% 60.75% 77ms 1.69% AbstractCellPopulation::CloseRoundRobinWritersFiles 14ms 0.31% 61.06% 77ms 1.69% MeshBasedCellPopulation::SpringIterator::SpringIterator 57ms 1.25% 62.31% 77ms 1.69% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 62.31% 76ms 1.66% AbstractCellBasedWriter::CloseFile 0 0% 62.31% 76ms 1.66% AbstractTetrahedralElement::CalculateInverseJacobian 76ms 1.66% 63.97% 76ms 1.66% incircle 1ms 0.022% 63.99% 76ms 1.66% std::basic_ofstream::close (inline) 1ms 0.022% 64.02% 75ms 1.64% std::basic_filebuf::close 17ms 0.37% 64.39% 73ms 1.60% std::num_put::_M_insert_int 0 0% 64.39% 67ms 1.47% std::_Vector_base::_M_allocate (inline) 2ms 0.044% 64.43% 65ms 1.42% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.044% 64.48% 64ms 1.40% boost::numeric::ublas::vector_assign (inline) 10ms 0.22% 64.70% 62ms 1.36% AbstractTetrahedralElement::RefreshJacobian 62ms 1.36% 66.05% 62ms 1.36% std::_Rb_tree_insert_and_rebalance 3ms 0.066% 66.12% 60ms 1.31% std::vector::push_back (inline) 10ms 0.22% 66.34% 59ms 1.29% std::type_info::operator== (inline) 2ms 0.044% 66.38% 58ms 1.27% Node::~Node 0 0% 66.38% 57ms 1.25% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 66.38% 57ms 1.25% std::filesystem::create_directory 6ms 0.13% 66.51% 56ms 1.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.022% 66.54% 56ms 1.23% AbstractCellPopulation::Iterator::operator++ (inline) 56ms 1.23% 67.76% 56ms 1.23% [libchaste_cell_based.so] 4ms 0.088% 67.85% 55ms 1.20% std::vector::_M_realloc_insert 1ms 0.022% 67.87% 53ms 1.16% std::basic_filebuf::_M_terminate_output 1ms 0.022% 67.89% 52ms 1.14% std::basic_filebuf::_M_convert_to_external 0 0% 67.89% 52ms 1.14% std::basic_filebuf::overflow 50ms 1.10% 68.99% 51ms 1.12% __GI___libc_write 0 0% 68.99% 51ms 1.12% std::__basic_file::xsputn 4ms 0.088% 69.08% 50ms 1.10% CellPropertyCollection::AddProperty 1ms 0.022% 69.10% 47ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 46ms 1.01% 70.11% 46ms 1.01% [libchaste_mesh.so] 17ms 0.37% 70.48% 46ms 1.01% boost::numeric::ublas::indexing_vector_assign 45ms 0.99% 71.46% 45ms 0.99% __GI___fstatat64 45ms 0.99% 72.45% 45ms 0.99% std::vector::size (inline) 4ms 0.088% 72.54% 44ms 0.96% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 31ms 0.68% 73.22% 44ms 0.96% std::basic_streambuf::xsputn 0 0% 73.22% 44ms 0.96% std::filesystem::status 0 0% 73.22% 43ms 0.94% CellPropertyCollection::~CellPropertyCollection (inline) 22ms 0.48% 73.70% 42ms 0.92% AbstractTetrahedralMesh::GetElement 1ms 0.022% 73.72% 42ms 0.92% Cell::GetCellId 1ms 0.022% 73.74% 41ms 0.9% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.61% 74.35% 40ms 0.88% AbstractElement::GetNodeLocation 0 0% 74.35% 40ms 0.88% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 74.35% 39ms 0.85% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 74.35% 39ms 0.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.35% 39ms 0.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 36ms 0.79% 75.14% 39ms 0.85% malloc_consolidate 24ms 0.53% 75.67% 39ms 0.85% std::basic_filebuf::xsputn 26ms 0.57% 76.24% 38ms 0.83% AbstractElement::GetNodeGlobalIndex 38ms 0.83% 77.07% 38ms 0.83% std::_Rb_tree_increment 2ms 0.044% 77.11% 37ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeB 37ms 0.81% 77.92% 37ms 0.81% [libstdc++.so.6.0.33] 4ms 0.088% 78.01% 36ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeA 36ms 0.79% 78.80% 36ms 0.79% counterclockwise 31ms 0.68% 79.48% 36ms 0.79% vertexsort 5ms 0.11% 79.59% 35ms 0.77% std::_Rb_tree_const_iterator::operator++ (inline) 34ms 0.74% 80.33% 34ms 0.74% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 28ms 0.61% 80.95% 33ms 0.72% CellPropertyCollection::GetProperty 33ms 0.72% 81.67% 33ms 0.72% __GI___mkdir 0 0% 81.67% 33ms 0.72% boost::numeric::ublas::norm_2 (inline) 3ms 0.066% 81.73% 33ms 0.72% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.044% 81.78% 33ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 15ms 0.33% 82.11% 32ms 0.7% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 82.11% 31ms 0.68% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 82.11% 31ms 0.68% _dl_init 0 0% 82.11% 31ms 0.68% call_init (inline) 0 0% 82.11% 30ms 0.66% CxxTest::RealWorldDescription::setUp 0 0% 82.11% 30ms 0.66% PetscInitialize 0 0% 82.11% 30ms 0.66% PetscSetup::setUpWorld 0 0% 82.11% 30ms 0.66% PetscSetupUtils::CommonSetup 0 0% 82.11% 30ms 0.66% PetscSetupUtils::InitialisePetsc 30ms 0.66% 82.76% 30ms 0.66% __memcpy_avx512_unaligned_erms 16ms 0.35% 83.11% 30ms 0.66% hack_digit 0 0% 83.11% 30ms 0.66% tcache_get (inline) 30ms 0.66% 83.77% 30ms 0.66% tcache_get_n (inline) 0 0% 83.77% 29ms 0.64% PMPI_Init_thread 23ms 0.5% 84.28% 29ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 84.28% 29ms 0.64% ompi_mpi_init 1ms 0.022% 84.30% 28ms 0.61% std::_Vector_base::_M_deallocate (inline) 1ms 0.022% 84.32% 27ms 0.59% 27ms 0.59% 84.91% 27ms 0.59% boost::numeric::ublas::c_vector::operator() 12ms 0.26% 85.17% 26ms 0.57% AbstractTetrahedralMesh::GetNumAllElements 2ms 0.044% 85.22% 25ms 0.55% Element::~Element 0 0% 85.22% 25ms 0.55% std::map::~map (inline) 1ms 0.022% 85.24% 24ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.24% 24ms 0.53% Node::ClearAppliedForce 0 0% 85.24% 24ms 0.53% Node::ConstructNodeAttributes (inline) 24ms 0.53% 85.76% 24ms 0.53% Node::GetIndex 0 0% 85.76% 24ms 0.53% _dl_start_user 0 0% 85.76% 24ms 0.53% std::vector::vector (inline) 1ms 0.022% 85.79% 23ms 0.5% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 5ms 0.11% 85.90% 23ms 0.5% Inverse 0 0% 85.90% 23ms 0.5% std::_Vector_base::_M_create_storage (inline) 0 0% 85.90% 23ms 0.5% std::_Vector_base::_Vector_base (inline)