File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5190ms, 86.44% of 6004ms total Dropped 512 nodes (cum <= 30.02ms) flat flat% sum% cum cum% 0 0% 0% 5976ms 99.53% __libc_start_call_main 0 0% 0% 5976ms 99.53% __libc_start_main_impl 0 0% 0% 5976ms 99.53% _start 0 0% 0% 5963ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5963ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5963ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5963ms 99.32% main 0 0% 0% 5928ms 98.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5928ms 98.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5928ms 98.73% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 5926ms 98.70% AbstractCellBasedSimulation::Solve 0 0% 0% 2608ms 43.44% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.083% 0.083% 2245ms 37.39% MeshBasedCellPopulation::Update 1ms 0.017% 0.1% 2241ms 37.33% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.1% 1103ms 18.37% MutableMesh::ReMesh 3ms 0.05% 0.15% 1091ms 18.17% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.017% 0.17% 1067ms 17.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.17% 946ms 15.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 20ms 0.33% 0.5% 932ms 15.52% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.033% 0.53% 907ms 15.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.15% 0.68% 827ms 13.77% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.05% 0.73% 766ms 12.76% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 362ms 6.03% 6.76% 747ms 12.44% std::_Rb_tree::_M_lower_bound (inline) 75ms 1.25% 8.01% 729ms 12.14% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.083% 8.09% 694ms 11.56% AbstractCellProperty::IsSubType (inline) 165ms 2.75% 10.84% 694ms 11.56% __dynamic_cast 3ms 0.05% 10.89% 665ms 11.08% CellPopulationElementWriter::Visit 4ms 0.067% 10.96% 645ms 10.74% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.033% 10.99% 598ms 9.96% AbstractTwoBodyInteractionForce::AddForceContribution 23ms 0.38% 11.38% 576ms 9.59% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.1% 11.48% 562ms 9.36% TetrahedralMesh::ImportFromMesher 28ms 0.47% 11.94% 506ms 8.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.033% 11.98% 505ms 8.41% Cell::GetCellProliferativeType 46ms 0.77% 12.74% 474ms 7.89% std::map::operator[] (partial-inline) 1ms 0.017% 12.76% 424ms 7.06% std::ostream::operator<< (inline) 68ms 1.13% 13.89% 420ms 7.00% std::ostream::_M_insert 22ms 0.37% 14.26% 419ms 6.98% operator new 4ms 0.067% 14.32% 407ms 6.78% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 14.32% 399ms 6.65% triangulate 11ms 0.18% 14.51% 397ms 6.61% std::_Rb_tree::find (inline) 5ms 0.083% 14.59% 393ms 6.55% std::set::insert (inline) 136ms 2.27% 16.86% 389ms 6.48% __GI___libc_malloc 4ms 0.067% 16.92% 388ms 6.46% std::_Rb_tree::_M_insert_unique 0 0% 16.92% 381ms 6.35% std::_Rb_tree::lower_bound (inline) 0 0% 16.92% 381ms 6.35% std::map::lower_bound (inline) 21ms 0.35% 17.27% 378ms 6.30% std::__new_allocator::allocate (inline) 0 0% 17.27% 374ms 6.23% std::allocator_traits::allocate (inline) 168ms 2.80% 20.07% 367ms 6.11% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.12% 20.19% 354ms 5.90% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.19% 353ms 5.88% delaunay 2ms 0.033% 20.22% 353ms 5.88% divconqdelaunay 352ms 5.86% 26.08% 352ms 5.86% __strcmp_evex 0 0% 26.08% 352ms 5.86% std::set::count (inline) 33ms 0.55% 26.63% 347ms 5.78% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.63% 330ms 5.50% std::set::~set (inline) 0 0% 26.63% 323ms 5.38% Cell::GetMutationState 53ms 0.88% 27.51% 311ms 5.18% std::_Rb_tree::_M_erase 0 0% 27.51% 288ms 4.80% std::_Rb_tree::_M_create_node (inline) 29ms 0.48% 28.00% 270ms 4.50% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.00% 268ms 4.46% std::_Rb_tree::_M_get_node (inline) 2ms 0.033% 28.03% 267ms 4.45% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.03% 267ms 4.45% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.03% 266ms 4.43% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.03% 265ms 4.41% OutputFileHandler::OpenOutputFile 83ms 1.38% 29.41% 262ms 4.36% __GI___libc_free 6ms 0.1% 29.51% 258ms 4.30% std::less::operator() (inline) 7ms 0.12% 29.63% 253ms 4.21% std::set::set (inline) 252ms 4.20% 33.83% 252ms 4.20% std::operator< (inline) 2ms 0.033% 33.86% 248ms 4.13% MeshBasedCellPopulation::GetDampingConstant 3ms 0.05% 33.91% 247ms 4.11% NodeLocationWriter::Visit 2ms 0.033% 33.94% 246ms 4.10% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.1% 34.04% 246ms 4.10% Element::Element 19ms 0.32% 34.36% 243ms 4.05% std::_Rb_tree::_M_insert_ (inline) 0 0% 34.36% 242ms 4.03% std::_Rb_tree::_M_drop_node (inline) 7ms 0.12% 34.48% 240ms 4.00% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.083% 34.56% 238ms 3.96% std::__new_allocator::deallocate (inline) 0 0% 34.56% 234ms 3.90% std::allocator_traits::deallocate (inline) 232ms 3.86% 38.42% 232ms 3.86% std::_Rb_tree::_S_right (inline) 2ms 0.033% 38.46% 228ms 3.80% Cell::ReadyToDivide 13ms 0.22% 38.67% 216ms 3.60% std::num_put::_M_insert_float 27ms 0.45% 39.12% 212ms 3.53% std::_Rb_tree::_M_copy (inline) 1ms 0.017% 39.14% 205ms 3.41% CellProliferativeTypesWriter::VisitCell 125ms 2.08% 41.22% 204ms 3.40% _int_malloc 4ms 0.067% 41.29% 201ms 3.35% divconqrecurse 0 0% 41.29% 201ms 3.35% std::_Rb_tree::_M_put_node (inline) 45ms 0.75% 42.04% 194ms 3.23% mergehulls 2ms 0.033% 42.07% 186ms 3.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.067% 42.14% 181ms 3.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 58ms 0.97% 43.10% 180ms 3.00% std::_Rb_tree::_M_clone_node (inline) 159ms 2.65% 45.75% 179ms 2.98% _int_free 2ms 0.033% 45.79% 175ms 2.91% std::__cxx11::collate::do_transform 3ms 0.05% 45.84% 173ms 2.88% ___vsnprintf 0 0% 45.84% 170ms 2.83% __vsnprintf_internal (inline) 23ms 0.38% 46.22% 167ms 2.78% __printf_buffer 3ms 0.05% 46.27% 152ms 2.53% Element::RegisterWithNodes (inline) 8ms 0.13% 46.40% 148ms 2.47% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.017% 46.42% 146ms 2.43% Node::AddElement 0 0% 46.42% 145ms 2.42% std::basic_ofstream::basic_ofstream (inline) 6ms 0.1% 46.52% 144ms 2.40% TetrahedralMesh::Clear 15ms 0.25% 46.77% 141ms 2.35% AbstractTetrahedralElement::CalculateJacobian 55ms 0.92% 47.68% 141ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 47.68% 141ms 2.35% std::basic_filebuf::open 0 0% 47.68% 141ms 2.35% std::basic_ofstream::open (inline) 1ms 0.017% 47.70% 130ms 2.17% OutputFileHandler::CommonConstructor 0 0% 47.70% 130ms 2.17% OutputFileHandler::OutputFileHandler 4ms 0.067% 47.77% 130ms 2.17% __printf_fp_l_buffer 0 0% 47.77% 130ms 2.17% __printf_fp_spec (inline) 0 0% 47.77% 128ms 2.13% TetrahedralMesh::RefreshJacobianCachedData 28ms 0.47% 48.23% 127ms 2.12% TetrahedralMesh::EdgesEnd (partial-inline) 7ms 0.12% 48.35% 126ms 2.10% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 48.35% 123ms 2.05% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.033% 48.38% 122ms 2.03% boost::numeric::ublas::vector_assign (inline) 64ms 1.07% 49.45% 120ms 2.00% __printf_fp_buffer_1 3ms 0.05% 49.50% 119ms 1.98% AbstractTetrahedralElement::CalculateInverseJacobian 46ms 0.77% 50.27% 118ms 1.97% std::__ostream_insert 0 0% 50.27% 112ms 1.87% std::__basic_file::open 0 0% 50.27% 111ms 1.85% _IO_new_fopen 1ms 0.017% 50.28% 111ms 1.85% __fopen_internal (inline) 0 0% 50.28% 108ms 1.80% _IO_new_file_fopen 0 0% 50.28% 107ms 1.78% __GI__IO_file_open 0 0% 50.28% 106ms 1.77% std::_Vector_base::_M_allocate (inline) 13ms 0.22% 50.50% 104ms 1.73% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 50.50% 104ms 1.73% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.083% 50.58% 104ms 1.73% Node::~Node 0 0% 50.58% 103ms 1.72% Cell::HasCellProperty (inline) 4ms 0.067% 50.65% 103ms 1.72% CellPropertyCollection::HasProperty 7ms 0.12% 50.77% 103ms 1.72% std::vector::push_back (inline) 0 0% 50.77% 101ms 1.68% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.77% 100ms 1.67% AbstractCellBasedWriter::CloseFile 1ms 0.017% 50.78% 100ms 1.67% std::basic_ofstream::close (inline) 62ms 1.03% 51.82% 99ms 1.65% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.017% 51.83% 99ms 1.65% std::basic_filebuf::close 19ms 0.32% 52.15% 98ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.033% 52.18% 97ms 1.62% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 52.18% 95ms 1.58% FilesystemPermissions::SetFilePermissions (inline) 95ms 1.58% 53.76% 95ms 1.58% __GI_fchmodat 0 0% 53.76% 95ms 1.58% std::filesystem::permissions 12ms 0.2% 53.96% 94ms 1.57% AbstractTetrahedralElement::RefreshJacobian 30ms 0.5% 54.46% 94ms 1.57% boost::numeric::ublas::indexing_vector_assign 0 0% 54.46% 94ms 1.57% std::operator<< (inline) 22ms 0.37% 54.83% 93ms 1.55% std::num_put::_M_insert_int 92ms 1.53% 56.36% 92ms 1.53% __libc_open64 2ms 0.033% 56.40% 90ms 1.50% alternateaxes 8ms 0.13% 56.53% 88ms 1.47% std::vector::_M_realloc_insert 80ms 1.33% 57.86% 88ms 1.47% vertexmedian 0 0% 57.86% 86ms 1.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.033% 57.89% 86ms 1.43% std::_Rb_tree_const_iterator::operator++ (inline) 86ms 1.43% 59.33% 86ms 1.43% std::_Rb_tree_increment 84ms 1.40% 60.73% 84ms 1.40% incircle 84ms 1.40% 62.13% 84ms 1.40% std::_Rb_tree_insert_and_rebalance 0 0% 62.13% 82ms 1.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.15% 62.28% 81ms 1.35% boost::detail::shared_count::~shared_count (inline) 42ms 0.7% 62.97% 81ms 1.35% boost::shared_ptr::shared_ptr (inline) 0 0% 62.97% 81ms 1.35% boost::shared_ptr::~shared_ptr (inline) 4ms 0.067% 63.04% 77ms 1.28% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.43% 63.47% 76ms 1.27% AbstractCellProperty::IsType (inline) 0 0% 63.47% 73ms 1.22% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 73ms 1.22% 64.69% 73ms 1.22% __GI___libc_write 0 0% 64.69% 73ms 1.22% std::__basic_file::xsputn 0 0% 64.69% 73ms 1.22% std::basic_filebuf::_M_convert_to_external 0 0% 64.69% 73ms 1.22% std::basic_filebuf::_M_terminate_output 0 0% 64.69% 73ms 1.22% std::basic_filebuf::overflow 1ms 0.017% 64.71% 73ms 1.22% std::filesystem::create_directory 72ms 1.20% 65.91% 72ms 1.20% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 35ms 0.58% 66.49% 71ms 1.18% std::basic_filebuf::xsputn 27ms 0.45% 66.94% 70ms 1.17% AbstractElement::GetNodeLocation 69ms 1.15% 68.09% 69ms 1.15% __GI___fstatat64 44ms 0.73% 68.82% 69ms 1.15% malloc_consolidate 0 0% 68.82% 69ms 1.15% std::filesystem::status 0 0% 68.82% 65ms 1.08% Cell::GetCellId 0 0% 68.82% 63ms 1.05% TetrahedralMesh::EdgeIterator::GetNodeB 63ms 1.05% 69.87% 63ms 1.05% [libchaste_cell_based.so] 60ms 1% 70.87% 63ms 1.05% boost::detail::sp_counted_base::release 62ms 1.03% 71.90% 62ms 1.03% counterclockwise 5ms 0.083% 71.99% 57ms 0.95% TetrahedralMesh::EdgeIterator::GetNodeA 33ms 0.55% 72.53% 54ms 0.9% boost::numeric::ublas::c_matrix::operator() (partial-inline) 45ms 0.75% 73.28% 54ms 0.9% std::num_put::do_put 54ms 0.9% 74.18% 54ms 0.9% std::vector::size (inline) 43ms 0.72% 74.90% 53ms 0.88% vertexsort 0 0% 74.90% 52ms 0.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.90% 52ms 0.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 38ms 0.63% 75.53% 52ms 0.87% std::basic_streambuf::xsputn 50ms 0.83% 76.37% 50ms 0.83% CellProperty::GetTypeId 18ms 0.3% 76.67% 49ms 0.82% Determinant (inline) 0 0% 76.67% 49ms 0.82% std::vector::vector (inline) 0 0% 76.67% 48ms 0.8% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.67% 47ms 0.78% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 47ms 0.78% 77.45% 47ms 0.78% __memcpy_avx512_unaligned_erms 2ms 0.033% 77.48% 47ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.48% 46ms 0.77% tcache_get (inline) 46ms 0.77% 78.25% 46ms 0.77% tcache_get_n (inline) 44ms 0.73% 78.98% 44ms 0.73% [libstdc++.so.6.0.33] 6ms 0.1% 79.08% 43ms 0.72% CellPropertyCollection::AddProperty 0 0% 79.08% 42ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 41ms 0.68% 79.76% 41ms 0.68% Node::GetIndex 0 0% 79.76% 41ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.76% 41ms 0.68% std::__new_allocator::destroy (inline) 0 0% 79.76% 41ms 0.68% std::allocator_traits::destroy (inline) 0 0% 79.76% 40ms 0.67% std::_Vector_base::_Vector_base (inline) 5ms 0.083% 79.85% 39ms 0.65% AbstractMesh::GetVectorFromAtoB 17ms 0.28% 80.13% 39ms 0.65% AbstractTetrahedralMesh::GetElement 1ms 0.017% 80.15% 39ms 0.65% Node::ClearAppliedForce 39ms 0.65% 80.80% 39ms 0.65% [libchaste_mesh.so] 38ms 0.63% 81.43% 39ms 0.65% boost::detail::shared_count::shared_count (inline) 0 0% 81.43% 39ms 0.65% std::_Vector_base::_M_create_storage (inline) 2ms 0.033% 81.46% 38ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 28ms 0.47% 81.93% 38ms 0.63% AbstractElement::GetNodeGlobalIndex 0 0% 81.93% 38ms 0.63% BoundaryNodeWriter::Visit 0 0% 81.93% 38ms 0.63% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.017% 81.95% 38ms 0.63% Node::ConstructNodeAttributes (inline) 0 0% 81.95% 38ms 0.63% boost::numeric::ublas::norm_2 (inline) 15ms 0.25% 82.20% 38ms 0.63% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.05% 82.25% 37ms 0.62% Inverse 37ms 0.62% 82.86% 37ms 0.62% boost::shared_ptr::operator-> (inline) 1ms 0.017% 82.88% 36ms 0.6% AbstractCentreBasedCellPopulation::IsMarkedSpring 3ms 0.05% 82.93% 36ms 0.6% std::_Vector_base::_M_deallocate (inline) 0 0% 82.93% 36ms 0.6% std::map::find (inline) 35ms 0.58% 83.51% 35ms 0.58% Node::rGetLocation 14ms 0.23% 83.74% 33ms 0.55% AbstractCellCycleModel::GetAge 33ms 0.55% 84.29% 33ms 0.55% boost::numeric::ublas::same_impl_ex 33ms 0.55% 84.84% 33ms 0.55% std::codecvt::do_always_noconv 33ms 0.55% 85.39% 33ms 0.55% unlink_chunk 32ms 0.53% 85.93% 32ms 0.53% Node::IsDeleted 0 0% 85.93% 31ms 0.52% CxxTest::RealWorldDescription::setUp 0 0% 85.93% 31ms 0.52% PMPI_Init_thread 0 0% 85.93% 31ms 0.52% PetscInitialize 0 0% 85.93% 31ms 0.52% PetscSetup::setUpWorld 0 0% 85.93% 31ms 0.52% PetscSetupUtils::CommonSetup 0 0% 85.93% 31ms 0.52% PetscSetupUtils::InitialisePetsc 31ms 0.52% 86.44% 31ms 0.52% __GI___mkdir 0 0% 86.44% 31ms 0.52% ompi_mpi_init