File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5202ms, 85.17% of 6108ms total Dropped 516 nodes (cum <= 30.54ms) flat flat% sum% cum cum% 0 0% 0% 6076ms 99.48% __libc_start_call_main 0 0% 0% 6076ms 99.48% __libc_start_main_impl 0 0% 0% 6076ms 99.48% _start 0 0% 0% 6062ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6062ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6062ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6062ms 99.25% main 0 0% 0% 6027ms 98.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6027ms 98.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6027ms 98.67% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6024ms 98.62% AbstractCellBasedSimulation::Solve 0 0% 0% 2602ms 42.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2249ms 36.82% MeshBasedCellPopulation::Update 1ms 0.016% 0.016% 2195ms 35.94% AbstractCellPopulation::WriteResultsToFiles 1ms 0.016% 0.033% 1219ms 19.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.033% 1105ms 18.09% MutableMesh::ReMesh 1ms 0.016% 0.049% 1091ms 17.86% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.065% 1079ms 17.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.033% 0.098% 1032ms 16.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.25% 0.34% 927ms 15.18% MeshBasedCellPopulation::SpringIterator::operator++ 84ms 1.38% 1.72% 743ms 12.16% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.72% 737ms 12.07% AbstractTwoBodyInteractionForce::AddForceContribution 358ms 5.86% 7.58% 729ms 11.94% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.58% 693ms 11.35% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 191ms 3.13% 10.71% 689ms 11.28% __dynamic_cast 5ms 0.082% 10.79% 677ms 11.08% CellPopulationElementWriter::Visit 42ms 0.69% 11.48% 651ms 10.66% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.082% 11.56% 647ms 10.59% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.28% 11.84% 613ms 10.04% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.065% 11.90% 572ms 9.36% MeshBasedCellPopulation::AcceptCellWriter 13ms 0.21% 12.12% 545ms 8.92% TetrahedralMesh::ImportFromMesher 0 0% 12.12% 535ms 8.76% AbstractCellProperty::IsSubType (inline) 30ms 0.49% 12.61% 455ms 7.45% std::map::operator[] (partial-inline) 0 0% 12.61% 443ms 7.25% std::ostream::operator<< (inline) 72ms 1.18% 13.79% 442ms 7.24% std::ostream::_M_insert 441ms 7.22% 21.01% 441ms 7.22% __strcmp_evex 1ms 0.016% 21.02% 423ms 6.93% triangulate 20ms 0.33% 21.35% 400ms 6.55% operator new 19ms 0.31% 21.66% 399ms 6.53% std::_Rb_tree::find (inline) 2ms 0.033% 21.69% 392ms 6.42% Cell::GetCellProliferativeType 6ms 0.098% 21.79% 380ms 6.22% std::set::insert (inline) 127ms 2.08% 23.87% 376ms 6.16% __GI___libc_malloc 0 0% 23.87% 375ms 6.14% delaunay 0 0% 23.87% 375ms 6.14% std::_Rb_tree::lower_bound (inline) 0 0% 23.87% 375ms 6.14% std::map::lower_bound (inline) 1ms 0.016% 23.89% 374ms 6.12% divconqdelaunay 5ms 0.082% 23.97% 374ms 6.12% std::_Rb_tree::_M_insert_unique 4ms 0.065% 24.03% 371ms 6.07% LegacyCellProliferativeTypesWriter::VisitCell 24ms 0.39% 24.43% 371ms 6.07% std::__new_allocator::allocate (inline) 0 0% 24.43% 367ms 6.01% std::allocator_traits::allocate (inline) 0 0% 24.43% 366ms 5.99% std::set::count (inline) 35ms 0.57% 25.00% 365ms 5.98% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.082% 25.08% 340ms 5.57% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.08% 338ms 5.53% std::set::~set (inline) 149ms 2.44% 27.52% 337ms 5.52% __cxxabiv1::__si_class_type_info::__do_dyncast 68ms 1.11% 28.63% 327ms 5.35% std::_Rb_tree::_M_erase 0 0% 28.63% 319ms 5.22% std::_Rb_tree::_M_create_node (inline) 0 0% 28.63% 296ms 4.85% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.63% 291ms 4.76% std::_Rb_tree::_M_get_node (inline) 97ms 1.59% 30.22% 286ms 4.68% __GI___libc_free 29ms 0.47% 30.70% 284ms 4.65% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 30.70% 268ms 4.39% NodeLocationWriter::Visit 1ms 0.016% 30.71% 262ms 4.29% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 30.71% 261ms 4.27% AbstractCellBasedWriter::OpenOutputFileForAppend 6ms 0.098% 30.81% 260ms 4.26% std::__new_allocator::deallocate (inline) 0 0% 30.81% 260ms 4.26% std::allocator_traits::deallocate (inline) 6ms 0.098% 30.91% 260ms 4.26% std::less::operator() (inline) 1ms 0.016% 30.93% 258ms 4.22% OutputFileHandler::OpenOutputFile 254ms 4.16% 35.09% 255ms 4.17% std::operator< (inline) 1ms 0.016% 35.10% 252ms 4.13% std::set::set (inline) 0 0% 35.10% 243ms 3.98% std::_Rb_tree::_M_drop_node (inline) 0 0% 35.10% 242ms 3.96% Cell::GetMutationState 23ms 0.38% 35.48% 239ms 3.91% std::num_put::_M_insert_float 6ms 0.098% 35.58% 233ms 3.81% Cell::ReadyToDivide 29ms 0.47% 36.05% 230ms 3.77% std::_Rb_tree::_M_copy (inline) 16ms 0.26% 36.31% 228ms 3.73% std::_Rb_tree::_M_insert_ (inline) 12ms 0.2% 36.51% 226ms 3.70% divconqrecurse 0 0% 36.51% 225ms 3.68% MeshBasedCellPopulation::GetDampingConstant 1ms 0.016% 36.53% 224ms 3.67% AbstractCentreBasedCellPopulation::GetDampingConstant 222ms 3.63% 40.16% 222ms 3.63% std::_Rb_tree::_S_right (inline) 0 0% 40.16% 211ms 3.45% Element::Element 0 0% 40.16% 211ms 3.45% std::_Rb_tree::_M_put_node (inline) 5ms 0.082% 40.24% 208ms 3.41% CellPropertyCollection::HasProperty 8ms 0.13% 40.37% 207ms 3.39% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.065% 40.44% 207ms 3.39% AbstractCellProperty::IsType (inline) 0 0% 40.44% 205ms 3.36% Cell::HasCellProperty (inline) 69ms 1.13% 41.57% 204ms 3.34% mergehulls 137ms 2.24% 43.81% 200ms 3.27% _int_malloc 1ms 0.016% 43.83% 195ms 3.19% std::__cxx11::collate::do_transform 165ms 2.70% 46.53% 189ms 3.09% _int_free 49ms 0.8% 47.33% 189ms 3.09% std::_Rb_tree::_M_clone_node (inline) 3ms 0.049% 47.38% 178ms 2.91% ___vsnprintf 1ms 0.016% 47.40% 177ms 2.90% CellProliferativeTypesWriter::VisitCell 20ms 0.33% 47.72% 175ms 2.87% __printf_buffer 0 0% 47.72% 175ms 2.87% __vsnprintf_internal (inline) 8ms 0.13% 47.86% 170ms 2.78% TetrahedralMesh::Clear 6ms 0.098% 47.95% 169ms 2.77% MeshBasedCellPopulation::SpringsEnd (inline) 31ms 0.51% 48.46% 166ms 2.72% AbstractCellProperty::IsSame 3ms 0.049% 48.51% 145ms 2.37% Element::RegisterWithNodes (inline) 2ms 0.033% 48.54% 143ms 2.34% __printf_fp_spec (inline) 2ms 0.033% 48.58% 142ms 2.32% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.098% 48.67% 141ms 2.31% __printf_fp_l_buffer 48ms 0.79% 49.46% 141ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.11% 49.57% 140ms 2.29% Node::AddElement 0 0% 49.57% 139ms 2.28% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 33ms 0.54% 50.11% 135ms 2.21% std::type_info::operator== (inline) 0 0% 50.11% 131ms 2.14% std::basic_ofstream::basic_ofstream (inline) 27ms 0.44% 50.56% 128ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.016% 50.57% 128ms 2.10% std::basic_ofstream::open (inline) 13ms 0.21% 50.79% 127ms 2.08% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.79% 127ms 2.08% std::basic_filebuf::open 70ms 1.15% 51.93% 125ms 2.05% __printf_fp_buffer_1 0 0% 51.93% 122ms 2.00% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.065% 52.00% 114ms 1.87% Node::~Node 2ms 0.033% 52.03% 113ms 1.85% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.21% 52.24% 113ms 1.85% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.016% 52.26% 113ms 1.85% OutputFileHandler::OutputFileHandler 60ms 0.98% 53.24% 113ms 1.85% boost::shared_ptr::shared_ptr (inline) 0 0% 53.24% 112ms 1.83% OutputFileHandler::CommonConstructor 74ms 1.21% 54.45% 111ms 1.82% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 54.45% 111ms 1.82% _IO_new_fopen 0 0% 54.45% 111ms 1.82% __fopen_internal (inline) 1ms 0.016% 54.47% 111ms 1.82% std::__basic_file::open 0 0% 54.47% 109ms 1.78% OutputFileHandler::MakeFoldersAndReturnFullPath 36ms 0.59% 55.06% 109ms 1.78% std::__ostream_insert 0 0% 55.06% 107ms 1.75% _IO_new_file_fopen 0 0% 55.06% 106ms 1.74% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.016% 55.08% 106ms 1.74% __GI__IO_file_open 0 0% 55.08% 104ms 1.70% AbstractCellBasedWriter::CloseFile 2ms 0.033% 55.11% 104ms 1.70% std::basic_filebuf::close 0 0% 55.11% 104ms 1.70% std::basic_ofstream::close (inline) 0 0% 55.11% 102ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 102ms 1.67% 56.78% 102ms 1.67% __GI_fchmodat 0 0% 56.78% 102ms 1.67% std::filesystem::permissions 97ms 1.59% 58.37% 97ms 1.59% __libc_open64 0 0% 58.37% 93ms 1.52% std::operator<< (inline) 2ms 0.033% 58.40% 92ms 1.51% boost::numeric::ublas::vector_assign (inline) 8ms 0.13% 58.53% 89ms 1.46% AbstractTetrahedralElement::RefreshJacobian 13ms 0.21% 58.74% 89ms 1.46% boost::detail::shared_count::~shared_count (inline) 5ms 0.082% 58.82% 89ms 1.46% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 58.82% 89ms 1.46% boost::shared_ptr::~shared_ptr (inline) 8ms 0.13% 58.96% 87ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 58.96% 87ms 1.42% alternateaxes 83ms 1.36% 60.31% 87ms 1.42% vertexmedian 0 0% 60.31% 86ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 85ms 1.39% 61.71% 85ms 1.39% incircle 1ms 0.016% 61.72% 84ms 1.38% std::basic_filebuf::_M_terminate_output 3ms 0.049% 61.77% 84ms 1.38% std::basic_filebuf::overflow 23ms 0.38% 62.15% 84ms 1.38% std::num_put::_M_insert_int 81ms 1.33% 63.47% 81ms 1.33% __GI___libc_write 0 0% 63.47% 81ms 1.33% std::__basic_file::xsputn 0 0% 63.47% 81ms 1.33% std::basic_filebuf::_M_convert_to_external 4ms 0.065% 63.54% 80ms 1.31% std::vector::push_back (inline) 1ms 0.016% 63.56% 77ms 1.26% std::_Vector_base::_M_allocate (inline) 1ms 0.016% 63.57% 73ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 73ms 1.20% 64.77% 73ms 1.20% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 69ms 1.13% 65.90% 72ms 1.18% boost::detail::sp_counted_base::release 4ms 0.065% 65.96% 71ms 1.16% std::vector::_M_realloc_insert 1ms 0.016% 65.98% 70ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.016% 66.00% 70ms 1.15% AbstractTetrahedralElement::AbstractTetrahedralElement 70ms 1.15% 67.14% 70ms 1.15% std::_Rb_tree_insert_and_rebalance 0 0% 67.14% 69ms 1.13% Cell::GetCellId 31ms 0.51% 67.65% 68ms 1.11% AbstractElement::GetNodeLocation 1ms 0.016% 67.67% 66ms 1.08% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.29% 67.96% 65ms 1.06% boost::numeric::ublas::indexing_vector_assign 60ms 0.98% 68.94% 60ms 0.98% [libchaste_cell_based.so] 55ms 0.9% 69.84% 59ms 0.97% vertexsort 56ms 0.92% 70.76% 56ms 0.92% __memcpy_avx512_unaligned_erms 2ms 0.033% 70.79% 55ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeA 47ms 0.77% 71.56% 55ms 0.9% std::num_put::do_put 55ms 0.9% 72.46% 55ms 0.9% std::vector::size (inline) 0 0% 72.46% 54ms 0.88% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 72.46% 54ms 0.88% std::filesystem::create_directory 4ms 0.065% 72.53% 53ms 0.87% CellPropertyCollection::AddProperty 48ms 0.79% 73.31% 53ms 0.87% boost::detail::shared_count::shared_count (inline) 38ms 0.62% 73.94% 53ms 0.87% std::basic_streambuf::xsputn 1ms 0.016% 73.95% 53ms 0.87% std::filesystem::status 38ms 0.62% 74.57% 52ms 0.85% AbstractElement::GetNodeGlobalIndex 1ms 0.016% 74.59% 52ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 52ms 0.85% 75.44% 52ms 0.85% __GI___fstatat64 36ms 0.59% 76.03% 52ms 0.85% malloc_consolidate 1ms 0.016% 76.05% 50ms 0.82% BoundaryNodeWriter::Visit 50ms 0.82% 76.87% 50ms 0.82% counterclockwise 3ms 0.049% 76.92% 50ms 0.82% std::_Rb_tree::_M_emplace_hint_unique 32ms 0.52% 77.44% 50ms 0.82% std::basic_filebuf::xsputn 3ms 0.049% 77.49% 49ms 0.8% std::_Rb_tree_const_iterator::operator++ (inline) 49ms 0.8% 78.29% 49ms 0.8% std::_Rb_tree_increment 0 0% 78.29% 49ms 0.8% tcache_get (inline) 49ms 0.8% 79.09% 49ms 0.8% tcache_get_n (inline) 0 0% 79.09% 47ms 0.77% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.016% 79.11% 45ms 0.74% Node::ConstructNodeAttributes (inline) 0 0% 79.11% 44ms 0.72% Node::ClearAppliedForce 0 0% 79.11% 44ms 0.72% std::_Vector_base::_M_deallocate (inline) 43ms 0.7% 79.81% 43ms 0.7% boost::shared_ptr::operator-> (inline) 42ms 0.69% 80.50% 42ms 0.69% [libchaste_mesh.so] 17ms 0.28% 80.78% 40ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 80.78% 40ms 0.65% std::vector::vector (inline) 39ms 0.64% 81.42% 39ms 0.64% Node::GetIndex 0 0% 81.42% 39ms 0.64% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 24ms 0.39% 81.81% 39ms 0.64% boost::numeric::ublas::c_matrix::operator() (partial-inline) 16ms 0.26% 82.07% 38ms 0.62% AbstractTetrahedralMesh::GetNumAllElements 0 0% 82.07% 37ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 3ms 0.049% 82.12% 37ms 0.61% NodeAttributes::NodeAttributes 22ms 0.36% 82.48% 36ms 0.59% hack_digit 1ms 0.016% 82.50% 36ms 0.59% std::__copy_move::__copy_m (inline) 0 0% 82.50% 36ms 0.59% std::__copy_move_a (inline) 0 0% 82.50% 36ms 0.59% std::__copy_move_a1 (inline) 0 0% 82.50% 36ms 0.59% std::__copy_move_a2 (inline) 0 0% 82.50% 36ms 0.59% std::copy (inline) 0 0% 82.50% 35ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.50% 35ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 35ms 0.57% 83.07% 35ms 0.57% Node::rGetLocation 0 0% 83.07% 35ms 0.57% std::_Vector_base::_Vector_base (inline) 23ms 0.38% 83.45% 34ms 0.56% AbstractCellCycleModel::GetAge 0 0% 83.45% 34ms 0.56% _dl_init 0 0% 83.45% 34ms 0.56% call_init (inline) 0 0% 83.45% 33ms 0.54% std::_Vector_base::_M_create_storage (inline) 1ms 0.016% 83.46% 33ms 0.54% std::__new_allocator::construct (inline) 0 0% 83.46% 33ms 0.54% std::allocator_traits::construct (inline) 0 0% 83.46% 33ms 0.54% std::map::map (inline) 0 0% 83.46% 32ms 0.52% CxxTest::RealWorldDescription::setUp 9ms 0.15% 83.61% 32ms 0.52% Determinant (inline) 0 0% 83.61% 32ms 0.52% PMPI_Init_thread 0 0% 83.61% 32ms 0.52% PetscInitialize 0 0% 83.61% 32ms 0.52% PetscSetup::setUpWorld 0 0% 83.61% 32ms 0.52% PetscSetupUtils::CommonSetup 0 0% 83.61% 32ms 0.52% PetscSetupUtils::InitialisePetsc 32ms 0.52% 84.14% 32ms 0.52% [libstdc++.so.6.0.33] 32ms 0.52% 84.66% 32ms 0.52% boost::numeric::ublas::same_impl_ex 0 0% 84.66% 32ms 0.52% ompi_mpi_init 0 0% 84.66% 32ms 0.52% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.66% 32ms 0.52% std::__new_allocator::destroy (inline) 0 0% 84.66% 32ms 0.52% std::allocator_traits::destroy (inline) 0 0% 84.66% 31ms 0.51% _dl_start_user 0 0% 84.66% 31ms 0.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 84.66% 31ms 0.51% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 31ms 0.51% 85.17% 31ms 0.51% std::ostream::sentry::sentry