File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6757ms, 84.24% of 8021ms total Dropped 579 nodes (cum <= 40.10ms) flat flat% sum% cum cum% 0 0% 0% 7979ms 99.48% __libc_start_call_main 0 0% 0% 7979ms 99.48% __libc_start_main_impl 0 0% 0% 7979ms 99.48% _start 0 0% 0% 7961ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7961ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7961ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7961ms 99.25% main 0 0% 0% 7916ms 98.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7916ms 98.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7916ms 98.69% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 7912ms 98.64% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3498ms 43.61% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.05% 0.062% 3026ms 37.73% MeshBasedCellPopulation::Update 2ms 0.025% 0.087% 2904ms 36.20% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.11% 1500ms 18.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.11% 1485ms 18.51% MutableMesh::ReMesh 3ms 0.037% 0.15% 1478ms 18.43% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.16% 1348ms 16.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.075% 0.24% 1295ms 16.15% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.49% 1262ms 15.73% MeshBasedCellPopulation::SpringIterator::operator++ 109ms 1.36% 1.85% 1003ms 12.50% TetrahedralMesh::EdgeIterator::operator++ 441ms 5.50% 7.34% 984ms 12.27% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.05% 7.39% 963ms 12.01% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.012% 7.41% 920ms 11.47% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.11% 7.52% 883ms 11.01% CellPropertyCollection::GetPropertiesType (inline) 248ms 3.09% 10.61% 882ms 11.00% __dynamic_cast 10ms 0.12% 10.73% 876ms 10.92% CellPopulationElementWriter::Visit 44ms 0.55% 11.28% 836ms 10.42% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.11% 11.40% 812ms 10.12% MeshBasedCellPopulation::AcceptCellWriter 38ms 0.47% 11.87% 784ms 9.77% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.02% 745ms 9.29% TetrahedralMesh::ImportFromMesher 2ms 0.025% 12.04% 695ms 8.66% AbstractCellProperty::IsSubType (inline) 60ms 0.75% 12.79% 619ms 7.72% std::map::operator[] (partial-inline) 0 0% 12.79% 573ms 7.14% std::ostream::operator<< (inline) 87ms 1.08% 13.88% 571ms 7.12% std::ostream::_M_insert 1ms 0.012% 13.89% 551ms 6.87% triangulate 34ms 0.42% 14.31% 548ms 6.83% operator new 11ms 0.14% 14.45% 547ms 6.82% Cell::GetCellProliferativeType 544ms 6.78% 21.23% 544ms 6.78% __strcmp_avx2 6ms 0.075% 21.31% 532ms 6.63% std::set::insert (inline) 5ms 0.062% 21.37% 526ms 6.56% std::_Rb_tree::_M_insert_unique 5ms 0.062% 21.43% 525ms 6.55% LegacyCellProliferativeTypesWriter::VisitCell 21ms 0.26% 21.69% 517ms 6.45% std::_Rb_tree::find (inline) 168ms 2.09% 23.79% 516ms 6.43% __GI___libc_malloc 0 0% 23.79% 507ms 6.32% std::_Rb_tree::lower_bound (inline) 0 0% 23.79% 507ms 6.32% std::map::lower_bound (inline) 30ms 0.37% 24.16% 493ms 6.15% std::__new_allocator::allocate (inline) 0 0% 24.16% 485ms 6.05% std::allocator_traits::allocate (inline) 0 0% 24.16% 482ms 6.01% delaunay 0 0% 24.16% 481ms 6.00% divconqdelaunay 0 0% 24.16% 474ms 5.91% std::set::count (inline) 7ms 0.087% 24.25% 458ms 5.71% AbstractCellBasedSimulation::DoCellBirth 200ms 2.49% 26.74% 442ms 5.51% __cxxabiv1::__si_class_type_info::__do_dyncast 39ms 0.49% 27.23% 436ms 5.44% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.23% 410ms 5.11% std::set::~set (inline) 0 0% 27.23% 404ms 5.04% std::_Rb_tree::_M_create_node (inline) 71ms 0.89% 28.11% 387ms 4.82% std::_Rb_tree::_M_erase 0 0% 28.11% 382ms 4.76% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.11% 366ms 4.56% std::_Rb_tree::_M_get_node (inline) 1ms 0.012% 28.13% 348ms 4.34% NodeLocationWriter::Visit 12ms 0.15% 28.28% 347ms 4.33% std::less::operator() (inline) 2ms 0.025% 28.30% 338ms 4.21% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 3ms 0.037% 28.34% 337ms 4.20% Cell::GetMutationState 15ms 0.19% 28.53% 336ms 4.19% std::_Rb_tree::_Rb_tree (partial-inline) 335ms 4.18% 32.70% 336ms 4.19% std::operator< (inline) 118ms 1.47% 34.17% 334ms 4.16% __GI___libc_free 0 0% 34.17% 333ms 4.15% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.17% 331ms 4.13% OutputFileHandler::OpenOutputFile 325ms 4.05% 38.22% 325ms 4.05% std::_Rb_tree::_S_right (inline) 21ms 0.26% 38.49% 321ms 4.00% std::_Rb_tree::_M_insert_ (inline) 6ms 0.075% 38.56% 320ms 3.99% Element::Element 1ms 0.012% 38.57% 319ms 3.98% Cell::ReadyToDivide 4ms 0.05% 38.62% 307ms 3.83% std::set::set (inline) 25ms 0.31% 38.94% 302ms 3.77% std::num_put::_M_insert_float 4ms 0.05% 38.99% 298ms 3.72% std::__new_allocator::deallocate (inline) 0 0% 38.99% 296ms 3.69% std::_Rb_tree::_M_drop_node (inline) 0 0% 38.99% 296ms 3.69% std::allocator_traits::deallocate (inline) 9ms 0.11% 39.10% 286ms 3.57% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.11% 39.21% 286ms 3.57% divconqrecurse 34ms 0.42% 39.63% 285ms 3.55% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 39.66% 281ms 3.50% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 39.66% 281ms 3.50% MeshBasedCellPopulation::GetDampingConstant 193ms 2.41% 42.06% 279ms 3.48% _int_malloc 79ms 0.98% 43.05% 269ms 3.35% mergehulls 0 0% 43.05% 266ms 3.32% Cell::HasCellProperty (inline) 4ms 0.05% 43.10% 266ms 3.32% CellPropertyCollection::HasProperty 2ms 0.025% 43.12% 261ms 3.25% AbstractCellProperty::IsType (inline) 0 0% 43.12% 252ms 3.14% std::_Rb_tree::_M_put_node (inline) 5ms 0.062% 43.19% 249ms 3.10% std::__cxx11::collate::do_transform 67ms 0.84% 44.02% 247ms 3.08% std::_Rb_tree::_M_clone_node (inline) 2ms 0.025% 44.05% 244ms 3.04% CellProliferativeTypesWriter::VisitCell 5ms 0.062% 44.11% 232ms 2.89% ___vsnprintf 0 0% 44.11% 227ms 2.83% __vsnprintf_internal (inline) 30ms 0.37% 44.48% 223ms 2.78% __printf_buffer 190ms 2.37% 46.85% 216ms 2.69% _int_free 3ms 0.037% 46.89% 213ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 7ms 0.087% 46.98% 207ms 2.58% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.17% 47.15% 207ms 2.58% TetrahedralMesh::Clear 9ms 0.11% 47.26% 205ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 38ms 0.47% 47.74% 204ms 2.54% AbstractCellProperty::IsSame 11ms 0.14% 47.87% 204ms 2.54% Element::RegisterWithNodes (inline) 73ms 0.91% 48.78% 200ms 2.49% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.05% 48.83% 193ms 2.41% Node::AddElement 14ms 0.17% 49.01% 177ms 2.21% AbstractTetrahedralElement::CalculateJacobian 6ms 0.075% 49.08% 175ms 2.18% __printf_fp_l_buffer 0 0% 49.08% 175ms 2.18% __printf_fp_spec (inline) 26ms 0.32% 49.41% 171ms 2.13% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.012% 49.42% 169ms 2.11% TetrahedralMesh::RefreshJacobianCachedData 28ms 0.35% 49.77% 166ms 2.07% std::type_info::operator== (inline) 96ms 1.20% 50.97% 163ms 2.03% __printf_fp_buffer_1 0 0% 50.97% 161ms 2.01% std::basic_ofstream::basic_ofstream (inline) 4ms 0.05% 51.02% 158ms 1.97% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.012% 51.03% 154ms 1.92% std::basic_filebuf::open 0 0% 51.03% 154ms 1.92% std::basic_ofstream::open (inline) 21ms 0.26% 51.29% 148ms 1.85% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 51.29% 147ms 1.83% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.29% 146ms 1.82% AbstractCellBasedWriter::CloseFile 54ms 0.67% 51.96% 146ms 1.82% std::__ostream_insert 1ms 0.012% 51.98% 146ms 1.82% std::basic_filebuf::close 0 0% 51.98% 146ms 1.82% std::basic_ofstream::close (inline) 0 0% 51.98% 144ms 1.80% FilesystemPermissions::SetFilePermissions (inline) 144ms 1.80% 53.77% 144ms 1.80% __GI_fchmodat 0 0% 53.77% 144ms 1.80% std::filesystem::permissions 1ms 0.012% 53.78% 139ms 1.73% OutputFileHandler::OutputFileHandler 0 0% 53.78% 138ms 1.72% OutputFileHandler::CommonConstructor 4ms 0.05% 53.83% 135ms 1.68% alternateaxes 1ms 0.012% 53.85% 131ms 1.63% OutputFileHandler::MakeFoldersAndReturnFullPath 123ms 1.53% 55.38% 131ms 1.63% vertexmedian 82ms 1.02% 56.40% 127ms 1.58% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 56.43% 127ms 1.58% std::operator<< (inline) 124ms 1.55% 57.97% 124ms 1.55% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 7ms 0.087% 58.06% 123ms 1.53% Node::~Node 0 0% 58.06% 122ms 1.52% _IO_new_fopen 1ms 0.012% 58.07% 122ms 1.52% __fopen_internal (inline) 0 0% 58.07% 122ms 1.52% std::__basic_file::open 1ms 0.012% 58.09% 120ms 1.50% std::_Vector_base::_M_allocate (inline) 0 0% 58.09% 119ms 1.48% AbstractTetrahedralElement::AbstractTetrahedralElement 21ms 0.26% 58.35% 119ms 1.48% AbstractTetrahedralElement::RefreshJacobian 2ms 0.025% 58.37% 119ms 1.48% _IO_new_file_fopen 117ms 1.46% 59.83% 117ms 1.46% incircle 6ms 0.075% 59.91% 117ms 1.46% std::vector::push_back (inline) 1ms 0.012% 59.92% 114ms 1.42% __GI__IO_file_open 6ms 0.075% 59.99% 113ms 1.41% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 60.02% 113ms 1.41% boost::numeric::ublas::vector_assign (inline) 7ms 0.087% 60.10% 110ms 1.37% boost::detail::shared_count::~shared_count (inline) 0 0% 60.10% 110ms 1.37% boost::shared_ptr::~shared_ptr (inline) 109ms 1.36% 61.46% 109ms 1.36% [libchaste_cell_based.so] 45ms 0.56% 62.02% 107ms 1.33% boost::shared_ptr::shared_ptr (inline) 21ms 0.26% 62.29% 106ms 1.32% std::num_put::_M_insert_int 9ms 0.11% 62.40% 105ms 1.31% std::vector::_M_realloc_insert 104ms 1.30% 63.70% 104ms 1.30% __libc_open64 2ms 0.025% 63.72% 104ms 1.30% std::basic_filebuf::overflow 12ms 0.15% 63.87% 103ms 1.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 103ms 1.28% 65.15% 103ms 1.28% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 65.17% 102ms 1.27% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 65.19% 101ms 1.26% std::__basic_file::xsputn 0 0% 65.19% 101ms 1.26% std::basic_filebuf::_M_terminate_output 0 0% 65.19% 100ms 1.25% AbstractCellPopulation::Iterator::operator++ (inline) 97ms 1.21% 66.40% 98ms 1.22% __GI___libc_write 95ms 1.18% 67.59% 96ms 1.20% boost::detail::sp_counted_base::release 11ms 0.14% 67.72% 94ms 1.17% std::_Rb_tree_const_iterator::operator++ (inline) 49ms 0.61% 68.33% 91ms 1.13% std::basic_filebuf::xsputn 5ms 0.062% 68.40% 87ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 30ms 0.37% 68.77% 85ms 1.06% AbstractElement::GetNodeLocation 84ms 1.05% 69.82% 84ms 1.05% std::_Rb_tree_increment 1ms 0.012% 69.83% 83ms 1.03% Cell::GetCellId 4ms 0.05% 69.88% 81ms 1.01% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 69.88% 79ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.037% 69.92% 78ms 0.97% TetrahedralMesh::EdgeIterator::GetNodeA 35ms 0.44% 70.35% 77ms 0.96% boost::numeric::ublas::indexing_vector_assign 1ms 0.012% 70.37% 75ms 0.94% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 3ms 0.037% 70.40% 75ms 0.94% std::filesystem::status 7ms 0.087% 70.49% 74ms 0.92% CellPropertyCollection::AddProperty 0 0% 70.49% 74ms 0.92% std::filesystem::create_directory 74ms 0.92% 71.41% 74ms 0.92% std::vector::size (inline) 1ms 0.012% 71.43% 73ms 0.91% AbstractCellPopulation::GetLocationIndexUsingCell 73ms 0.91% 72.34% 73ms 0.91% __GI___fstatat64 52ms 0.65% 72.98% 71ms 0.89% malloc_consolidate 49ms 0.61% 73.59% 70ms 0.87% AbstractElement::GetNodeGlobalIndex 45ms 0.56% 74.16% 70ms 0.87% boost::numeric::ublas::c_matrix::operator() (partial-inline) 69ms 0.86% 75.02% 69ms 0.86% counterclockwise 56ms 0.7% 75.71% 69ms 0.86% std::num_put::do_put 39ms 0.49% 76.20% 66ms 0.82% AbstractTetrahedralMesh::GetElement 0 0% 76.20% 64ms 0.8% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 76.20% 64ms 0.8% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 61ms 0.76% 76.96% 62ms 0.77% boost::detail::shared_count::shared_count (inline) 0 0% 76.96% 62ms 0.77% tcache_get (inline) 62ms 0.77% 77.73% 62ms 0.77% tcache_get_n (inline) 21ms 0.26% 78.00% 61ms 0.76% Determinant (inline) 60ms 0.75% 78.74% 60ms 0.75% boost::shared_ptr::operator-> (inline) 59ms 0.74% 79.48% 59ms 0.74% __memcpy_avx_unaligned_erms 1ms 0.012% 79.49% 58ms 0.72% Node::ConstructNodeAttributes (inline) 0 0% 79.49% 57ms 0.71% Node::ClearAppliedForce 0 0% 79.49% 55ms 0.69% AbstractCentreBasedCellPopulation::CreateCellPair 52ms 0.65% 80.14% 55ms 0.69% vertexsort 0 0% 80.14% 53ms 0.66% BoundaryNodeWriter::Visit 53ms 0.66% 80.80% 53ms 0.66% Node::GetIndex 12ms 0.15% 80.95% 52ms 0.65% Inverse 3ms 0.037% 80.99% 52ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 22ms 0.27% 81.26% 50ms 0.62% AbstractTetrahedralMesh::GetNumAllElements 31ms 0.39% 81.65% 50ms 0.62% std::basic_streambuf::xsputn 0 0% 81.65% 50ms 0.62% std::vector::vector (inline) 49ms 0.61% 82.26% 49ms 0.61% std::ostream::sentry::sentry 0 0% 82.26% 48ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 82.26% 47ms 0.59% std::_Vector_base::_M_create_storage (inline) 0 0% 82.26% 46ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 82.26% 46ms 0.57% _dl_init 0 0% 82.26% 46ms 0.57% call_init (inline) 4ms 0.05% 82.31% 46ms 0.57% std::_Vector_base::_M_deallocate (inline) 2ms 0.025% 82.33% 45ms 0.56% NodeAttributes::NodeAttributes 44ms 0.55% 82.88% 44ms 0.55% Node::rGetLocation 0 0% 82.88% 44ms 0.55% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.88% 44ms 0.55% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 82.88% 44ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.88% 44ms 0.55% std::__new_allocator::destroy (inline) 0 0% 82.88% 44ms 0.55% std::allocator_traits::destroy (inline) 0 0% 82.88% 42ms 0.52% std::__basic_file::close 3ms 0.037% 82.92% 42ms 0.52% std::__copy_move::__copy_m (inline) 0 0% 82.92% 42ms 0.52% std::__copy_move_a (inline) 0 0% 82.92% 42ms 0.52% std::__copy_move_a1 (inline) 0 0% 82.92% 42ms 0.52% std::__copy_move_a2 (inline) 0 0% 82.92% 42ms 0.52% std::copy (inline) 0 0% 82.92% 41ms 0.51% CxxTest::RealWorldDescription::setUp 0 0% 82.92% 41ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.92% 41ms 0.51% PetscInitialize 0 0% 82.92% 41ms 0.51% PetscSetup::setUpWorld 0 0% 82.92% 41ms 0.51% PetscSetupUtils::CommonSetup 0 0% 82.92% 41ms 0.51% PetscSetupUtils::InitialisePetsc 41ms 0.51% 83.43% 41ms 0.51% [libchaste_mesh.so] 2ms 0.025% 83.46% 41ms 0.51% _IO_new_fclose 20ms 0.25% 83.71% 41ms 0.51% hack_digit 2ms 0.025% 83.73% 41ms 0.51% std::__new_allocator::construct (inline) 0 0% 83.73% 41ms 0.51% std::allocator_traits::construct (inline) 41ms 0.51% 84.24% 41ms 0.51% std::codecvt::do_always_noconv