File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6847ms, 84.81% of 8073ms total Dropped 557 nodes (cum <= 40.37ms) flat flat% sum% cum cum% 0 0% 0% 8032ms 99.49% __libc_start_call_main 0 0% 0% 8032ms 99.49% __libc_start_main_impl 0 0% 0% 8032ms 99.49% _start 0 0% 0% 8013ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8013ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8013ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8013ms 99.26% main 0 0% 0% 7969ms 98.71% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7969ms 98.71% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7969ms 98.71% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7965ms 98.66% AbstractCellBasedSimulation::Solve 0 0% 0% 3413ms 42.28% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 3003ms 37.20% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.05% 2987ms 37.00% MeshBasedCellPopulation::Update 0 0% 0.05% 1540ms 19.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.062% 0.11% 1478ms 18.31% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.11% 1455ms 18.02% MutableMesh::ReMesh 0 0% 0.11% 1385ms 17.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.14% 0.25% 1328ms 16.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 26ms 0.32% 0.57% 1266ms 15.68% MeshBasedCellPopulation::SpringIterator::operator++ 121ms 1.50% 2.07% 1000ms 12.39% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 2.11% 983ms 12.18% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 445ms 5.51% 7.62% 939ms 11.63% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.12% 7.74% 918ms 11.37% CellPopulationElementWriter::Visit 266ms 3.29% 11.04% 912ms 11.30% __dynamic_cast 3ms 0.037% 11.07% 890ms 11.02% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.14% 11.21% 873ms 10.81% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.062% 11.27% 813ms 10.07% MeshBasedCellPopulation::AcceptCellWriter 54ms 0.67% 11.94% 801ms 9.92% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 34ms 0.42% 12.36% 768ms 9.51% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.087% 12.45% 726ms 8.99% TetrahedralMesh::ImportFromMesher 1ms 0.012% 12.46% 705ms 8.73% AbstractCellProperty::IsSubType (inline) 0 0% 12.46% 608ms 7.53% std::ostream::operator<< (inline) 100ms 1.24% 13.70% 606ms 7.51% std::ostream::_M_insert 46ms 0.57% 14.27% 572ms 7.09% std::map::operator[] (partial-inline) 561ms 6.95% 21.22% 561ms 6.95% __strcmp_avx2 0 0% 21.22% 559ms 6.92% triangulate 34ms 0.42% 21.64% 532ms 6.59% operator new 6ms 0.074% 21.71% 522ms 6.47% Cell::GetCellProliferativeType 5ms 0.062% 21.78% 514ms 6.37% LegacyCellProliferativeTypesWriter::VisitCell 18ms 0.22% 22.00% 506ms 6.27% std::_Rb_tree::find (inline) 11ms 0.14% 22.14% 500ms 6.19% std::set::insert (inline) 147ms 1.82% 23.96% 497ms 6.16% __GI___libc_malloc 0 0% 23.96% 489ms 6.06% delaunay 5ms 0.062% 24.02% 489ms 6.06% std::_Rb_tree::_M_insert_unique 1ms 0.012% 24.03% 486ms 6.02% divconqdelaunay 0 0% 24.03% 476ms 5.90% std::_Rb_tree::lower_bound (inline) 0 0% 24.03% 476ms 5.90% std::map::lower_bound (inline) 35ms 0.43% 24.46% 473ms 5.86% std::_Rb_tree::~_Rb_tree (inline) 34ms 0.42% 24.89% 469ms 5.81% std::__new_allocator::allocate (inline) 0 0% 24.89% 465ms 5.76% std::set::count (inline) 0 0% 24.89% 463ms 5.74% std::allocator_traits::allocate (inline) 0 0% 24.89% 444ms 5.50% std::set::~set (inline) 76ms 0.94% 25.83% 426ms 5.28% std::_Rb_tree::_M_erase 191ms 2.37% 28.19% 421ms 5.21% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.05% 28.24% 414ms 5.13% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.24% 400ms 4.95% std::_Rb_tree::_M_create_node (inline) 0 0% 28.24% 376ms 4.66% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.099% 28.34% 367ms 4.55% Cell::GetMutationState 0 0% 28.34% 361ms 4.47% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.012% 28.35% 359ms 4.45% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.35% 357ms 4.42% std::_Rb_tree::_M_get_node (inline) 18ms 0.22% 28.58% 355ms 4.40% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.58% 354ms 4.38% OutputFileHandler::OpenOutputFile 2ms 0.025% 28.60% 346ms 4.29% NodeLocationWriter::Visit 103ms 1.28% 29.88% 339ms 4.20% __GI___libc_free 3ms 0.037% 29.91% 338ms 4.19% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 29.94% 335ms 4.15% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.062% 30.00% 330ms 4.09% std::set::set (inline) 6ms 0.074% 30.08% 322ms 3.99% std::less::operator() (inline) 0 0% 30.08% 321ms 3.98% std::_Rb_tree::_M_drop_node (inline) 316ms 3.91% 33.99% 316ms 3.91% std::_Rb_tree::_S_right (inline) 316ms 3.91% 37.90% 316ms 3.91% std::operator< (inline) 4ms 0.05% 37.95% 307ms 3.80% Element::Element 17ms 0.21% 38.16% 306ms 3.79% std::_Rb_tree::_M_insert_ (inline) 7ms 0.087% 38.25% 302ms 3.74% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.087% 38.34% 301ms 3.73% std::__new_allocator::deallocate (inline) 27ms 0.33% 38.67% 300ms 3.72% std::num_put::_M_insert_float 23ms 0.28% 38.96% 299ms 3.70% std::_Rb_tree::_M_copy (inline) 0 0% 38.96% 296ms 3.67% std::allocator_traits::deallocate (inline) 6ms 0.074% 39.03% 281ms 3.48% divconqrecurse 165ms 2.04% 41.08% 274ms 3.39% _int_malloc 76ms 0.94% 42.02% 271ms 3.36% mergehulls 88ms 1.09% 43.11% 266ms 3.29% std::_Rb_tree::_M_clone_node (inline) 3ms 0.037% 43.14% 264ms 3.27% Cell::ReadyToDivide 0 0% 43.14% 259ms 3.21% std::_Rb_tree::_M_put_node (inline) 1ms 0.012% 43.16% 254ms 3.15% CellProliferativeTypesWriter::VisitCell 4ms 0.05% 43.21% 238ms 2.95% std::__cxx11::collate::do_transform 200ms 2.48% 45.68% 236ms 2.92% _int_free 4ms 0.05% 45.73% 231ms 2.86% AbstractCellProperty::IsType (inline) 2ms 0.025% 45.76% 229ms 2.84% __vsnprintf_internal (inline) 0 0% 45.76% 228ms 2.82% ___vsnprintf 17ms 0.21% 45.97% 221ms 2.74% TetrahedralMesh::Clear 36ms 0.45% 46.41% 221ms 2.74% __printf_buffer 0 0% 46.41% 218ms 2.70% Cell::HasCellProperty (inline) 7ms 0.087% 46.50% 217ms 2.69% CellPropertyCollection::HasProperty 9ms 0.11% 46.61% 205ms 2.54% MeshBasedCellPopulation::SpringsEnd (inline) 35ms 0.43% 47.05% 194ms 2.40% TetrahedralMesh::EdgesEnd (partial-inline) 8ms 0.099% 47.14% 191ms 2.37% Element::RegisterWithNodes (inline) 0 0% 47.14% 184ms 2.28% std::basic_ofstream::basic_ofstream (inline) 3ms 0.037% 47.18% 183ms 2.27% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.012% 47.19% 183ms 2.27% std::basic_filebuf::open 0 0% 47.19% 183ms 2.27% std::basic_ofstream::open (inline) 2ms 0.025% 47.22% 181ms 2.24% Node::AddElement 63ms 0.78% 48.00% 178ms 2.20% std::_Rb_tree::_M_get_insert_unique_pos (inline) 39ms 0.48% 48.48% 176ms 2.18% AbstractCellProperty::IsSame 5ms 0.062% 48.54% 176ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.074% 48.62% 164ms 2.03% __printf_fp_l_buffer 0 0% 48.62% 164ms 2.03% __printf_fp_spec (inline) 2ms 0.025% 48.64% 161ms 1.99% OutputFileHandler::OutputFileHandler 0 0% 48.64% 159ms 1.97% OutputFileHandler::CommonConstructor 12ms 0.15% 48.79% 158ms 1.96% AbstractTetrahedralElement::CalculateJacobian 2ms 0.025% 48.82% 156ms 1.93% AbstractCellBasedWriter::CloseFile 0 0% 48.82% 156ms 1.93% AbstractCellPopulation::CloseRoundRobinWritersFiles 85ms 1.05% 49.87% 155ms 1.92% __printf_fp_buffer_1 1ms 0.012% 49.88% 154ms 1.91% std::basic_ofstream::close (inline) 0 0% 49.88% 153ms 1.90% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 49.88% 153ms 1.90% std::basic_filebuf::close 0 0% 49.88% 145ms 1.80% TetrahedralMesh::RefreshJacobianCachedData 98ms 1.21% 51.10% 144ms 1.78% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 51ms 0.63% 51.73% 144ms 1.78% std::__ostream_insert 1ms 0.012% 51.74% 142ms 1.76% Node::~Node 1ms 0.012% 51.75% 141ms 1.75% _IO_new_file_fopen 0 0% 51.75% 141ms 1.75% _IO_new_fopen 0 0% 51.75% 141ms 1.75% __fopen_internal (inline) 0 0% 51.75% 141ms 1.75% std::__basic_file::open 0 0% 51.75% 139ms 1.72% __GI__IO_file_open 1ms 0.012% 51.77% 139ms 1.72% alternateaxes 19ms 0.24% 52.00% 138ms 1.71% boost::detail::shared_count::~shared_count (inline) 0 0% 52.00% 138ms 1.71% boost::shared_ptr::~shared_ptr (inline) 127ms 1.57% 53.57% 138ms 1.71% vertexmedian 43ms 0.53% 54.11% 137ms 1.70% std::num_put::_M_insert_int 32ms 0.4% 54.50% 137ms 1.70% std::type_info::operator== (inline) 10ms 0.12% 54.63% 136ms 1.68% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.63% 135ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 135ms 1.67% 56.30% 135ms 1.67% __GI_fchmodat 0 0% 56.30% 135ms 1.67% std::filesystem::permissions 15ms 0.19% 56.48% 131ms 1.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 60ms 0.74% 57.23% 131ms 1.62% boost::shared_ptr::shared_ptr (inline) 123ms 1.52% 58.75% 123ms 1.52% incircle 15ms 0.19% 58.94% 120ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.037% 58.97% 119ms 1.47% std::operator<< (inline) 0 0% 58.97% 117ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.05% 59.02% 117ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 116ms 1.44% 60.46% 116ms 1.44% __libc_open64 10ms 0.12% 60.58% 115ms 1.42% AbstractTetrahedralElement::RefreshJacobian 109ms 1.35% 61.93% 115ms 1.42% boost::detail::sp_counted_base::release 2ms 0.025% 61.96% 115ms 1.42% boost::numeric::ublas::vector_assign (inline) 3ms 0.037% 62.00% 108ms 1.34% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 62.00% 106ms 1.31% std::_Vector_base::_M_allocate (inline) 5ms 0.062% 62.06% 106ms 1.31% std::vector::push_back (inline) 104ms 1.29% 63.35% 104ms 1.29% std::_Rb_tree_insert_and_rebalance 99ms 1.23% 64.57% 99ms 1.23% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 60ms 0.74% 65.32% 99ms 1.23% std::basic_filebuf::xsputn 7ms 0.087% 65.40% 98ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 98ms 1.21% 66.62% 98ms 1.21% std::_Rb_tree_increment 10ms 0.12% 66.74% 97ms 1.20% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.012% 66.75% 93ms 1.15% std::basic_filebuf::overflow 14ms 0.17% 66.93% 93ms 1.15% std::vector::_M_realloc_insert 1ms 0.012% 66.94% 92ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 92ms 1.14% 68.08% 92ms 1.14% [libchaste_cell_based.so] 92ms 1.14% 69.22% 92ms 1.14% __GI___libc_write 0 0% 69.22% 92ms 1.14% std::__basic_file::xsputn 0 0% 69.22% 92ms 1.14% std::basic_filebuf::_M_convert_to_external 0 0% 69.22% 92ms 1.14% std::basic_filebuf::_M_terminate_output 1ms 0.012% 69.23% 86ms 1.07% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 69.26% 85ms 1.05% std::filesystem::create_directory 4ms 0.05% 69.31% 84ms 1.04% TetrahedralMesh::EdgeIterator::GetNodeB 61ms 0.76% 70.06% 83ms 1.03% malloc_consolidate 43ms 0.53% 70.59% 82ms 1.02% AbstractElement::GetNodeLocation 30ms 0.37% 70.96% 81ms 1.00% boost::numeric::ublas::indexing_vector_assign 3ms 0.037% 71.00% 80ms 0.99% AbstractCellPopulation::GetLocationIndexUsingCell 79ms 0.98% 71.98% 79ms 0.98% std::vector::size (inline) 5ms 0.062% 72.04% 77ms 0.95% TetrahedralMesh::EdgeIterator::GetNodeA 73ms 0.9% 72.95% 73ms 0.9% __GI___fstatat64 1ms 0.012% 72.96% 72ms 0.89% std::filesystem::status 70ms 0.87% 73.83% 71ms 0.88% boost::detail::shared_count::shared_count (inline) 70ms 0.87% 74.69% 70ms 0.87% __memcpy_avx_unaligned_erms 51ms 0.63% 75.33% 69ms 0.85% AbstractElement::GetNodeGlobalIndex 2ms 0.025% 75.35% 68ms 0.84% Cell::GetCellId 68ms 0.84% 76.19% 68ms 0.84% counterclockwise 44ms 0.55% 76.74% 68ms 0.84% std::basic_streambuf::xsputn 35ms 0.43% 77.17% 66ms 0.82% AbstractTetrahedralMesh::GetElement 0 0% 77.17% 66ms 0.82% tcache_get (inline) 66ms 0.82% 77.99% 66ms 0.82% tcache_get_n (inline) 65ms 0.81% 78.79% 65ms 0.81% Node::GetIndex 30ms 0.37% 79.17% 64ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.17% 62ms 0.77% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.17% 62ms 0.77% std::__new_allocator::destroy (inline) 0 0% 79.17% 62ms 0.77% std::allocator_traits::destroy (inline) 46ms 0.57% 79.73% 60ms 0.74% std::num_put::do_put 57ms 0.71% 80.44% 60ms 0.74% vertexsort 0 0% 80.44% 58ms 0.72% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.012% 80.45% 58ms 0.72% std::__basic_file::close 1ms 0.012% 80.47% 57ms 0.71% _IO_new_fclose 2ms 0.025% 80.49% 55ms 0.68% Node::ClearAppliedForce 7ms 0.087% 80.58% 54ms 0.67% CellPropertyCollection::AddProperty 0 0% 80.58% 54ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 2ms 0.025% 80.60% 54ms 0.67% Node::ConstructNodeAttributes (inline) 24ms 0.3% 80.90% 53ms 0.66% AbstractCellCycleModel::GetAge 0 0% 80.90% 50ms 0.62% BoundaryNodeWriter::Visit 0 0% 80.90% 50ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.012% 80.91% 50ms 0.62% _IO_new_file_close_it 0 0% 80.91% 50ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.91% 50ms 0.62% std::vector::vector (inline) 49ms 0.61% 81.52% 49ms 0.61% [libchaste_mesh.so] 49ms 0.61% 82.13% 49ms 0.61% __GI___close_nocancel 0 0% 82.13% 48ms 0.59% std::__new_allocator::construct (inline) 0 0% 82.13% 48ms 0.59% std::allocator_traits::construct (inline) 16ms 0.2% 82.32% 47ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 0 0% 82.32% 46ms 0.57% std::_Vector_base::_Vector_base (inline) 0 0% 82.32% 45ms 0.56% CellPropertyCollection::~CellPropertyCollection (inline) 9ms 0.11% 82.44% 45ms 0.56% Inverse 0 0% 82.44% 45ms 0.56% _dl_init 0 0% 82.44% 45ms 0.56% call_init (inline) 0 0% 82.44% 44ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 16ms 0.2% 82.63% 44ms 0.55% Determinant (inline) 44ms 0.55% 83.18% 44ms 0.55% [libstdc++.so.6.0.33] 1ms 0.012% 83.19% 44ms 0.55% std::_Vector_base::_M_create_storage (inline) 43ms 0.53% 83.72% 43ms 0.53% __GI___mkdir 0 0% 83.72% 43ms 0.53% std::_Rb_tree::_M_construct_node (inline) 41ms 0.51% 84.23% 41ms 0.51% Node::IsDeleted 41ms 0.51% 84.74% 41ms 0.51% boost::shared_ptr::operator-> (inline) 5ms 0.062% 84.80% 41ms 0.51% std::_Vector_base::_M_deallocate (inline) 1ms 0.012% 84.81% 41ms 0.51% std::__copy_move::__copy_m (inline) 0 0% 84.81% 41ms 0.51% std::__copy_move_a (inline) 0 0% 84.81% 41ms 0.51% std::__copy_move_a1 (inline) 0 0% 84.81% 41ms 0.51% std::__copy_move_a2 (inline) 0 0% 84.81% 41ms 0.51% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 84.81% 41ms 0.51% std::copy (inline)