File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6835ms, 84.88% of 8053ms total Dropped 595 nodes (cum <= 40.27ms) flat flat% sum% cum cum% 0 0% 0% 8015ms 99.53% __libc_start_call_main 0 0% 0% 8015ms 99.53% __libc_start_main_impl 0 0% 0% 8015ms 99.53% _start 0 0% 0% 7996ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7996ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7996ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7996ms 99.29% main 0 0% 0% 7954ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7954ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7953ms 98.76% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7951ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3433ms 42.63% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2997ms 37.22% MeshBasedCellPopulation::Update 1ms 0.012% 0.012% 2992ms 37.15% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.025% 1515ms 18.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.037% 1470ms 18.25% MutableMesh::ReMesh 0 0% 0.037% 1465ms 18.19% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.05% 1355ms 16.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.087% 0.14% 1301ms 16.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 31ms 0.38% 0.52% 1252ms 15.55% MeshBasedCellPopulation::SpringIterator::operator++ 105ms 1.30% 1.83% 1004ms 12.47% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.062% 1.89% 981ms 12.18% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 428ms 5.31% 7.20% 954ms 11.85% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.075% 7.28% 938ms 11.65% CellPopulationElementWriter::Visit 257ms 3.19% 10.47% 932ms 11.57% __dynamic_cast 1ms 0.012% 10.48% 906ms 11.25% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.099% 10.58% 890ms 11.05% CellPropertyCollection::GetPropertiesType (inline) 52ms 0.65% 11.23% 825ms 10.24% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.099% 11.32% 811ms 10.07% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.32% 11.65% 794ms 9.86% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.037% 11.69% 747ms 9.28% AbstractCellProperty::IsSubType (inline) 10ms 0.12% 11.81% 726ms 9.02% TetrahedralMesh::ImportFromMesher 0 0% 11.81% 632ms 7.85% std::ostream::operator<< (inline) 97ms 1.20% 13.01% 630ms 7.82% std::ostream::_M_insert 58ms 0.72% 13.73% 591ms 7.34% std::map::operator[] (partial-inline) 574ms 7.13% 20.86% 574ms 7.13% __strcmp_avx2 1ms 0.012% 20.87% 568ms 7.05% triangulate 4ms 0.05% 20.92% 540ms 6.71% Cell::GetCellProliferativeType 24ms 0.3% 21.22% 538ms 6.68% operator new 3ms 0.037% 21.26% 533ms 6.62% std::set::insert (inline) 7ms 0.087% 21.35% 530ms 6.58% std::_Rb_tree::_M_insert_unique 24ms 0.3% 21.64% 520ms 6.46% std::_Rb_tree::find (inline) 7ms 0.087% 21.73% 510ms 6.33% LegacyCellProliferativeTypesWriter::VisitCell 170ms 2.11% 23.84% 507ms 6.30% __GI___libc_malloc 0 0% 23.84% 493ms 6.12% delaunay 2ms 0.025% 23.87% 492ms 6.11% divconqdelaunay 37ms 0.46% 24.33% 490ms 6.08% std::__new_allocator::allocate (inline) 0 0% 24.33% 486ms 6.04% std::_Rb_tree::lower_bound (inline) 64ms 0.79% 25.12% 486ms 6.04% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.12% 486ms 6.04% std::map::lower_bound (inline) 203ms 2.52% 27.64% 479ms 5.95% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.64% 479ms 5.95% std::allocator_traits::allocate (inline) 0 0% 27.64% 466ms 5.79% std::set::count (inline) 0 0% 27.64% 456ms 5.66% std::set::~set (inline) 0 0% 27.64% 426ms 5.29% std::_Rb_tree::_M_create_node (inline) 2ms 0.025% 27.67% 420ms 5.22% AbstractCellBasedSimulation::DoCellBirth 82ms 1.02% 28.68% 419ms 5.20% std::_Rb_tree::_M_erase 0 0% 28.68% 410ms 5.09% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.68% 389ms 4.83% std::_Rb_tree::_M_get_node (inline) 19ms 0.24% 28.92% 376ms 4.67% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.025% 28.95% 363ms 4.51% NodeLocationWriter::Visit 0 0% 28.95% 351ms 4.36% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.95% 350ms 4.35% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.025% 28.97% 348ms 4.32% Cell::GetMutationState 0 0% 28.97% 346ms 4.30% OutputFileHandler::OpenOutputFile 11ms 0.14% 29.11% 346ms 4.30% std::less::operator() (inline) 2ms 0.025% 29.13% 343ms 4.26% std::set::set (inline) 7ms 0.087% 29.22% 337ms 4.18% Element::Element 335ms 4.16% 33.38% 335ms 4.16% std::operator< (inline) 29ms 0.36% 33.74% 332ms 4.12% std::num_put::_M_insert_float 111ms 1.38% 35.12% 329ms 4.09% __GI___libc_free 29ms 0.36% 35.48% 325ms 4.04% std::_Rb_tree::_M_insert_ (inline) 40ms 0.5% 35.97% 318ms 3.95% std::_Rb_tree::_M_copy (inline) 4ms 0.05% 36.02% 317ms 3.94% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 36.02% 314ms 3.90% std::_Rb_tree::_M_drop_node (inline) 2ms 0.025% 36.05% 313ms 3.89% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 36.05% 313ms 3.89% MeshBasedCellPopulation::GetDampingConstant 311ms 3.86% 39.91% 311ms 3.86% std::_Rb_tree::_S_right (inline) 5ms 0.062% 39.97% 296ms 3.68% Cell::ReadyToDivide 7ms 0.087% 40.06% 293ms 3.64% std::__new_allocator::deallocate (inline) 0 0% 40.06% 289ms 3.59% std::allocator_traits::deallocate (inline) 11ms 0.14% 40.20% 288ms 3.58% divconqrecurse 70ms 0.87% 41.07% 270ms 3.35% mergehulls 83ms 1.03% 42.10% 269ms 3.34% std::_Rb_tree::_M_clone_node (inline) 190ms 2.36% 44.46% 259ms 3.22% _int_malloc 2ms 0.025% 44.48% 258ms 3.20% CellProliferativeTypesWriter::VisitCell 0 0% 44.48% 253ms 3.14% std::_Rb_tree::_M_put_node (inline) 4ms 0.05% 44.53% 252ms 3.13% std::__cxx11::collate::do_transform 4ms 0.05% 44.58% 248ms 3.08% AbstractCellProperty::IsType (inline) 9ms 0.11% 44.69% 246ms 3.05% CellPropertyCollection::HasProperty 0 0% 44.69% 244ms 3.03% Cell::HasCellProperty (inline) 0 0% 44.69% 238ms 2.96% ___vsnprintf 0 0% 44.69% 238ms 2.96% __vsnprintf_internal (inline) 36ms 0.45% 45.14% 237ms 2.94% __printf_buffer 6ms 0.075% 45.21% 222ms 2.76% Element::RegisterWithNodes (inline) 180ms 2.24% 47.45% 217ms 2.69% _int_free 6ms 0.075% 47.52% 212ms 2.63% Node::AddElement 9ms 0.11% 47.63% 209ms 2.60% TetrahedralMesh::Clear 12ms 0.15% 47.78% 207ms 2.57% MeshBasedCellPopulation::SpringsEnd (inline) 78ms 0.97% 48.75% 198ms 2.46% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.05% 48.80% 197ms 2.45% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.062% 48.86% 192ms 2.38% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.11% 48.98% 190ms 2.36% __printf_fp_l_buffer 0 0% 48.98% 190ms 2.36% __printf_fp_spec (inline) 32ms 0.4% 49.37% 186ms 2.31% AbstractCellProperty::IsSame 18ms 0.22% 49.60% 177ms 2.20% AbstractTetrahedralElement::CalculateJacobian 79ms 0.98% 50.58% 174ms 2.16% __printf_fp_buffer_1 0 0% 50.58% 171ms 2.12% std::basic_ofstream::basic_ofstream (inline) 27ms 0.34% 50.91% 167ms 2.07% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.91% 162ms 2.01% std::basic_ofstream::open (inline) 1ms 0.012% 50.93% 161ms 2.00% std::basic_filebuf::open 36ms 0.45% 51.37% 154ms 1.91% std::type_info::operator== (inline) 1ms 0.012% 51.38% 152ms 1.89% AbstractCellBasedWriter::CloseFile 0 0% 51.38% 152ms 1.89% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 51.41% 151ms 1.88% std::basic_filebuf::close 1ms 0.012% 51.42% 151ms 1.88% std::basic_ofstream::close (inline) 0 0% 51.42% 148ms 1.84% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.42% 147ms 1.83% FilesystemPermissions::SetFilePermissions (inline) 0 0% 51.42% 146ms 1.81% std::filesystem::permissions 145ms 1.80% 53.22% 145ms 1.80% __GI_fchmodat 92ms 1.14% 54.36% 142ms 1.76% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.062% 54.43% 138ms 1.71% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.43% 138ms 1.71% alternateaxes 7ms 0.087% 54.51% 137ms 1.70% Node::~Node 119ms 1.48% 55.99% 137ms 1.70% vertexmedian 57ms 0.71% 56.70% 136ms 1.69% std::__ostream_insert 15ms 0.19% 56.89% 132ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 131ms 1.63% 58.51% 131ms 1.63% incircle 0 0% 58.51% 129ms 1.60% std::__basic_file::open 0 0% 58.51% 126ms 1.56% _IO_new_fopen 0 0% 58.51% 126ms 1.56% __fopen_internal (inline) 2ms 0.025% 58.54% 124ms 1.54% _IO_new_file_fopen 23ms 0.29% 58.82% 123ms 1.53% AbstractTetrahedralElement::RefreshJacobian 0 0% 58.82% 122ms 1.51% OutputFileHandler::CommonConstructor 0 0% 58.82% 122ms 1.51% OutputFileHandler::OutputFileHandler 7ms 0.087% 58.91% 122ms 1.51% boost::detail::shared_count::~shared_count (inline) 0 0% 58.91% 122ms 1.51% boost::shared_ptr::~shared_ptr (inline) 30ms 0.37% 59.28% 122ms 1.51% std::num_put::_M_insert_int 0 0% 59.28% 121ms 1.50% OutputFileHandler::MakeFoldersAndReturnFullPath 7ms 0.087% 59.37% 120ms 1.49% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.037% 59.41% 120ms 1.49% __GI__IO_file_open 9ms 0.11% 59.52% 113ms 1.40% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 59.52% 113ms 1.40% std::basic_filebuf::_M_terminate_output 111ms 1.38% 60.90% 112ms 1.39% __GI___libc_write 1ms 0.012% 60.91% 112ms 1.39% std::basic_filebuf::_M_convert_to_external 0 0% 60.91% 112ms 1.39% std::basic_filebuf::overflow 0 0% 60.91% 111ms 1.38% std::__basic_file::xsputn 53ms 0.66% 61.57% 110ms 1.37% boost::shared_ptr::shared_ptr (inline) 109ms 1.35% 62.92% 109ms 1.35% __libc_open64 1ms 0.012% 62.93% 108ms 1.34% std::operator<< (inline) 105ms 1.30% 64.24% 105ms 1.30% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.025% 64.26% 104ms 1.29% boost::numeric::ublas::vector_assign (inline) 102ms 1.27% 65.53% 102ms 1.27% boost::detail::sp_counted_base::release 10ms 0.12% 65.65% 95ms 1.18% AbstractCellPopulation::Iterator::IsRealCell (inline) 95ms 1.18% 66.83% 95ms 1.18% [libchaste_cell_based.so] 0 0% 66.83% 94ms 1.17% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.012% 66.84% 91ms 1.13% std::_Vector_base::_M_allocate (inline) 35ms 0.43% 67.28% 89ms 1.11% AbstractElement::GetNodeLocation 3ms 0.037% 67.32% 88ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.012% 67.33% 88ms 1.09% std::vector::push_back (inline) 0 0% 67.33% 87ms 1.08% Cell::GetCellId 6ms 0.075% 67.40% 85ms 1.06% std::vector::_M_realloc_insert 2ms 0.025% 67.43% 81ms 1.01% TetrahedralMesh::EdgeIterator::GetNodeA 80ms 0.99% 68.42% 80ms 0.99% std::_Rb_tree_insert_and_rebalance 62ms 0.77% 69.19% 79ms 0.98% AbstractElement::GetNodeGlobalIndex 48ms 0.6% 69.79% 79ms 0.98% std::basic_filebuf::xsputn 5ms 0.062% 69.85% 76ms 0.94% std::_Rb_tree_const_iterator::operator++ (inline) 76ms 0.94% 70.79% 76ms 0.94% std::_Rb_tree_increment 0 0% 70.79% 75ms 0.93% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.012% 70.81% 72ms 0.89% AbstractCellPopulation::GetLocationIndexUsingCell 19ms 0.24% 71.04% 72ms 0.89% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 71.07% 72ms 0.89% std::filesystem::status 72ms 0.89% 71.96% 72ms 0.89% std::vector::size (inline) 70ms 0.87% 72.83% 70ms 0.87% Node::GetIndex 70ms 0.87% 73.70% 70ms 0.87% __GI___fstatat64 6ms 0.075% 73.77% 69ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 68ms 0.84% 74.62% 68ms 0.84% counterclockwise 0 0% 74.62% 68ms 0.84% tcache_get (inline) 68ms 0.84% 75.46% 68ms 0.84% tcache_get_n (inline) 1ms 0.012% 75.47% 67ms 0.83% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 75.50% 66ms 0.82% std::filesystem::create_directory 57ms 0.71% 76.21% 65ms 0.81% std::num_put::do_put 28ms 0.35% 76.56% 63ms 0.78% AbstractTetrahedralMesh::GetElement 42ms 0.52% 77.08% 63ms 0.78% malloc_consolidate 0 0% 77.08% 61ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.08% 61ms 0.76% std::__new_allocator::destroy (inline) 0 0% 77.08% 61ms 0.76% std::allocator_traits::destroy (inline) 43ms 0.53% 77.61% 61ms 0.76% std::basic_streambuf::xsputn 8ms 0.099% 77.71% 58ms 0.72% CellPropertyCollection::AddProperty 0 0% 77.71% 57ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 57ms 0.71% 78.42% 57ms 0.71% __memcpy_avx_unaligned_erms 56ms 0.7% 79.11% 57ms 0.71% boost::detail::shared_count::shared_count (inline) 53ms 0.66% 79.77% 56ms 0.7% vertexsort 2ms 0.025% 79.80% 52ms 0.65% Node::ConstructNodeAttributes (inline) 52ms 0.65% 80.44% 52ms 0.65% std::ostream::sentry::sentry 0 0% 80.44% 51ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.012% 80.45% 51ms 0.63% Node::ClearAppliedForce 0 0% 80.45% 51ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 51ms 0.63% 81.09% 51ms 0.63% [libstdc++.so.6.0.33] 0 0% 81.09% 47ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 3ms 0.037% 81.13% 47ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.13% 47ms 0.58% std::map::find (inline) 17ms 0.21% 81.34% 46ms 0.57% Determinant (inline) 31ms 0.38% 81.72% 45ms 0.56% boost::numeric::ublas::c_matrix::operator() 27ms 0.34% 82.06% 45ms 0.56% hack_digit 0 0% 82.06% 44ms 0.55% BoundaryNodeWriter::Visit 44ms 0.55% 82.60% 44ms 0.55% Node::rGetLocation 44ms 0.55% 83.15% 44ms 0.55% [libchaste_mesh.so] 44ms 0.55% 83.70% 44ms 0.55% operator delete 0 0% 83.70% 42ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.70% 42ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 35ms 0.43% 84.13% 42ms 0.52% writeedges 19ms 0.24% 84.37% 41ms 0.51% AbstractCellCycleModel::GetAge 0 0% 84.37% 41ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 41ms 0.51% 84.88% 41ms 0.51% boost::numeric::ublas::c_vector::operator() (inline)