File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6784ms, 84.66% of 8013ms total Dropped 591 nodes (cum <= 40.06ms) flat flat% sum% cum cum% 0 0% 0% 7977ms 99.55% __libc_start_call_main 0 0% 0% 7977ms 99.55% __libc_start_main_impl 0 0% 0% 7977ms 99.55% _start 0 0% 0% 7962ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7962ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7962ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7962ms 99.36% main 0 0% 0% 7926ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7926ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7926ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 7923ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3382ms 42.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.025% 2920ms 36.44% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.05% 2843ms 35.48% MeshBasedCellPopulation::Update 0 0% 0.05% 1609ms 20.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.075% 1476ms 18.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.17% 1411ms 17.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.012% 0.19% 1393ms 17.38% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.19% 1382ms 17.25% MutableMesh::ReMesh 23ms 0.29% 0.47% 1230ms 15.35% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.037% 0.51% 1027ms 12.82% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 428ms 5.34% 5.85% 1004ms 12.53% std::_Rb_tree::_M_lower_bound (inline) 96ms 1.20% 7.05% 1000ms 12.48% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.012% 7.06% 988ms 12.33% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.15% 7.21% 983ms 12.27% CellPropertyCollection::GetPropertiesType (inline) 262ms 3.27% 10.48% 945ms 11.79% __dynamic_cast 14ms 0.17% 10.66% 932ms 11.63% CellPopulationElementWriter::Visit 47ms 0.59% 11.24% 871ms 10.87% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.037% 11.28% 838ms 10.46% MeshBasedCellPopulation::AcceptCellWriter 29ms 0.36% 11.64% 800ms 9.98% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.062% 11.71% 765ms 9.55% AbstractCellProperty::IsSubType (inline) 9ms 0.11% 11.82% 684ms 8.54% TetrahedralMesh::ImportFromMesher 52ms 0.65% 12.47% 632ms 7.89% std::map::operator[] (partial-inline) 4ms 0.05% 12.52% 585ms 7.30% Cell::GetCellProliferativeType 567ms 7.08% 19.59% 567ms 7.08% __strcmp_avx2 54ms 0.67% 20.27% 564ms 7.04% operator new 3ms 0.037% 20.30% 564ms 7.04% std::ostream::operator<< (inline) 74ms 0.92% 21.23% 561ms 7.00% std::ostream::_M_insert 4ms 0.05% 21.28% 557ms 6.95% triangulate 7ms 0.087% 21.37% 546ms 6.81% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 21.37% 529ms 6.60% std::_Rb_tree::lower_bound (inline) 0 0% 21.37% 529ms 6.60% std::map::lower_bound (inline) 9ms 0.11% 21.48% 528ms 6.59% std::set::insert (inline) 20ms 0.25% 21.73% 527ms 6.58% std::_Rb_tree::find (inline) 4ms 0.05% 21.78% 523ms 6.53% AbstractCellBasedSimulation::DoCellBirth 10ms 0.12% 21.90% 519ms 6.48% std::_Rb_tree::_M_insert_unique 31ms 0.39% 22.29% 513ms 6.40% std::__new_allocator::allocate (inline) 170ms 2.12% 24.41% 510ms 6.36% __GI___libc_malloc 0 0% 24.41% 507ms 6.33% std::allocator_traits::allocate (inline) 0 0% 24.41% 479ms 5.98% delaunay 2ms 0.025% 24.44% 479ms 5.98% divconqdelaunay 0 0% 24.44% 477ms 5.95% std::set::count (inline) 228ms 2.85% 27.28% 472ms 5.89% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.28% 434ms 5.42% std::_Rb_tree::_M_create_node (inline) 0 0% 27.28% 412ms 5.14% std::_Rb_tree::_Alloc_node::operator() (inline) 35ms 0.44% 27.72% 409ms 5.10% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.72% 399ms 4.98% std::_Rb_tree::_M_get_node (inline) 0 0% 27.72% 398ms 4.97% Cell::GetMutationState 16ms 0.2% 27.92% 383ms 4.78% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.075% 27.99% 381ms 4.75% Cell::ReadyToDivide 0 0% 27.99% 381ms 4.75% std::set::~set (inline) 67ms 0.84% 28.83% 374ms 4.67% std::_Rb_tree::_M_erase 17ms 0.21% 29.04% 367ms 4.58% std::less::operator() (inline) 2ms 0.025% 29.07% 359ms 4.48% std::set::set (inline) 352ms 4.39% 33.46% 352ms 4.39% std::_Rb_tree::_S_right (inline) 350ms 4.37% 37.83% 350ms 4.37% std::operator< (inline) 42ms 0.52% 38.35% 343ms 4.28% std::_Rb_tree::_M_copy (inline) 22ms 0.27% 38.62% 340ms 4.24% std::_Rb_tree::_M_insert_ (inline) 0 0% 38.62% 330ms 4.12% MeshBasedCellPopulation::GetDampingConstant 1ms 0.012% 38.64% 329ms 4.11% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.012% 38.65% 323ms 4.03% NodeLocationWriter::Visit 11ms 0.14% 38.79% 322ms 4.02% AbstractCellPopulation::IsCellAttachedToLocationIndex 118ms 1.47% 40.26% 301ms 3.76% __GI___libc_free 97ms 1.21% 41.47% 300ms 3.74% std::_Rb_tree::_M_clone_node (inline) 1ms 0.012% 41.48% 296ms 3.69% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 41.48% 295ms 3.68% AbstractCellBasedWriter::OpenOutputFileForAppend 27ms 0.34% 41.82% 293ms 3.66% std::num_put::_M_insert_float 7ms 0.087% 41.91% 291ms 3.63% Element::Element 0 0% 41.91% 291ms 3.63% OutputFileHandler::OpenOutputFile 1ms 0.012% 41.92% 287ms 3.58% AbstractCellProperty::IsType (inline) 0 0% 41.92% 278ms 3.47% std::_Rb_tree::_M_drop_node (inline) 5ms 0.062% 41.98% 271ms 3.38% CellPropertyCollection::HasProperty 0 0% 41.98% 269ms 3.36% Cell::HasCellProperty (inline) 17ms 0.21% 42.19% 269ms 3.36% divconqrecurse 10ms 0.12% 42.32% 265ms 3.31% std::__new_allocator::deallocate (inline) 0 0% 42.32% 261ms 3.26% std::allocator_traits::deallocate (inline) 173ms 2.16% 44.48% 258ms 3.22% _int_malloc 5ms 0.062% 44.54% 257ms 3.21% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.062% 44.60% 256ms 3.19% CellProliferativeTypesWriter::VisitCell 13ms 0.16% 44.76% 245ms 3.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 67ms 0.84% 45.60% 240ms 3.00% mergehulls 56ms 0.7% 46.30% 224ms 2.80% AbstractCellProperty::IsSame 6ms 0.075% 46.37% 224ms 2.80% std::__cxx11::collate::do_transform 0 0% 46.37% 217ms 2.71% std::_Rb_tree::_M_put_node (inline) 4ms 0.05% 46.42% 210ms 2.62% ___vsnprintf 0 0% 46.42% 206ms 2.57% __vsnprintf_internal (inline) 20ms 0.25% 46.67% 200ms 2.50% __printf_buffer 5ms 0.062% 46.74% 199ms 2.48% Element::RegisterWithNodes (inline) 4ms 0.05% 46.79% 190ms 2.37% Node::AddElement 157ms 1.96% 48.75% 183ms 2.28% _int_free 11ms 0.14% 48.88% 181ms 2.26% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.25% 49.13% 181ms 2.26% TetrahedralMesh::Clear 63ms 0.79% 49.92% 170ms 2.12% std::_Rb_tree::_M_get_insert_unique_pos (inline) 36ms 0.45% 50.37% 168ms 2.10% std::type_info::operator== (inline) 1ms 0.012% 50.38% 166ms 2.07% __printf_fp_spec (inline) 4ms 0.05% 50.43% 165ms 2.06% __printf_fp_l_buffer 91ms 1.14% 51.57% 156ms 1.95% __printf_fp_buffer_1 6ms 0.075% 51.64% 156ms 1.95% boost::numeric::ublas::vector_assign (inline) 6ms 0.075% 51.72% 147ms 1.83% boost::numeric::ublas::c_vector::c_vector (inline) 33ms 0.41% 52.13% 145ms 1.81% TetrahedralMesh::EdgesEnd (partial-inline) 15ms 0.19% 52.31% 143ms 1.78% AbstractTetrahedralElement::CalculateJacobian 1ms 0.012% 52.33% 142ms 1.77% OutputFileHandler::CommonConstructor 0 0% 52.33% 142ms 1.77% OutputFileHandler::OutputFileHandler 0 0% 52.33% 140ms 1.75% std::basic_ofstream::basic_ofstream (inline) 64ms 0.8% 53.13% 138ms 1.72% std::__ostream_insert 0 0% 53.13% 136ms 1.70% std::basic_filebuf::open 0 0% 53.13% 136ms 1.70% std::basic_ofstream::open (inline) 37ms 0.46% 53.59% 136ms 1.70% std::num_put::_M_insert_int 1ms 0.012% 53.60% 134ms 1.67% OutputFileHandler::MakeFoldersAndReturnFullPath 16ms 0.2% 53.80% 133ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 53.80% 133ms 1.66% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 53.83% 128ms 1.60% alternateaxes 116ms 1.45% 55.27% 126ms 1.57% vertexmedian 15ms 0.19% 55.46% 125ms 1.56% std::_Rb_tree_const_iterator::operator++ (inline) 124ms 1.55% 57.01% 124ms 1.55% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 57.02% 120ms 1.50% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.012% 57.03% 120ms 1.50% TetrahedralMesh::RefreshJacobianCachedData 0 0% 57.03% 119ms 1.49% FilesystemPermissions::SetFilePermissions (inline) 119ms 1.49% 58.52% 119ms 1.49% __GI_fchmodat 0 0% 58.52% 119ms 1.49% std::filesystem::permissions 6ms 0.075% 58.59% 119ms 1.49% std::operator<< (inline) 0 0% 58.59% 118ms 1.47% AbstractCellBasedWriter::CloseFile 1ms 0.012% 58.60% 118ms 1.47% std::basic_ofstream::close (inline) 1ms 0.012% 58.62% 117ms 1.46% std::basic_filebuf::close 114ms 1.42% 60.04% 114ms 1.42% std::_Rb_tree_increment 112ms 1.40% 61.44% 113ms 1.41% boost::detail::sp_counted_base::release 1ms 0.012% 61.45% 112ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.05% 61.50% 112ms 1.40% AbstractTetrahedralElement::CalculateInverseJacobian 35ms 0.44% 61.94% 112ms 1.40% boost::numeric::ublas::indexing_vector_assign 20ms 0.25% 62.19% 111ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 109ms 1.36% 63.55% 109ms 1.36% incircle 1ms 0.012% 63.56% 109ms 1.36% std::_Vector_base::_M_allocate (inline) 0 0% 63.56% 107ms 1.34% _IO_new_fopen 0 0% 63.56% 107ms 1.34% __fopen_internal (inline) 0 0% 63.56% 107ms 1.34% std::__basic_file::open 22ms 0.27% 63.83% 105ms 1.31% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 63.83% 105ms 1.31% std::vector::push_back (inline) 0 0% 63.83% 103ms 1.29% _IO_new_file_fopen 1ms 0.012% 63.85% 103ms 1.29% __GI__IO_file_open 7ms 0.087% 63.93% 101ms 1.26% std::vector::_M_realloc_insert 8ms 0.1% 64.03% 100ms 1.25% AbstractTetrahedralElement::RefreshJacobian 7ms 0.087% 64.12% 100ms 1.25% Node::~Node 3ms 0.037% 64.16% 97ms 1.21% AbstractTetrahedralElement::AbstractTetrahedralElement 61ms 0.76% 64.92% 97ms 1.21% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 95ms 1.19% 66.11% 95ms 1.19% __libc_open64 43ms 0.54% 66.64% 90ms 1.12% boost::shared_ptr::shared_ptr (inline) 1ms 0.012% 66.65% 88ms 1.10% std::basic_filebuf::_M_terminate_output 1ms 0.012% 66.67% 87ms 1.09% std::__basic_file::xsputn 0 0% 66.67% 87ms 1.09% std::basic_filebuf::_M_convert_to_external 0 0% 66.67% 87ms 1.09% std::basic_filebuf::overflow 1ms 0.012% 66.68% 86ms 1.07% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 85ms 1.06% 67.74% 85ms 1.06% __GI___libc_write 3ms 0.037% 67.78% 84ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.012% 67.79% 84ms 1.05% Cell::GetCellId 84ms 1.05% 68.84% 84ms 1.05% [libchaste_cell_based.so] 50ms 0.62% 69.46% 82ms 1.02% std::basic_streambuf::xsputn 37ms 0.46% 69.92% 77ms 0.96% AbstractElement::GetNodeLocation 77ms 0.96% 70.88% 77ms 0.96% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 70.88% 76ms 0.95% tcache_get (inline) 76ms 0.95% 71.83% 76ms 0.95% tcache_get_n (inline) 0 0% 71.83% 75ms 0.94% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.83% 72ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 71.83% 72ms 0.9% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.83% 72ms 0.9% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 43ms 0.54% 72.37% 72ms 0.9% std::basic_filebuf::xsputn 1ms 0.012% 72.38% 72ms 0.9% std::filesystem::create_directory 54ms 0.67% 73.06% 71ms 0.89% malloc_consolidate 67ms 0.84% 73.89% 67ms 0.84% __memcpy_avx_unaligned_erms 66ms 0.82% 74.72% 66ms 0.82% __GI___fstatat64 0 0% 74.72% 66ms 0.82% std::filesystem::status 62ms 0.77% 75.49% 65ms 0.81% vertexsort 64ms 0.8% 76.29% 64ms 0.8% Node::GetIndex 64ms 0.8% 77.09% 64ms 0.8% std::vector::size (inline) 6ms 0.075% 77.16% 63ms 0.79% CellPropertyCollection::AddProperty 63ms 0.79% 77.95% 63ms 0.79% counterclockwise 0 0% 77.95% 61ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.95% 61ms 0.76% std::__new_allocator::destroy (inline) 0 0% 77.95% 61ms 0.76% std::allocator_traits::destroy (inline) 36ms 0.45% 78.40% 59ms 0.74% boost::numeric::ublas::c_matrix::operator() (partial-inline) 51ms 0.64% 79.03% 58ms 0.72% AbstractElement::GetNodeGlobalIndex 28ms 0.35% 79.38% 58ms 0.72% AbstractTetrahedralMesh::GetElement 6ms 0.075% 79.46% 58ms 0.72% TetrahedralMesh::EdgeIterator::GetNodeB 26ms 0.32% 79.78% 55ms 0.69% AbstractCellCycleModel::GetAge 0 0% 79.78% 55ms 0.69% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 79.78% 55ms 0.69% boost::numeric::ublas::norm_2 (inline) 19ms 0.24% 80.02% 55ms 0.69% boost::numeric::ublas::vector_norm_2::apply (inline) 43ms 0.54% 80.56% 55ms 0.69% std::num_put::do_put 2ms 0.025% 80.58% 53ms 0.66% Node::ConstructNodeAttributes (inline) 53ms 0.66% 81.24% 53ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 81.24% 52ms 0.65% Node::ClearAppliedForce 4ms 0.05% 81.29% 52ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 2ms 0.025% 81.32% 51ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 19ms 0.24% 81.55% 50ms 0.62% AbstractTetrahedralMesh::GetNumAllElements 49ms 0.61% 82.17% 49ms 0.61% [libchaste_mesh.so] 48ms 0.6% 82.77% 48ms 0.6% boost::numeric::ublas::c_vector::operator() 45ms 0.56% 83.33% 47ms 0.59% boost::detail::shared_count::shared_count (inline) 4ms 0.05% 83.38% 46ms 0.57% std::_Vector_base::_M_deallocate (inline) 46ms 0.57% 83.95% 46ms 0.57% std::ostream::sentry::sentry 0 0% 83.95% 45ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.95% 45ms 0.56% std::map::find (inline) 44ms 0.55% 84.50% 44ms 0.55% Node::IsDeleted 0 0% 84.50% 44ms 0.55% std::vector::vector (inline) 0 0% 84.50% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.05% 84.55% 43ms 0.54% NodeAttributes::NodeAttributes 9ms 0.11% 84.66% 42ms 0.52% Determinant (inline) 0 0% 84.66% 42ms 0.52% std::_Vector_base::_Vector_base (inline)