File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6749ms, 85.78% of 7868ms total Dropped 583 nodes (cum <= 39.34ms) flat flat% sum% cum cum% 0 0% 0% 7834ms 99.57% __libc_start_call_main 0 0% 0% 7834ms 99.57% __libc_start_main_impl 0 0% 0% 7834ms 99.57% _start 0 0% 0% 7819ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7819ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7819ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7819ms 99.38% main 0 0% 0% 7782ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7782ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7782ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7780ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0% 3386ms 43.04% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2920ms 37.11% MeshBasedCellPopulation::Update 0 0% 0.025% 2878ms 36.58% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.051% 1508ms 19.17% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1460ms 18.56% MutableMesh::ReMesh 1ms 0.013% 0.064% 1410ms 17.92% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.051% 0.11% 1378ms 17.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.076% 0.19% 1321ms 16.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.17% 0.36% 1234ms 15.68% MeshBasedCellPopulation::SpringIterator::operator++ 132ms 1.68% 2.03% 1027ms 13.05% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.051% 2.08% 934ms 11.87% AbstractTwoBodyInteractionForce::AddForceContribution 447ms 5.68% 7.77% 924ms 11.74% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 7.80% 922ms 11.72% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 6ms 0.076% 7.88% 913ms 11.60% CellPopulationElementWriter::Visit 262ms 3.33% 11.21% 888ms 11.29% __dynamic_cast 11ms 0.14% 11.35% 880ms 11.18% CellPropertyCollection::GetPropertiesType (inline) 23ms 0.29% 11.64% 821ms 10.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.025% 11.67% 775ms 9.85% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 12.01% 734ms 9.33% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 12.13% 729ms 9.27% TetrahedralMesh::ImportFromMesher 4ms 0.051% 12.18% 692ms 8.80% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 12.20% 583ms 7.41% std::ostream::operator<< (inline) 84ms 1.07% 13.27% 579ms 7.36% std::ostream::_M_insert 48ms 0.61% 13.88% 571ms 7.26% operator new 2ms 0.025% 13.90% 554ms 7.04% triangulate 38ms 0.48% 14.39% 546ms 6.94% std::map::operator[] (partial-inline) 8ms 0.1% 14.49% 534ms 6.79% Cell::GetCellProliferativeType 23ms 0.29% 14.78% 518ms 6.58% std::_Rb_tree::find (inline) 9ms 0.11% 14.90% 518ms 6.58% std::set::insert (inline) 170ms 2.16% 17.06% 517ms 6.57% __GI___libc_malloc 36ms 0.46% 17.51% 517ms 6.57% std::__new_allocator::allocate (inline) 0 0% 17.51% 512ms 6.51% std::allocator_traits::allocate (inline) 13ms 0.17% 17.68% 509ms 6.47% std::_Rb_tree::_M_insert_unique 2ms 0.025% 17.70% 493ms 6.27% delaunay 2ms 0.025% 17.73% 490ms 6.23% divconqdelaunay 488ms 6.20% 23.93% 488ms 6.20% __strcmp_avx2 0 0% 23.93% 475ms 6.04% std::set::count (inline) 3ms 0.038% 23.97% 470ms 5.97% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.97% 465ms 5.91% std::_Rb_tree::lower_bound (inline) 0 0% 23.97% 465ms 5.91% std::map::lower_bound (inline) 213ms 2.71% 26.68% 460ms 5.85% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.68% 456ms 5.80% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.68% 425ms 5.40% std::_Rb_tree::_M_create_node (inline) 0 0% 26.68% 409ms 5.20% std::_Rb_tree::_Alloc_node::operator() (inline) 22ms 0.28% 26.96% 396ms 5.03% std::_Rb_tree::_Rb_tree (partial-inline) 35ms 0.44% 27.40% 389ms 4.94% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.051% 27.45% 377ms 4.79% NodeLocationWriter::Visit 0 0% 27.45% 377ms 4.79% std::_Rb_tree::_M_get_node (inline) 0 0% 27.45% 368ms 4.68% std::set::~set (inline) 2ms 0.025% 27.48% 361ms 4.59% std::set::set (inline) 3ms 0.038% 27.52% 348ms 4.42% Cell::GetMutationState 76ms 0.97% 28.48% 347ms 4.41% std::_Rb_tree::_M_erase 44ms 0.56% 29.04% 341ms 4.33% std::_Rb_tree::_M_copy (inline) 10ms 0.13% 29.17% 327ms 4.16% std::less::operator() (inline) 4ms 0.051% 29.22% 325ms 4.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 21ms 0.27% 29.49% 323ms 4.11% std::num_put::_M_insert_float 21ms 0.27% 29.75% 317ms 4.03% std::_Rb_tree::_M_insert_ (inline) 317ms 4.03% 33.78% 317ms 4.03% std::operator< (inline) 2ms 0.025% 33.81% 313ms 3.98% Element::Element 1ms 0.013% 33.82% 310ms 3.94% Cell::ReadyToDivide 0 0% 33.82% 308ms 3.91% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.82% 306ms 3.89% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.038% 33.86% 301ms 3.83% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 33.90% 298ms 3.79% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.013% 33.91% 298ms 3.79% OutputFileHandler::OpenOutputFile 84ms 1.07% 34.98% 292ms 3.71% std::_Rb_tree::_M_clone_node (inline) 291ms 3.70% 38.68% 291ms 3.70% std::_Rb_tree::_S_right (inline) 184ms 2.34% 41.01% 276ms 3.51% _int_malloc 10ms 0.13% 41.14% 276ms 3.51% divconqrecurse 91ms 1.16% 42.30% 271ms 3.44% __GI___libc_free 1ms 0.013% 42.31% 259ms 3.29% CellProliferativeTypesWriter::VisitCell 7ms 0.089% 42.40% 259ms 3.29% std::__cxx11::collate::do_transform 83ms 1.05% 43.45% 256ms 3.25% mergehulls 0 0% 43.45% 252ms 3.20% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.45% 249ms 3.16% ___vsnprintf 0 0% 43.45% 249ms 3.16% __vsnprintf_internal (inline) 20ms 0.25% 43.71% 245ms 3.11% __printf_buffer 11ms 0.14% 43.85% 243ms 3.09% std::__new_allocator::deallocate (inline) 0 0% 43.85% 242ms 3.08% std::allocator_traits::deallocate (inline) 5ms 0.064% 43.91% 233ms 2.96% AbstractCellProperty::IsType (inline) 0 0% 43.91% 228ms 2.90% Cell::HasCellProperty (inline) 3ms 0.038% 43.95% 228ms 2.90% CellPropertyCollection::HasProperty 7ms 0.089% 44.04% 212ms 2.69% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.013% 44.05% 204ms 2.59% __printf_fp_spec (inline) 13ms 0.17% 44.22% 203ms 2.58% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.13% 44.34% 203ms 2.58% __printf_fp_l_buffer 4ms 0.051% 44.40% 197ms 2.50% Element::RegisterWithNodes (inline) 0 0% 44.40% 193ms 2.45% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 44.46% 190ms 2.41% Node::AddElement 106ms 1.35% 45.81% 188ms 2.39% __printf_fp_buffer_1 23ms 0.29% 46.10% 184ms 2.34% TetrahedralMesh::Clear 17ms 0.22% 46.31% 181ms 2.30% AbstractTetrahedralElement::CalculateJacobian 144ms 1.83% 48.14% 180ms 2.29% _int_free 73ms 0.93% 49.07% 179ms 2.28% std::_Rb_tree::_M_get_insert_unique_pos (inline) 45ms 0.57% 49.64% 164ms 2.08% AbstractCellProperty::IsSame 6ms 0.076% 49.72% 157ms 2.00% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 49.72% 153ms 1.94% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 49.73% 152ms 1.93% OutputFileHandler::OutputFileHandler 47ms 0.6% 50.33% 152ms 1.93% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.33% 151ms 1.92% OutputFileHandler::CommonConstructor 79ms 1.00% 51.33% 145ms 1.84% std::__ostream_insert 4ms 0.051% 51.39% 143ms 1.82% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 51.39% 142ms 1.80% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.39% 141ms 1.79% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.038% 51.42% 138ms 1.75% std::_Vector_base::_M_allocate (inline) 0 0% 51.42% 138ms 1.75% std::basic_ofstream::open (inline) 0 0% 51.42% 136ms 1.73% FilesystemPermissions::SetFilePermissions (inline) 136ms 1.73% 53.15% 136ms 1.73% __GI_fchmodat 0 0% 53.15% 136ms 1.73% std::filesystem::permissions 1ms 0.013% 53.16% 135ms 1.72% std::basic_filebuf::open 3ms 0.038% 53.20% 131ms 1.66% boost::numeric::ublas::vector_assign (inline) 2ms 0.025% 53.23% 130ms 1.65% alternateaxes 19ms 0.24% 53.47% 129ms 1.64% AbstractTetrahedralElement::RefreshJacobian 63ms 0.8% 54.27% 127ms 1.61% boost::shared_ptr::shared_ptr (inline) 119ms 1.51% 55.78% 127ms 1.61% vertexmedian 10ms 0.13% 55.91% 126ms 1.60% std::vector::push_back (inline) 0 0% 55.91% 121ms 1.54% AbstractCellPopulation::CloseRoundRobinWritersFiles 6ms 0.076% 55.99% 121ms 1.54% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 56.02% 120ms 1.53% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.089% 56.11% 120ms 1.53% boost::detail::shared_count::~shared_count (inline) 0 0% 56.11% 120ms 1.53% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 56.14% 119ms 1.51% AbstractCellBasedWriter::CloseFile 25ms 0.32% 56.46% 119ms 1.51% std::type_info::operator== (inline) 1ms 0.013% 56.47% 118ms 1.50% std::basic_filebuf::close 0 0% 56.47% 117ms 1.49% std::basic_ofstream::close (inline) 16ms 0.2% 56.67% 116ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 56.67% 112ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.33% 57.00% 111ms 1.41% std::num_put::_M_insert_int 8ms 0.1% 57.10% 111ms 1.41% std::vector::_M_realloc_insert 12ms 0.15% 57.26% 110ms 1.40% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 57.28% 110ms 1.40% std::operator<< (inline) 108ms 1.37% 58.66% 108ms 1.37% boost::detail::sp_counted_base::release 107ms 1.36% 60.02% 107ms 1.36% std::_Rb_tree_increment 4ms 0.051% 60.07% 106ms 1.35% Node::~Node 13ms 0.17% 60.23% 105ms 1.33% MeshBasedCellPopulation::SpringIterator::SpringIterator 104ms 1.32% 61.55% 104ms 1.32% [libchaste_cell_based.so] 104ms 1.32% 62.87% 104ms 1.32% incircle 104ms 1.32% 64.20% 104ms 1.32% std::_Rb_tree_insert_and_rebalance 24ms 0.31% 64.50% 98ms 1.25% boost::numeric::ublas::indexing_vector_assign 46ms 0.58% 65.09% 97ms 1.23% AbstractElement::GetNodeLocation 2ms 0.025% 65.11% 96ms 1.22% std::__basic_file::open 1ms 0.013% 65.12% 95ms 1.21% std::basic_filebuf::overflow 92ms 1.17% 66.29% 94ms 1.19% __GI___libc_write 0 0% 66.29% 94ms 1.19% std::__basic_file::xsputn 0 0% 66.29% 94ms 1.19% std::basic_filebuf::_M_convert_to_external 0 0% 66.29% 94ms 1.19% std::basic_filebuf::_M_terminate_output 0 0% 66.29% 92ms 1.17% _IO_new_fopen 0 0% 66.29% 92ms 1.17% __fopen_internal (inline) 58ms 0.74% 67.03% 89ms 1.13% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 67.03% 89ms 1.13% _IO_new_file_fopen 0 0% 67.03% 88ms 1.12% __GI__IO_file_open 2ms 0.025% 67.06% 87ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 67.08% 85ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 85ms 1.08% 68.16% 85ms 1.08% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 68.16% 81ms 1.03% Cell::GetCellId 58ms 0.74% 68.90% 79ms 1.00% malloc_consolidate 77ms 0.98% 69.88% 77ms 0.98% __libc_open64 2ms 0.025% 69.90% 77ms 0.98% std::filesystem::status 0 0% 69.90% 75ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 69.90% 75ms 0.95% std::filesystem::create_directory 74ms 0.94% 70.84% 74ms 0.94% Node::GetIndex 74ms 0.94% 71.78% 74ms 0.94% __GI___fstatat64 68ms 0.86% 72.65% 73ms 0.93% vertexsort 70ms 0.89% 73.54% 70ms 0.89% counterclockwise 5ms 0.064% 73.60% 69ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 54ms 0.69% 74.29% 69ms 0.88% std::basic_streambuf::xsputn 2ms 0.025% 74.31% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 66ms 0.84% 75.15% 66ms 0.84% std::vector::size (inline) 0 0% 75.15% 65ms 0.83% tcache_get (inline) 65ms 0.83% 75.98% 65ms 0.83% tcache_get_n (inline) 63ms 0.8% 76.78% 64ms 0.81% boost::detail::shared_count::shared_count (inline) 31ms 0.39% 77.17% 64ms 0.81% std::basic_filebuf::xsputn 0 0% 77.17% 64ms 0.81% std::vector::vector (inline) 4ms 0.051% 77.22% 63ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 33ms 0.42% 77.64% 61ms 0.78% AbstractTetrahedralMesh::GetElement 47ms 0.6% 78.24% 61ms 0.78% std::num_put::do_put 0 0% 78.24% 59ms 0.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.24% 59ms 0.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.24% 59ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.24% 59ms 0.75% std::__new_allocator::destroy (inline) 0 0% 78.24% 59ms 0.75% std::allocator_traits::destroy (inline) 45ms 0.57% 78.81% 58ms 0.74% AbstractElement::GetNodeGlobalIndex 9ms 0.11% 78.93% 58ms 0.74% CellPropertyCollection::AddProperty 56ms 0.71% 79.64% 56ms 0.71% [libchaste_mesh.so] 0 0% 79.64% 55ms 0.7% std::_Vector_base::_Vector_base (inline) 7ms 0.089% 79.73% 54ms 0.69% Node::ConstructNodeAttributes (inline) 52ms 0.66% 80.39% 52ms 0.66% __memcpy_avx_unaligned_erms 52ms 0.66% 81.05% 52ms 0.66% boost::shared_ptr::operator-> (inline) 2ms 0.025% 81.08% 52ms 0.66% std::__new_allocator::construct (inline) 0 0% 81.08% 52ms 0.66% std::allocator_traits::construct (inline) 0 0% 81.08% 51ms 0.65% std::_Vector_base::_M_create_storage (inline) 5ms 0.064% 81.14% 51ms 0.65% std::_Vector_base::_M_deallocate (inline) 0 0% 81.14% 50ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.14% 48ms 0.61% Node::ClearAppliedForce 48ms 0.61% 81.75% 48ms 0.61% Node::IsDeleted 0 0% 81.75% 48ms 0.61% std::_Rb_tree::_M_construct_node (inline) 24ms 0.31% 82.05% 47ms 0.6% AbstractMesh::GetNode 34ms 0.43% 82.49% 47ms 0.6% boost::numeric::ublas::c_matrix::operator() 15ms 0.19% 82.68% 46ms 0.58% Determinant (inline) 0 0% 82.68% 46ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 82.68% 46ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 45ms 0.57% 83.25% 45ms 0.57% [libstdc++.so.6.0.33] 0 0% 83.25% 45ms 0.57% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 83.43% 45ms 0.57% boost::numeric::ublas::vector_norm_2::apply (inline) 33ms 0.42% 83.85% 45ms 0.57% hack_digit 23ms 0.29% 84.14% 44ms 0.56% AbstractCellCycleModel::GetAge 0 0% 84.14% 44ms 0.56% BoundaryNodeWriter::Visit 44ms 0.56% 84.70% 44ms 0.56% Node::rGetLocation 2ms 0.025% 84.72% 43ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 43ms 0.55% 85.27% 43ms 0.55% std::ostream::sentry::sentry 0 0% 85.27% 41ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline) 40ms 0.51% 85.78% 40ms 0.51% boost::numeric::ublas::c_vector::operator()