File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6391ms, 84.40% of 7572ms total Dropped 552 nodes (cum <= 37.86ms) flat flat% sum% cum cum% 0 0% 0% 7538ms 99.55% __libc_start_call_main 0 0% 0% 7538ms 99.55% __libc_start_main_impl 0 0% 0% 7538ms 99.55% _start 0 0% 0% 7523ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7523ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7523ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7523ms 99.35% main 0 0% 0% 7489ms 98.90% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7489ms 98.90% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7489ms 98.90% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7487ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3247ms 42.88% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2812ms 37.14% MeshBasedCellPopulation::Update 2ms 0.026% 0.04% 2725ms 35.99% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.053% 1505ms 19.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.026% 0.079% 1398ms 18.46% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.079% 1358ms 17.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.079% 1352ms 17.86% MutableMesh::ReMesh 9ms 0.12% 0.2% 1308ms 17.27% AbstractNumericalMethod::ComputeForcesIncludingDamping 11ms 0.15% 0.34% 1201ms 15.86% MeshBasedCellPopulation::SpringIterator::operator++ 464ms 6.13% 6.47% 986ms 13.02% std::_Rb_tree::_M_lower_bound (inline) 115ms 1.52% 7.99% 971ms 12.82% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.04% 8.03% 944ms 12.47% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 6ms 0.079% 8.11% 905ms 11.95% CellPopulationElementWriter::Visit 6ms 0.079% 8.19% 903ms 11.93% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.092% 8.28% 882ms 11.65% CellPropertyCollection::GetPropertiesType (inline) 240ms 3.17% 11.45% 882ms 11.65% __dynamic_cast 30ms 0.4% 11.85% 798ms 10.54% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.026% 11.87% 790ms 10.43% MeshBasedCellPopulation::AcceptCellWriter 24ms 0.32% 12.19% 720ms 9.51% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.16% 12.35% 698ms 9.22% TetrahedralMesh::ImportFromMesher 6ms 0.079% 12.43% 683ms 9.02% AbstractCellProperty::IsSubType (inline) 42ms 0.55% 12.98% 596ms 7.87% std::map::operator[] (partial-inline) 0 0% 12.98% 586ms 7.74% std::ostream::operator<< (inline) 97ms 1.28% 14.26% 585ms 7.73% std::ostream::_M_insert 33ms 0.44% 14.70% 534ms 7.05% operator new 3ms 0.04% 14.74% 521ms 6.88% Cell::GetCellProliferativeType 0 0% 14.74% 513ms 6.77% std::_Rb_tree::lower_bound (inline) 0 0% 14.74% 513ms 6.77% std::map::lower_bound (inline) 18ms 0.24% 14.98% 508ms 6.71% std::_Rb_tree::find (inline) 2ms 0.026% 15.00% 500ms 6.60% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 15.00% 495ms 6.54% triangulate 494ms 6.52% 21.53% 494ms 6.52% __strcmp_avx2 164ms 2.17% 23.69% 491ms 6.48% __GI___libc_malloc 8ms 0.11% 23.80% 489ms 6.46% std::set::insert (inline) 24ms 0.32% 24.12% 486ms 6.42% std::__new_allocator::allocate (inline) 10ms 0.13% 24.25% 481ms 6.35% std::_Rb_tree::_M_insert_unique 0 0% 24.25% 481ms 6.35% std::allocator_traits::allocate (inline) 223ms 2.95% 27.19% 469ms 6.19% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.19% 458ms 6.05% std::set::count (inline) 1ms 0.013% 27.21% 440ms 5.81% delaunay 3ms 0.04% 27.25% 439ms 5.80% divconqdelaunay 4ms 0.053% 27.30% 429ms 5.67% AbstractCellBasedSimulation::DoCellBirth 25ms 0.33% 27.63% 420ms 5.55% std::_Rb_tree::~_Rb_tree (inline) 78ms 1.03% 28.66% 392ms 5.18% std::_Rb_tree::_M_erase 0 0% 28.66% 390ms 5.15% std::set::~set (inline) 0 0% 28.66% 389ms 5.14% std::_Rb_tree::_M_create_node (inline) 0 0% 28.66% 367ms 4.85% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.026% 28.68% 359ms 4.74% Cell::GetMutationState 0 0% 28.68% 349ms 4.61% std::_Rb_tree::_M_get_node (inline) 12ms 0.16% 28.84% 347ms 4.58% std::less::operator() (inline) 1ms 0.013% 28.86% 343ms 4.53% NodeLocationWriter::Visit 18ms 0.24% 29.09% 340ms 4.49% std::_Rb_tree::_Rb_tree (partial-inline) 335ms 4.42% 33.52% 335ms 4.42% std::operator< (inline) 120ms 1.58% 35.10% 323ms 4.27% __GI___libc_free 5ms 0.066% 35.17% 318ms 4.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 35.18% 305ms 4.03% MeshBasedCellPopulation::GetDampingConstant 0 0% 35.18% 304ms 4.01% AbstractCentreBasedCellPopulation::GetDampingConstant 304ms 4.01% 39.20% 304ms 4.01% std::_Rb_tree::_S_right (inline) 2ms 0.026% 39.22% 303ms 4.00% std::set::set (inline) 16ms 0.21% 39.43% 302ms 3.99% std::num_put::_M_insert_float 0 0% 39.43% 298ms 3.94% std::_Rb_tree::_M_drop_node (inline) 36ms 0.48% 39.91% 295ms 3.90% std::_Rb_tree::_M_copy (inline) 9ms 0.12% 40.03% 292ms 3.86% std::__new_allocator::deallocate (inline) 26ms 0.34% 40.37% 289ms 3.82% std::_Rb_tree::_M_insert_ (inline) 0 0% 40.37% 289ms 3.82% std::allocator_traits::deallocate (inline) 2ms 0.026% 40.40% 287ms 3.79% Cell::ReadyToDivide 4ms 0.053% 40.45% 285ms 3.76% Element::Element 13ms 0.17% 40.62% 256ms 3.38% divconqrecurse 4ms 0.053% 40.68% 253ms 3.34% CellProliferativeTypesWriter::VisitCell 163ms 2.15% 42.83% 250ms 3.30% _int_malloc 79ms 1.04% 43.87% 249ms 3.29% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.87% 249ms 3.29% std::_Rb_tree::_M_put_node (inline) 20ms 0.26% 44.14% 247ms 3.26% std::__cxx11::collate::do_transform 62ms 0.82% 44.96% 238ms 3.14% mergehulls 6ms 0.079% 45.03% 230ms 3.04% CellPropertyCollection::HasProperty 0 0% 45.03% 228ms 3.01% Cell::HasCellProperty (inline) 3ms 0.04% 45.07% 225ms 2.97% AbstractCellProperty::IsType (inline) 1ms 0.013% 45.09% 219ms 2.89% ___vsnprintf 1ms 0.013% 45.10% 218ms 2.88% __vsnprintf_internal (inline) 34ms 0.45% 45.55% 211ms 2.79% __printf_buffer 176ms 2.32% 47.87% 202ms 2.67% _int_free 6ms 0.079% 47.95% 197ms 2.60% AbstractPhaseBasedCellCycleModel::ReadyToDivide 17ms 0.22% 48.18% 197ms 2.60% TetrahedralMesh::Clear 8ms 0.11% 48.28% 191ms 2.52% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.17% 48.45% 189ms 2.50% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 66ms 0.87% 49.33% 182ms 2.40% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.053% 49.38% 177ms 2.34% Element::RegisterWithNodes (inline) 51ms 0.67% 50.05% 176ms 2.32% TetrahedralMesh::EdgesEnd (partial-inline) 33ms 0.44% 50.49% 169ms 2.23% AbstractCellProperty::IsSame 3ms 0.04% 50.53% 169ms 2.23% Node::AddElement 17ms 0.22% 50.75% 163ms 2.15% AbstractTetrahedralElement::CalculateJacobian 2ms 0.026% 50.78% 163ms 2.15% __printf_fp_spec (inline) 6ms 0.079% 50.86% 161ms 2.13% __printf_fp_l_buffer 0 0% 50.86% 148ms 1.95% AbstractCellBasedWriter::CloseFile 0 0% 50.86% 148ms 1.95% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 50.87% 148ms 1.95% std::basic_filebuf::close 0 0% 50.87% 148ms 1.95% std::basic_ofstream::close (inline) 1ms 0.013% 50.88% 145ms 1.91% OutputFileHandler::OutputFileHandler 0 0% 50.88% 145ms 1.91% TetrahedralMesh::RefreshJacobianCachedData 84ms 1.11% 51.99% 145ms 1.91% __printf_fp_buffer_1 0 0% 51.99% 144ms 1.90% OutputFileHandler::CommonConstructor 0 0% 51.99% 141ms 1.86% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 52.01% 140ms 1.85% AbstractCellBasedWriter::OpenOutputFileForAppend 35ms 0.46% 52.47% 140ms 1.85% std::num_put::_M_insert_int 69ms 0.91% 53.38% 137ms 1.81% std::__ostream_insert 1ms 0.013% 53.39% 136ms 1.80% OutputFileHandler::MakeFoldersAndReturnFullPath 35ms 0.46% 53.86% 136ms 1.80% std::type_info::operator== (inline) 0 0% 53.86% 135ms 1.78% OutputFileHandler::OpenOutputFile 1ms 0.013% 53.87% 133ms 1.76% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 53.88% 133ms 1.76% std::_Vector_base::_M_allocate (inline) 0 0% 53.88% 132ms 1.74% std::basic_ofstream::basic_ofstream (inline) 7ms 0.092% 53.98% 131ms 1.73% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.079% 54.05% 128ms 1.69% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 54.07% 128ms 1.69% std::basic_ofstream::open (inline) 0 0% 54.07% 127ms 1.68% std::basic_filebuf::open 14ms 0.18% 54.25% 124ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 8ms 0.11% 54.36% 120ms 1.58% Node::~Node 3ms 0.04% 54.40% 116ms 1.53% alternateaxes 13ms 0.17% 54.57% 114ms 1.51% AbstractTetrahedralElement::RefreshJacobian 105ms 1.39% 55.96% 113ms 1.49% vertexmedian 48ms 0.63% 56.59% 112ms 1.48% boost::shared_ptr::shared_ptr (inline) 16ms 0.21% 56.80% 111ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 56.80% 111ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 111ms 1.47% 58.27% 111ms 1.47% incircle 11ms 0.15% 58.41% 110ms 1.45% boost::detail::shared_count::~shared_count (inline) 0 0% 58.41% 110ms 1.45% boost::shared_ptr::~shared_ptr (inline) 3ms 0.04% 58.45% 108ms 1.43% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.04% 58.49% 108ms 1.43% std::operator<< (inline) 9ms 0.12% 58.61% 107ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 58.62% 107ms 1.41% std::basic_filebuf::_M_terminate_output 105ms 1.39% 60.01% 105ms 1.39% std::_Rb_tree_increment 1ms 0.013% 60.02% 105ms 1.39% std::basic_filebuf::overflow 104ms 1.37% 61.40% 104ms 1.37% __GI___libc_write 0 0% 61.40% 104ms 1.37% std::__basic_file::xsputn 0 0% 61.40% 104ms 1.37% std::basic_filebuf::_M_convert_to_external 4ms 0.053% 61.45% 104ms 1.37% std::vector::push_back (inline) 75ms 0.99% 62.44% 103ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 62.45% 101ms 1.33% std::__basic_file::open 37ms 0.49% 62.94% 99ms 1.31% boost::numeric::ublas::indexing_vector_assign 0 0% 62.94% 98ms 1.29% _IO_new_fopen 0 0% 62.94% 98ms 1.29% __fopen_internal (inline) 97ms 1.28% 64.22% 98ms 1.29% boost::detail::sp_counted_base::release 1ms 0.013% 64.24% 95ms 1.25% _IO_new_file_fopen 5ms 0.066% 64.30% 94ms 1.24% std::vector::_M_realloc_insert 0 0% 64.30% 93ms 1.23% __GI__IO_file_open 4ms 0.053% 64.36% 89ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 86ms 1.14% 65.49% 86ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 86ms 1.14% 66.63% 86ms 1.14% __libc_open64 43ms 0.57% 67.19% 84ms 1.11% AbstractElement::GetNodeLocation 2ms 0.026% 67.22% 83ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 83ms 1.10% 68.32% 83ms 1.10% [libchaste_cell_based.so] 8ms 0.11% 68.42% 82ms 1.08% CellPropertyCollection::AddProperty 61ms 0.81% 69.23% 80ms 1.06% AbstractElement::GetNodeGlobalIndex 43ms 0.57% 69.80% 79ms 1.04% std::basic_filebuf::xsputn 0 0% 69.80% 77ms 1.02% Cell::GetCellId 2ms 0.026% 69.82% 76ms 1.00% std::filesystem::create_directory 75ms 0.99% 70.81% 75ms 0.99% std::vector::size (inline) 3ms 0.04% 70.85% 74ms 0.98% std::filesystem::status 7ms 0.092% 70.95% 73ms 0.96% TetrahedralMesh::EdgeIterator::GetNodeB 3ms 0.04% 70.99% 72ms 0.95% AbstractCellPopulation::GetLocationIndexUsingCell 72ms 0.95% 71.94% 72ms 0.95% __GI___fstatat64 57ms 0.75% 72.69% 72ms 0.95% malloc_consolidate 70ms 0.92% 73.61% 70ms 0.92% std::_Rb_tree_insert_and_rebalance 48ms 0.63% 74.25% 69ms 0.91% std::basic_streambuf::xsputn 68ms 0.9% 75.15% 68ms 0.9% [libchaste_mesh.so] 63ms 0.83% 75.98% 64ms 0.85% boost::detail::shared_count::shared_count (inline) 2ms 0.026% 76.00% 62ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.00% 61ms 0.81% tcache_get (inline) 61ms 0.81% 76.81% 61ms 0.81% tcache_get_n (inline) 59ms 0.78% 77.59% 59ms 0.78% counterclockwise 0 0% 77.59% 57ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 77.59% 56ms 0.74% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 54ms 0.71% 78.30% 56ms 0.74% vertexsort 5ms 0.066% 78.37% 55ms 0.73% Node::ConstructNodeAttributes (inline) 55ms 0.73% 79.09% 55ms 0.73% Node::GetIndex 28ms 0.37% 79.46% 54ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 38ms 0.5% 79.97% 53ms 0.7% std::num_put::do_put 0 0% 79.97% 53ms 0.7% std::vector::vector (inline) 1ms 0.013% 79.98% 52ms 0.69% BoundaryNodeWriter::Visit 2ms 0.026% 80.01% 52ms 0.69% Node::ClearAppliedForce 51ms 0.67% 80.68% 51ms 0.67% [libstdc++.so.6.0.33] 50ms 0.66% 81.34% 50ms 0.66% __memcpy_avx_unaligned_erms 28ms 0.37% 81.71% 49ms 0.65% AbstractCellCycleModel::GetAge 0 0% 81.71% 49ms 0.65% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.71% 49ms 0.65% std::_Vector_base::_Vector_base (inline) 0 0% 81.71% 49ms 0.65% std::__new_allocator::destroy (inline) 0 0% 81.71% 49ms 0.65% std::allocator_traits::destroy (inline) 32ms 0.42% 82.13% 48ms 0.63% AbstractTetrahedralMesh::GetElement 23ms 0.3% 82.44% 48ms 0.63% Determinant (inline) 1ms 0.013% 82.45% 48ms 0.63% std::_Vector_base::_M_create_storage (inline) 0 0% 82.45% 47ms 0.62% AbstractCentreBasedCellPopulation::IsMarkedSpring 46ms 0.61% 83.06% 46ms 0.61% Node::IsDeleted 0 0% 83.06% 45ms 0.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.06% 45ms 0.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 11ms 0.15% 83.20% 44ms 0.58% Inverse 44ms 0.58% 83.78% 44ms 0.58% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 83.78% 44ms 0.58% std::__new_allocator::construct (inline) 0 0% 83.78% 44ms 0.58% std::allocator_traits::construct (inline) 1ms 0.013% 83.80% 42ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.55% 84.35% 42ms 0.55% boost::shared_ptr::operator-> (inline) 2ms 0.026% 84.38% 41ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.026% 84.40% 41ms 0.54% std::_Vector_base::_M_deallocate (inline) 0 0% 84.40% 40ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.40% 40ms 0.53% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.40% 40ms 0.53% std::map::map (inline) 0 0% 84.40% 39ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline)