File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6473ms, 85.07% of 7609ms total Dropped 551 nodes (cum <= 38.05ms) flat flat% sum% cum cum% 0 0% 0% 7572ms 99.51% __libc_start_call_main 0 0% 0% 7572ms 99.51% __libc_start_main_impl 0 0% 0% 7572ms 99.51% _start 0 0% 0% 7554ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7554ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7554ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7554ms 99.28% main 0 0% 0% 7512ms 98.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7512ms 98.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7512ms 98.73% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7509ms 98.69% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.026% 3357ms 44.12% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.053% 2962ms 38.93% MeshBasedCellPopulation::Update 0 0% 0.053% 2637ms 34.66% AbstractCellPopulation::WriteResultsToFiles 3ms 0.039% 0.092% 1510ms 19.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.092% 1495ms 19.65% MutableMesh::ReMesh 1ms 0.013% 0.11% 1415ms 18.60% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.11% 1350ms 17.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.12% 1291ms 16.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 18ms 0.24% 0.35% 1207ms 15.86% MeshBasedCellPopulation::SpringIterator::operator++ 117ms 1.54% 1.89% 961ms 12.63% TetrahedralMesh::EdgeIterator::operator++ 248ms 3.26% 5.15% 916ms 12.04% __dynamic_cast 2ms 0.026% 5.18% 903ms 11.87% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.053% 5.23% 885ms 11.63% AbstractTwoBodyInteractionForce::AddForceContribution 422ms 5.55% 10.78% 874ms 11.49% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.12% 10.89% 870ms 11.43% CellPopulationElementWriter::Visit 12ms 0.16% 11.05% 866ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 34ms 0.45% 11.50% 783ms 10.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 9ms 0.12% 11.62% 770ms 10.12% MeshBasedCellPopulation::AcceptCellWriter 16ms 0.21% 11.83% 723ms 9.50% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 11.97% 721ms 9.48% TetrahedralMesh::ImportFromMesher 2ms 0.026% 12.00% 700ms 9.20% AbstractCellProperty::IsSubType (inline) 3ms 0.039% 12.04% 594ms 7.81% triangulate 28ms 0.37% 12.41% 573ms 7.53% operator new 0 0% 12.41% 555ms 7.29% std::ostream::operator<< (inline) 99ms 1.30% 13.71% 554ms 7.28% std::ostream::_M_insert 56ms 0.74% 14.44% 547ms 7.19% std::map::operator[] (partial-inline) 207ms 2.72% 17.16% 541ms 7.11% __GI___libc_malloc 9ms 0.12% 17.28% 538ms 7.07% std::set::insert (inline) 0 0% 17.28% 531ms 6.98% delaunay 2ms 0.026% 17.31% 530ms 6.97% divconqdelaunay 8ms 0.11% 17.41% 529ms 6.95% std::_Rb_tree::_M_insert_unique 520ms 6.83% 24.25% 520ms 6.83% __strcmp_avx2 17ms 0.22% 24.47% 516ms 6.78% std::__new_allocator::allocate (inline) 0 0% 24.47% 507ms 6.66% std::allocator_traits::allocate (inline) 9ms 0.12% 24.59% 497ms 6.53% LegacyCellProliferativeTypesWriter::VisitCell 6ms 0.079% 24.67% 485ms 6.37% Cell::GetCellProliferativeType 227ms 2.98% 27.65% 483ms 6.35% __cxxabiv1::__si_class_type_info::__do_dyncast 14ms 0.18% 27.84% 472ms 6.20% std::_Rb_tree::find (inline) 0 0% 27.84% 436ms 5.73% std::_Rb_tree::lower_bound (inline) 0 0% 27.84% 436ms 5.73% std::map::lower_bound (inline) 0 0% 27.84% 434ms 5.70% std::set::count (inline) 0 0% 27.84% 423ms 5.56% std::_Rb_tree::_M_create_node (inline) 37ms 0.49% 28.32% 420ms 5.52% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.32% 399ms 5.24% std::set::~set (inline) 0 0% 28.32% 396ms 5.20% std::_Rb_tree::_M_get_node (inline) 0 0% 28.32% 393ms 5.16% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.026% 28.35% 388ms 5.10% AbstractCellBasedSimulation::DoCellBirth 2ms 0.026% 28.37% 386ms 5.07% Cell::GetMutationState 86ms 1.13% 29.50% 379ms 4.98% std::_Rb_tree::_M_erase 39ms 0.51% 30.02% 362ms 4.76% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 30.03% 338ms 4.44% NodeLocationWriter::Visit 6ms 0.079% 30.11% 332ms 4.36% Element::Element 10ms 0.13% 30.24% 328ms 4.31% std::less::operator() (inline) 1ms 0.013% 30.25% 321ms 4.22% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 30.27% 320ms 4.21% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.013% 30.28% 319ms 4.19% std::set::set (inline) 318ms 4.18% 34.46% 318ms 4.18% std::operator< (inline) 26ms 0.34% 34.80% 316ms 4.15% std::_Rb_tree::_M_insert_ (inline) 11ms 0.14% 34.95% 292ms 3.84% divconqrecurse 33ms 0.43% 35.38% 290ms 3.81% std::_Rb_tree::_M_copy (inline) 87ms 1.14% 36.52% 286ms 3.76% __GI___libc_free 30ms 0.39% 36.92% 282ms 3.71% std::num_put::_M_insert_float 94ms 1.24% 38.15% 273ms 3.59% mergehulls 0 0% 38.15% 273ms 3.59% std::_Rb_tree::_M_drop_node (inline) 268ms 3.52% 41.67% 268ms 3.52% std::_Rb_tree::_S_right (inline) 6ms 0.079% 41.75% 266ms 3.50% AbstractCellPopulation::IsCellAttachedToLocationIndex 160ms 2.10% 43.86% 254ms 3.34% _int_malloc 8ms 0.11% 43.96% 254ms 3.34% std::__new_allocator::deallocate (inline) 6ms 0.079% 44.04% 252ms 3.31% Cell::ReadyToDivide 0 0% 44.04% 251ms 3.30% std::allocator_traits::deallocate (inline) 62ms 0.81% 44.85% 250ms 3.29% std::_Rb_tree::_M_clone_node (inline) 6ms 0.079% 44.93% 233ms 3.06% std::__cxx11::collate::do_transform 3ms 0.039% 44.97% 231ms 3.04% CellProliferativeTypesWriter::VisitCell 7ms 0.092% 45.07% 227ms 2.98% AbstractCellProperty::IsType (inline) 7ms 0.092% 45.16% 226ms 2.97% CellPropertyCollection::HasProperty 0 0% 45.16% 225ms 2.96% Cell::HasCellProperty (inline) 9ms 0.12% 45.28% 220ms 2.89% Element::RegisterWithNodes (inline) 2ms 0.026% 45.30% 217ms 2.85% ___vsnprintf 0 0% 45.30% 216ms 2.84% std::_Rb_tree::_M_put_node (inline) 0 0% 45.30% 215ms 2.83% __vsnprintf_internal (inline) 29ms 0.38% 45.68% 214ms 2.81% __printf_buffer 8ms 0.11% 45.79% 209ms 2.75% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.039% 45.83% 206ms 2.71% Node::AddElement 74ms 0.97% 46.80% 205ms 2.69% std::_Rb_tree::_M_get_insert_unique_pos (inline) 169ms 2.22% 49.02% 199ms 2.62% _int_free 3ms 0.039% 49.06% 184ms 2.42% AbstractPhaseBasedCellCycleModel::ReadyToDivide 13ms 0.17% 49.23% 183ms 2.41% AbstractTetrahedralElement::CalculateJacobian 12ms 0.16% 49.39% 180ms 2.37% TetrahedralMesh::Clear 5ms 0.066% 49.45% 179ms 2.35% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.026% 49.48% 174ms 2.29% __printf_fp_l_buffer 0 0% 49.48% 174ms 2.29% __printf_fp_spec (inline) 39ms 0.51% 49.99% 170ms 2.23% TetrahedralMesh::EdgesEnd (partial-inline) 95ms 1.25% 51.24% 167ms 2.19% __printf_fp_buffer_1 0 0% 51.24% 161ms 2.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.24% 161ms 2.12% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 38ms 0.5% 51.74% 161ms 2.12% AbstractCellProperty::IsSame 0 0% 51.74% 156ms 2.05% OutputFileHandler::OpenOutputFile 0 0% 51.74% 155ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.74% 154ms 2.02% std::basic_ofstream::basic_ofstream (inline) 2ms 0.026% 51.77% 152ms 2.00% std::basic_filebuf::open 0 0% 51.77% 152ms 2.00% std::basic_ofstream::open (inline) 4ms 0.053% 51.82% 145ms 1.91% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 51.82% 145ms 1.91% OutputFileHandler::CommonConstructor 0 0% 51.82% 145ms 1.91% OutputFileHandler::OutputFileHandler 0 0% 51.82% 145ms 1.91% boost::numeric::ublas::vector_assign (inline) 0 0% 51.82% 143ms 1.88% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 51.83% 142ms 1.87% alternateaxes 5ms 0.066% 51.90% 140ms 1.84% boost::numeric::ublas::c_vector::c_vector (inline) 125ms 1.64% 53.54% 140ms 1.84% vertexmedian 1ms 0.013% 53.56% 138ms 1.81% AbstractCellBasedWriter::CloseFile 0 0% 53.56% 138ms 1.81% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 53.57% 137ms 1.80% std::basic_filebuf::close 0 0% 53.57% 137ms 1.80% std::basic_ofstream::close (inline) 19ms 0.25% 53.82% 133ms 1.75% AbstractTetrahedralElement::RefreshJacobian 41ms 0.54% 54.36% 132ms 1.73% std::__ostream_insert 15ms 0.2% 54.55% 128ms 1.68% boost::detail::shared_count::~shared_count (inline) 0 0% 54.55% 128ms 1.68% boost::shared_ptr::~shared_ptr (inline) 36ms 0.47% 55.03% 125ms 1.64% std::num_put::_M_insert_int 17ms 0.22% 55.25% 124ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 29ms 0.38% 55.63% 123ms 1.62% std::type_info::operator== (inline) 1ms 0.013% 55.64% 117ms 1.54% _IO_new_fopen 0 0% 55.64% 117ms 1.54% std::__basic_file::open 1ms 0.013% 55.66% 116ms 1.52% __fopen_internal (inline) 116ms 1.52% 57.18% 116ms 1.52% incircle 2ms 0.026% 57.21% 115ms 1.51% Node::~Node 114ms 1.50% 58.71% 114ms 1.50% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 58.72% 113ms 1.49% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 58.73% 113ms 1.49% _IO_new_file_fopen 2ms 0.026% 58.76% 113ms 1.49% std::_Vector_base::_M_allocate (inline) 2ms 0.026% 58.79% 112ms 1.47% __GI__IO_file_open 0 0% 58.79% 112ms 1.47% std::operator<< (inline) 9ms 0.12% 58.90% 112ms 1.47% std::vector::push_back (inline) 79ms 1.04% 59.94% 111ms 1.46% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 13ms 0.17% 60.11% 109ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 60.11% 106ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 103ms 1.35% 61.47% 103ms 1.35% [libchaste_cell_based.so] 34ms 0.45% 61.91% 102ms 1.34% boost::numeric::ublas::indexing_vector_assign 100ms 1.31% 63.23% 100ms 1.31% __libc_open64 93ms 1.22% 64.45% 100ms 1.31% boost::detail::sp_counted_base::release 1ms 0.013% 64.46% 97ms 1.27% std::basic_filebuf::overflow 96ms 1.26% 65.72% 96ms 1.26% __GI___libc_write 0 0% 65.72% 96ms 1.26% std::__basic_file::xsputn 0 0% 65.72% 96ms 1.26% std::basic_filebuf::_M_convert_to_external 8ms 0.11% 65.83% 96ms 1.26% std::vector::_M_realloc_insert 0 0% 65.83% 95ms 1.25% std::basic_filebuf::_M_terminate_output 41ms 0.54% 66.37% 92ms 1.21% AbstractElement::GetNodeLocation 5ms 0.066% 66.43% 91ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 39ms 0.51% 66.95% 90ms 1.18% boost::shared_ptr::shared_ptr (inline) 72ms 0.95% 67.89% 87ms 1.14% vertexsort 2ms 0.026% 67.92% 86ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 45ms 0.59% 68.51% 86ms 1.13% std::basic_filebuf::xsputn 84ms 1.10% 69.61% 84ms 1.10% std::_Rb_tree_insert_and_rebalance 83ms 1.09% 70.71% 83ms 1.09% std::vector::size (inline) 82ms 1.08% 71.78% 82ms 1.08% std::_Rb_tree_increment 0 0% 71.78% 81ms 1.06% std::filesystem::create_directory 55ms 0.72% 72.51% 80ms 1.05% malloc_consolidate 6ms 0.079% 72.59% 80ms 1.05% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.053% 72.64% 76ms 1% TetrahedralMesh::EdgeIterator::GetNodeA 5ms 0.066% 72.70% 74ms 0.97% TetrahedralMesh::EdgeIterator::GetNodeB 46ms 0.6% 73.31% 70ms 0.92% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 73.31% 70ms 0.92% tcache_get (inline) 70ms 0.92% 74.23% 70ms 0.92% tcache_get_n (inline) 1ms 0.013% 74.24% 67ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 66ms 0.87% 75.11% 66ms 0.87% __GI___fstatat64 1ms 0.013% 75.12% 65ms 0.85% std::filesystem::status 47ms 0.62% 75.74% 61ms 0.8% AbstractElement::GetNodeGlobalIndex 61ms 0.8% 76.54% 61ms 0.8% counterclockwise 1ms 0.013% 76.55% 59ms 0.78% Node::ConstructNodeAttributes (inline) 0 0% 76.55% 59ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.55% 59ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 45ms 0.59% 77.15% 59ms 0.78% std::num_put::do_put 9ms 0.12% 77.26% 58ms 0.76% CellPropertyCollection::AddProperty 0 0% 77.26% 58ms 0.76% Node::ClearAppliedForce 0 0% 77.26% 58ms 0.76% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 57ms 0.75% 78.01% 57ms 0.75% __memcpy_avx_unaligned_erms 39ms 0.51% 78.53% 57ms 0.75% hack_digit 0 0% 78.53% 57ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.53% 57ms 0.75% std::__new_allocator::destroy (inline) 0 0% 78.53% 57ms 0.75% std::allocator_traits::destroy (inline) 0 0% 78.53% 55ms 0.72% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 55ms 0.72% 79.25% 55ms 0.72% [libchaste_mesh.so] 3ms 0.039% 79.29% 55ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 33ms 0.43% 79.72% 55ms 0.72% std::basic_streambuf::xsputn 14ms 0.18% 79.91% 54ms 0.71% Determinant (inline) 0 0% 79.91% 52ms 0.68% Cell::GetCellId 0 0% 79.91% 52ms 0.68% std::vector::vector (inline) 51ms 0.67% 80.58% 51ms 0.67% Node::GetIndex 50ms 0.66% 81.23% 51ms 0.67% boost::detail::shared_count::shared_count (inline) 49ms 0.64% 81.88% 49ms 0.64% Node::rGetLocation 48ms 0.63% 82.51% 48ms 0.63% boost::shared_ptr::operator-> (inline) 47ms 0.62% 83.13% 47ms 0.62% __GI___mkdir 25ms 0.33% 83.45% 46ms 0.6% AbstractTetrahedralMesh::GetElement 16ms 0.21% 83.66% 46ms 0.6% AbstractTetrahedralMesh::GetNumAllElements 0 0% 83.66% 45ms 0.59% BoundaryNodeWriter::Visit 5ms 0.066% 83.73% 45ms 0.59% NodeAttributes::NodeAttributes 0 0% 83.73% 45ms 0.59% std::_Vector_base::_Vector_base (inline) 44ms 0.58% 84.31% 44ms 0.58% [libstdc++.so.6.0.33] 0 0% 84.31% 44ms 0.58% std::_Vector_base::_M_create_storage (inline) 0 0% 84.31% 44ms 0.58% std::map::map (inline) 43ms 0.57% 84.87% 43ms 0.57% boost::numeric::ublas::c_vector::operator() 0 0% 84.87% 42ms 0.55% boost::numeric::ublas::norm_2 (inline) 15ms 0.2% 85.07% 42ms 0.55% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 85.07% 39ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 85.07% 39ms 0.51% _dl_init 0 0% 85.07% 39ms 0.51% call_init (inline)