File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6503ms, 84.97% of 7653ms total Dropped 541 nodes (cum <= 38.27ms) flat flat% sum% cum cum% 0 0% 0% 7617ms 99.53% __libc_start_call_main 0 0% 0% 7617ms 99.53% __libc_start_main_impl 0 0% 0% 7617ms 99.53% _start 0 0% 0% 7603ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7603ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7603ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7603ms 99.35% main 0 0% 0% 7566ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7566ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7566ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7563ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3253ms 42.51% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.039% 2800ms 36.59% MeshBasedCellPopulation::Update 2ms 0.026% 0.065% 2727ms 35.63% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.065% 1572ms 20.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.078% 1438ms 18.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.078% 1404ms 18.35% MutableMesh::ReMesh 7ms 0.091% 0.17% 1396ms 18.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.026% 0.2% 1340ms 17.51% MeshBasedCellPopulation::UpdateNodePairs 18ms 0.24% 0.43% 1172ms 15.31% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.091% 0.52% 960ms 12.54% AbstractTwoBodyInteractionForce::AddForceContribution 107ms 1.40% 1.92% 960ms 12.54% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 1.95% 930ms 12.15% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 411ms 5.37% 7.32% 912ms 11.92% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.12% 7.43% 908ms 11.86% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.14% 7.58% 896ms 11.71% CellPopulationElementWriter::Visit 256ms 3.35% 10.92% 882ms 11.52% __dynamic_cast 30ms 0.39% 11.32% 830ms 10.85% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.065% 11.38% 769ms 10.05% TetrahedralMesh::ImportFromMesher 2ms 0.026% 11.41% 762ms 9.96% MeshBasedCellPopulation::AcceptCellWriter 34ms 0.44% 11.85% 721ms 9.42% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.052% 11.90% 701ms 9.16% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.92% 657ms 8.58% std::ostream::operator<< (inline) 96ms 1.25% 13.17% 655ms 8.56% std::ostream::_M_insert 46ms 0.6% 13.77% 631ms 8.25% operator new 41ms 0.54% 14.31% 575ms 7.51% std::__new_allocator::allocate (inline) 206ms 2.69% 17.00% 573ms 7.49% __GI___libc_malloc 0 0% 17.00% 569ms 7.43% std::allocator_traits::allocate (inline) 9ms 0.12% 17.12% 560ms 7.32% std::set::insert (inline) 54ms 0.71% 17.82% 557ms 7.28% std::map::operator[] (partial-inline) 9ms 0.12% 17.94% 551ms 7.20% std::_Rb_tree::_M_insert_unique 521ms 6.81% 24.75% 521ms 6.81% __strcmp_avx2 5ms 0.065% 24.81% 500ms 6.53% Cell::GetCellProliferativeType 2ms 0.026% 24.84% 491ms 6.42% triangulate 22ms 0.29% 25.13% 478ms 6.25% std::_Rb_tree::find (inline) 0 0% 25.13% 468ms 6.12% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 25.13% 463ms 6.05% std::_Rb_tree::_M_create_node (inline) 0 0% 25.13% 463ms 6.05% std::_Rb_tree::lower_bound (inline) 0 0% 25.13% 463ms 6.05% std::map::lower_bound (inline) 189ms 2.47% 27.60% 453ms 5.92% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.60% 447ms 5.84% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.091% 27.69% 439ms 5.74% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.69% 424ms 5.54% std::_Rb_tree::_M_get_node (inline) 0 0% 27.69% 418ms 5.46% delaunay 2ms 0.026% 27.71% 417ms 5.45% divconqdelaunay 0 0% 27.71% 417ms 5.45% std::set::count (inline) 1ms 0.013% 27.73% 385ms 5.03% NodeLocationWriter::Visit 4ms 0.052% 27.78% 378ms 4.94% Cell::GetMutationState 19ms 0.25% 28.03% 377ms 4.93% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.26% 28.29% 376ms 4.91% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.29% 355ms 4.64% std::set::~set (inline) 88ms 1.15% 29.44% 352ms 4.60% std::_Rb_tree::_M_erase 5ms 0.065% 29.50% 350ms 4.57% std::set::set (inline) 12ms 0.16% 29.66% 342ms 4.47% std::_Rb_tree::_M_insert_ (inline) 27ms 0.35% 30.01% 337ms 4.40% std::num_put::_M_insert_float 1ms 0.013% 30.03% 336ms 4.39% MeshBasedCellPopulation::GetDampingConstant 3ms 0.039% 30.07% 335ms 4.38% AbstractCentreBasedCellPopulation::GetDampingConstant 324ms 4.23% 34.30% 324ms 4.23% std::_Rb_tree::_S_right (inline) 34ms 0.44% 34.74% 321ms 4.19% std::_Rb_tree::_M_copy (inline) 14ms 0.18% 34.93% 321ms 4.19% std::less::operator() (inline) 3ms 0.039% 34.97% 313ms 4.09% Element::Element 307ms 4.01% 38.98% 307ms 4.01% std::operator< (inline) 186ms 2.43% 41.41% 300ms 3.92% _int_malloc 8ms 0.1% 41.51% 299ms 3.91% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.039% 41.55% 286ms 3.74% Cell::ReadyToDivide 76ms 0.99% 42.55% 282ms 3.68% std::_Rb_tree::_M_clone_node (inline) 94ms 1.23% 43.77% 278ms 3.63% __GI___libc_free 4ms 0.052% 43.83% 271ms 3.54% std::__cxx11::collate::do_transform 3ms 0.039% 43.87% 266ms 3.48% CellProliferativeTypesWriter::VisitCell 9ms 0.12% 43.98% 265ms 3.46% divconqrecurse 2ms 0.026% 44.01% 261ms 3.41% ___vsnprintf 1ms 0.013% 44.02% 259ms 3.38% __vsnprintf_internal (inline) 42ms 0.55% 44.57% 252ms 3.29% __printf_buffer 0 0% 44.57% 251ms 3.28% std::_Rb_tree::_M_drop_node (inline) 75ms 0.98% 45.55% 247ms 3.23% mergehulls 9ms 0.12% 45.67% 236ms 3.08% std::__new_allocator::deallocate (inline) 0 0% 45.67% 234ms 3.06% std::allocator_traits::deallocate (inline) 4ms 0.052% 45.72% 226ms 2.95% AbstractCellProperty::IsType (inline) 9ms 0.12% 45.84% 220ms 2.87% CellPropertyCollection::HasProperty 0 0% 45.84% 219ms 2.86% Cell::HasCellProperty (inline) 18ms 0.24% 46.07% 216ms 2.82% TetrahedralMesh::Clear 3ms 0.039% 46.11% 215ms 2.81% Element::RegisterWithNodes (inline) 5ms 0.065% 46.18% 211ms 2.76% Node::AddElement 59ms 0.77% 46.95% 200ms 2.61% std::_Rb_tree::_M_get_insert_unique_pos (inline) 16ms 0.21% 47.16% 192ms 2.51% __printf_fp_l_buffer 0 0% 47.16% 192ms 2.51% __printf_fp_spec (inline) 0 0% 47.16% 192ms 2.51% std::_Rb_tree::_M_put_node (inline) 4ms 0.052% 47.21% 191ms 2.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 10ms 0.13% 47.34% 186ms 2.43% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 159ms 2.08% 49.42% 184ms 2.40% _int_free 6ms 0.078% 49.50% 177ms 2.31% MeshBasedCellPopulation::SpringsEnd (inline) 45ms 0.59% 50.08% 174ms 2.27% AbstractCellProperty::IsSame 81ms 1.06% 51.14% 165ms 2.16% __printf_fp_buffer_1 0 0% 51.14% 157ms 2.05% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.14% 157ms 2.05% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 51.14% 155ms 2.03% OutputFileHandler::OpenOutputFile 0 0% 51.14% 152ms 1.99% std::basic_ofstream::basic_ofstream (inline) 4ms 0.052% 51.20% 151ms 1.97% boost::numeric::ublas::vector_assign (inline) 3ms 0.039% 51.23% 148ms 1.93% std::basic_filebuf::open 0 0% 51.23% 148ms 1.93% std::basic_ofstream::open (inline) 32ms 0.42% 51.65% 147ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.65% 145ms 1.89% std::_Vector_base::_M_allocate (inline) 62ms 0.81% 52.46% 143ms 1.87% std::__ostream_insert 12ms 0.16% 52.62% 142ms 1.86% AbstractTetrahedralElement::CalculateJacobian 40ms 0.52% 53.14% 141ms 1.84% std::num_put::_M_insert_int 4ms 0.052% 53.19% 139ms 1.82% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 53.21% 136ms 1.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 53.21% 135ms 1.76% AbstractCellBasedWriter::CloseFile 2ms 0.026% 53.23% 135ms 1.76% std::basic_filebuf::close 0 0% 53.23% 135ms 1.76% std::basic_ofstream::close (inline) 23ms 0.3% 53.53% 131ms 1.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 15ms 0.2% 53.73% 131ms 1.71% boost::detail::shared_count::~shared_count (inline) 0 0% 53.73% 131ms 1.71% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 53.74% 129ms 1.69% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 53.74% 129ms 1.69% OutputFileHandler::OutputFileHandler 29ms 0.38% 54.12% 129ms 1.69% std::type_info::operator== (inline) 0 0% 54.12% 128ms 1.67% OutputFileHandler::CommonConstructor 5ms 0.065% 54.19% 128ms 1.67% std::operator<< (inline) 1ms 0.013% 54.20% 127ms 1.66% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.091% 54.29% 127ms 1.66% std::_Rb_tree_const_iterator::operator++ (inline) 8ms 0.1% 54.40% 125ms 1.63% Node::~Node 0 0% 54.40% 125ms 1.63% OutputFileHandler::MakeFoldersAndReturnFullPath 6ms 0.078% 54.48% 123ms 1.61% std::vector::push_back (inline) 122ms 1.59% 56.07% 122ms 1.59% std::_Rb_tree_increment 118ms 1.54% 57.61% 118ms 1.54% incircle 10ms 0.13% 57.74% 116ms 1.52% AbstractTetrahedralElement::CalculateInverseJacobian 37ms 0.48% 58.23% 113ms 1.48% boost::numeric::ublas::indexing_vector_assign 112ms 1.46% 59.69% 112ms 1.46% boost::detail::sp_counted_base::release 8ms 0.1% 59.79% 112ms 1.46% std::vector::_M_realloc_insert 0 0% 59.79% 111ms 1.45% _IO_new_fopen 0 0% 59.79% 111ms 1.45% __fopen_internal (inline) 0 0% 59.79% 111ms 1.45% std::__basic_file::open 0 0% 59.79% 109ms 1.42% _IO_new_file_fopen 1ms 0.013% 59.81% 108ms 1.41% __GI__IO_file_open 10ms 0.13% 59.94% 105ms 1.37% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.13% 60.07% 105ms 1.37% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 60.08% 102ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 102ms 1.33% 61.41% 102ms 1.33% __GI___libc_write 44ms 0.57% 61.99% 102ms 1.33% boost::shared_ptr::shared_ptr (inline) 0 0% 61.99% 102ms 1.33% std::__basic_file::xsputn 0 0% 61.99% 102ms 1.33% std::basic_filebuf::_M_convert_to_external 0 0% 61.99% 102ms 1.33% std::basic_filebuf::_M_terminate_output 0 0% 61.99% 102ms 1.33% std::basic_filebuf::overflow 62ms 0.81% 62.80% 99ms 1.29% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 14ms 0.18% 62.98% 97ms 1.27% AbstractTetrahedralElement::RefreshJacobian 0 0% 62.98% 96ms 1.25% alternateaxes 94ms 1.23% 64.21% 95ms 1.24% __libc_open64 89ms 1.16% 65.37% 95ms 1.24% vertexmedian 1ms 0.013% 65.39% 92ms 1.20% AbstractCellPopulation::GetLocationIndexUsingCell 92ms 1.20% 66.59% 92ms 1.20% std::_Rb_tree_insert_and_rebalance 0 0% 66.59% 91ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.052% 66.64% 91ms 1.19% Cell::GetCellId 86ms 1.12% 67.76% 86ms 1.12% [libchaste_cell_based.so] 65ms 0.85% 68.61% 83ms 1.08% malloc_consolidate 46ms 0.6% 69.21% 78ms 1.02% std::basic_filebuf::xsputn 77ms 1.01% 70.22% 77ms 1.01% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 56ms 0.73% 70.95% 75ms 0.98% AbstractElement::GetNodeGlobalIndex 74ms 0.97% 71.92% 74ms 0.97% __memcpy_avx_unaligned_erms 45ms 0.59% 72.51% 74ms 0.97% std::basic_streambuf::xsputn 30ms 0.39% 72.90% 73ms 0.95% AbstractElement::GetNodeLocation 56ms 0.73% 73.63% 69ms 0.9% std::num_put::do_put 68ms 0.89% 74.52% 68ms 0.89% std::vector::size (inline) 6ms 0.078% 74.60% 67ms 0.88% Node::ConstructNodeAttributes (inline) 67ms 0.88% 75.47% 67ms 0.88% Node::GetIndex 0 0% 75.47% 67ms 0.88% std::filesystem::create_directory 2ms 0.026% 75.50% 66ms 0.86% std::filesystem::status 0 0% 75.50% 66ms 0.86% std::vector::vector (inline) 65ms 0.85% 76.35% 65ms 0.85% __GI___fstatat64 0 0% 76.35% 63ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.35% 63ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 76.35% 63ms 0.82% tcache_get (inline) 63ms 0.82% 77.17% 63ms 0.82% tcache_get_n (inline) 0 0% 77.17% 62ms 0.81% Node::ClearAppliedForce 6ms 0.078% 77.25% 60ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 6ms 0.078% 77.33% 59ms 0.77% CellPropertyCollection::AddProperty 0 0% 77.33% 59ms 0.77% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.33% 59ms 0.77% std::__new_allocator::destroy (inline) 0 0% 77.33% 59ms 0.77% std::allocator_traits::destroy (inline) 54ms 0.71% 78.03% 58ms 0.76% boost::detail::shared_count::shared_count (inline) 58ms 0.76% 78.79% 58ms 0.76% std::ostream::sentry::sentry 0 0% 78.79% 56ms 0.73% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 78.81% 55ms 0.72% std::_Vector_base::_M_create_storage (inline) 0 0% 78.81% 54ms 0.71% std::map::find (inline) 0 0% 78.81% 53ms 0.69% BoundaryNodeWriter::Visit 53ms 0.69% 79.50% 53ms 0.69% boost::shared_ptr::operator-> (inline) 0 0% 79.50% 52ms 0.68% AbstractCentreBasedCellPopulation::IsMarkedSpring 51ms 0.67% 80.16% 51ms 0.67% boost::numeric::ublas::c_vector::operator() (partial-inline) 51ms 0.67% 80.83% 51ms 0.67% counterclockwise 27ms 0.35% 81.18% 50ms 0.65% hack_digit 46ms 0.6% 81.78% 48ms 0.63% vertexsort 47ms 0.61% 82.40% 47ms 0.61% Node::IsDeleted 5ms 0.065% 82.46% 47ms 0.61% TetrahedralMesh::EdgeIterator::GetNodeA 47ms 0.61% 83.08% 47ms 0.61% [libchaste_mesh.so] 0 0% 83.08% 46ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.052% 83.13% 46ms 0.6% NodeAttributes::NodeAttributes 0 0% 83.13% 46ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.052% 83.18% 46ms 0.6% std::_Vector_base::_M_deallocate (inline) 21ms 0.27% 83.46% 45ms 0.59% AbstractCellCycleModel::GetAge 0 0% 83.46% 45ms 0.59% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.46% 45ms 0.59% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 83.64% 45ms 0.59% boost::numeric::ublas::vector_norm_2::apply (inline) 44ms 0.57% 84.22% 44ms 0.57% [libstdc++.so.6.0.33] 17ms 0.22% 84.44% 43ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 84.45% 43ms 0.56% std::__new_allocator::construct (inline) 0 0% 84.45% 43ms 0.56% std::allocator_traits::construct (inline) 24ms 0.31% 84.76% 40ms 0.52% boost::numeric::ublas::c_matrix::operator() 2ms 0.026% 84.79% 40ms 0.52% std::_Rb_tree::_M_emplace_hint_unique 14ms 0.18% 84.97% 39ms 0.51% Determinant (inline) 0 0% 84.97% 39ms 0.51% std::_Rb_tree::_M_construct_node (inline)