File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6681ms, 84.99% of 7861ms total Dropped 563 nodes (cum <= 39.30ms) flat flat% sum% cum cum% 0 0% 0% 7826ms 99.55% __libc_start_call_main 0 0% 0% 7826ms 99.55% __libc_start_main_impl 0 0% 0% 7826ms 99.55% _start 0 0% 0% 7808ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7808ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7808ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7808ms 99.33% main 0 0% 0% 7765ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7765ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7765ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7762ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3419ms 43.49% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.038% 2991ms 38.05% MeshBasedCellPopulation::Update 1ms 0.013% 0.051% 2788ms 35.47% AbstractCellPopulation::WriteResultsToFiles 5ms 0.064% 0.11% 1546ms 19.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.11% 1484ms 18.88% MutableMesh::ReMesh 1ms 0.013% 0.13% 1434ms 18.24% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.14% 1397ms 17.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.089% 0.23% 1342ms 17.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.17% 0.39% 1244ms 15.82% MeshBasedCellPopulation::SpringIterator::operator++ 122ms 1.55% 1.95% 1020ms 12.98% TetrahedralMesh::EdgeIterator::operator++ 470ms 5.98% 7.93% 1019ms 12.96% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 7.96% 995ms 12.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.013% 7.98% 949ms 12.07% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.025% 8.00% 905ms 11.51% CellPropertyCollection::GetPropertiesType (inline) 251ms 3.19% 11.19% 905ms 11.51% __dynamic_cast 8ms 0.1% 11.30% 879ms 11.18% CellPopulationElementWriter::Visit 53ms 0.67% 11.97% 834ms 10.61% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 8ms 0.1% 12.07% 821ms 10.44% MeshBasedCellPopulation::AcceptCellWriter 24ms 0.31% 12.38% 808ms 10.28% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.53% 768ms 9.77% TetrahedralMesh::ImportFromMesher 2ms 0.025% 12.56% 721ms 9.17% AbstractCellProperty::IsSubType (inline) 60ms 0.76% 13.32% 620ms 7.89% std::map::operator[] (partial-inline) 40ms 0.51% 13.83% 600ms 7.63% operator new 1ms 0.013% 13.84% 594ms 7.56% std::ostream::operator<< (inline) 106ms 1.35% 15.19% 587ms 7.47% std::ostream::_M_insert 184ms 2.34% 17.53% 557ms 7.09% __GI___libc_malloc 12ms 0.15% 17.68% 545ms 6.93% std::_Rb_tree::find (inline) 30ms 0.38% 18.06% 543ms 6.91% std::__new_allocator::allocate (inline) 0 0% 18.06% 542ms 6.89% std::allocator_traits::allocate (inline) 7ms 0.089% 18.15% 538ms 6.84% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.013% 18.17% 535ms 6.81% triangulate 532ms 6.77% 24.93% 532ms 6.77% __strcmp_avx2 7ms 0.089% 25.02% 518ms 6.59% std::set::insert (inline) 7ms 0.089% 25.11% 514ms 6.54% Cell::GetCellProliferativeType 9ms 0.11% 25.23% 511ms 6.50% std::_Rb_tree::_M_insert_unique 0 0% 25.23% 510ms 6.49% std::_Rb_tree::lower_bound (inline) 0 0% 25.23% 510ms 6.49% std::map::lower_bound (inline) 0 0% 25.23% 500ms 6.36% std::set::count (inline) 0 0% 25.23% 476ms 6.06% delaunay 1ms 0.013% 25.24% 474ms 6.03% divconqdelaunay 202ms 2.57% 27.81% 464ms 5.90% __cxxabiv1::__si_class_type_info::__do_dyncast 54ms 0.69% 28.50% 461ms 5.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.50% 435ms 5.53% std::set::~set (inline) 0 0% 28.50% 426ms 5.42% std::_Rb_tree::_M_create_node (inline) 5ms 0.064% 28.56% 418ms 5.32% AbstractCellBasedSimulation::DoCellBirth 82ms 1.04% 29.60% 402ms 5.11% std::_Rb_tree::_M_erase 0 0% 29.60% 400ms 5.09% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.051% 29.65% 398ms 5.06% Cell::GetMutationState 0 0% 29.65% 391ms 4.97% std::_Rb_tree::_M_get_node (inline) 29ms 0.37% 30.02% 390ms 4.96% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.089% 30.11% 369ms 4.69% std::set::set (inline) 8ms 0.1% 30.21% 350ms 4.45% std::less::operator() (inline) 1ms 0.013% 30.23% 342ms 4.35% NodeLocationWriter::Visit 342ms 4.35% 34.58% 342ms 4.35% std::operator< (inline) 44ms 0.56% 35.14% 336ms 4.27% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 35.16% 327ms 4.16% MeshBasedCellPopulation::GetDampingConstant 327ms 4.16% 39.32% 327ms 4.16% std::_Rb_tree::_S_right (inline) 2ms 0.025% 39.35% 325ms 4.13% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.051% 39.40% 320ms 4.07% Element::Element 11ms 0.14% 39.54% 319ms 4.06% AbstractCellPopulation::IsCellAttachedToLocationIndex 28ms 0.36% 39.89% 317ms 4.03% std::_Rb_tree::_M_insert_ (inline) 94ms 1.20% 41.09% 314ms 3.99% __GI___libc_free 0 0% 41.09% 302ms 3.84% std::_Rb_tree::_M_drop_node (inline) 27ms 0.34% 41.43% 301ms 3.83% std::num_put::_M_insert_float 185ms 2.35% 43.79% 289ms 3.68% _int_malloc 86ms 1.09% 44.88% 281ms 3.57% std::_Rb_tree::_M_clone_node (inline) 14ms 0.18% 45.06% 273ms 3.47% std::__new_allocator::deallocate (inline) 0 0% 45.06% 270ms 3.43% std::allocator_traits::deallocate (inline) 2ms 0.025% 45.08% 267ms 3.40% Cell::ReadyToDivide 12ms 0.15% 45.24% 250ms 3.18% divconqrecurse 2ms 0.025% 45.26% 238ms 3.03% CellProliferativeTypesWriter::VisitCell 0 0% 45.26% 236ms 3.00% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 45.30% 228ms 2.90% AbstractCellProperty::IsType (inline) 8ms 0.1% 45.40% 228ms 2.90% std::__cxx11::collate::do_transform 9ms 0.11% 45.52% 225ms 2.86% TetrahedralMesh::Clear 68ms 0.87% 46.38% 223ms 2.84% mergehulls 5ms 0.064% 46.44% 221ms 2.81% CellPropertyCollection::HasProperty 0 0% 46.44% 220ms 2.80% Cell::HasCellProperty (inline) 191ms 2.43% 48.87% 219ms 2.79% _int_free 13ms 0.17% 49.04% 215ms 2.74% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 49.04% 210ms 2.67% ___vsnprintf 0 0% 49.04% 210ms 2.67% __vsnprintf_internal (inline) 31ms 0.39% 49.43% 206ms 2.62% __printf_buffer 1ms 0.013% 49.45% 199ms 2.53% Element::RegisterWithNodes (inline) 5ms 0.064% 49.51% 193ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.064% 49.57% 191ms 2.43% Node::AddElement 5ms 0.064% 49.64% 185ms 2.35% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 74ms 0.94% 50.58% 185ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 50.59% 178ms 2.26% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.59% 177ms 2.25% AbstractCellBasedWriter::CloseFile 0 0% 50.59% 177ms 2.25% std::basic_filebuf::close 0 0% 50.59% 177ms 2.25% std::basic_ofstream::close (inline) 34ms 0.43% 51.02% 175ms 2.23% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.15% 51.18% 170ms 2.16% AbstractTetrahedralElement::CalculateJacobian 34ms 0.43% 51.61% 166ms 2.11% AbstractCellProperty::IsSame 7ms 0.089% 51.70% 165ms 2.10% __printf_fp_l_buffer 0 0% 51.70% 165ms 2.10% __printf_fp_spec (inline) 0 0% 51.70% 163ms 2.07% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.70% 163ms 2.07% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 51.70% 161ms 2.05% OutputFileHandler::OpenOutputFile 0 0% 51.70% 160ms 2.04% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 51.71% 157ms 2.00% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 51.72% 156ms 1.98% std::basic_ofstream::open (inline) 92ms 1.17% 52.89% 155ms 1.97% __printf_fp_buffer_1 1ms 0.013% 52.91% 155ms 1.97% std::basic_filebuf::open 55ms 0.7% 53.61% 154ms 1.96% std::__ostream_insert 1ms 0.013% 53.62% 152ms 1.93% std::_Vector_base::_M_allocate (inline) 6ms 0.076% 53.70% 146ms 1.86% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.22% 53.91% 143ms 1.82% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.076% 53.99% 143ms 1.82% Node::~Node 0 0% 53.99% 143ms 1.82% alternateaxes 132ms 1.68% 55.67% 143ms 1.82% vertexmedian 0 0% 55.67% 141ms 1.79% OutputFileHandler::CommonConstructor 0 0% 55.67% 141ms 1.79% OutputFileHandler::OutputFileHandler 2ms 0.025% 55.69% 133ms 1.69% OutputFileHandler::MakeFoldersAndReturnFullPath 26ms 0.33% 56.02% 132ms 1.68% std::type_info::operator== (inline) 11ms 0.14% 56.16% 131ms 1.67% boost::detail::shared_count::~shared_count (inline) 0 0% 56.16% 131ms 1.67% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 56.19% 130ms 1.65% std::basic_filebuf::overflow 96ms 1.22% 57.41% 129ms 1.64% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 57.41% 129ms 1.64% std::basic_filebuf::_M_terminate_output 1ms 0.013% 57.42% 129ms 1.64% std::operator<< (inline) 0 0% 57.42% 128ms 1.63% std::__basic_file::xsputn 0 0% 57.42% 128ms 1.63% std::basic_filebuf::_M_convert_to_external 5ms 0.064% 57.49% 127ms 1.62% AbstractTetrahedralElement::AbstractTetrahedralElement 126ms 1.60% 59.09% 127ms 1.62% __GI___libc_write 9ms 0.11% 59.20% 124ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 21ms 0.27% 59.47% 124ms 1.58% AbstractTetrahedralElement::RefreshJacobian 8ms 0.1% 59.57% 123ms 1.56% std::vector::push_back (inline) 0 0% 59.57% 122ms 1.55% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.089% 59.66% 112ms 1.42% std::vector::_M_realloc_insert 32ms 0.41% 60.07% 111ms 1.41% std::num_put::_M_insert_int 1ms 0.013% 60.08% 110ms 1.40% std::__basic_file::open 0 0% 60.08% 109ms 1.39% _IO_new_fopen 1ms 0.013% 60.09% 109ms 1.39% __fopen_internal (inline) 2ms 0.025% 60.12% 108ms 1.37% _IO_new_file_fopen 107ms 1.36% 61.48% 107ms 1.36% [libchaste_cell_based.so] 101ms 1.28% 62.77% 107ms 1.36% boost::detail::sp_counted_base::release 2ms 0.025% 62.79% 106ms 1.35% __GI__IO_file_open 46ms 0.59% 63.38% 102ms 1.30% boost::shared_ptr::shared_ptr (inline) 102ms 1.30% 64.67% 102ms 1.30% incircle 6ms 0.076% 64.75% 98ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 4ms 0.051% 64.80% 98ms 1.25% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.089% 64.89% 98ms 1.25% boost::numeric::ublas::vector_assign (inline) 98ms 1.25% 66.14% 98ms 1.25% std::_Rb_tree_increment 0 0% 66.14% 97ms 1.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 72ms 0.92% 67.05% 97ms 1.23% malloc_consolidate 6ms 0.076% 67.13% 97ms 1.23% std::_Rb_tree_const_iterator::operator++ (inline) 67ms 0.85% 67.98% 97ms 1.23% std::basic_filebuf::xsputn 36ms 0.46% 68.44% 91ms 1.16% AbstractElement::GetNodeLocation 91ms 1.16% 69.60% 91ms 1.16% std::_Rb_tree_insert_and_rebalance 0 0% 69.60% 89ms 1.13% Cell::GetCellId 89ms 1.13% 70.73% 89ms 1.13% __libc_open64 4ms 0.051% 70.78% 84ms 1.07% AbstractCellPopulation::GetLocationIndexUsingCell 78ms 0.99% 71.77% 78ms 0.99% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 77ms 0.98% 72.75% 77ms 0.98% std::vector::size (inline) 0 0% 72.75% 77ms 0.98% tcache_get (inline) 77ms 0.98% 73.73% 77ms 0.98% tcache_get_n (inline) 14ms 0.18% 73.91% 76ms 0.97% CellPropertyCollection::AddProperty 73ms 0.93% 74.84% 73ms 0.93% __GI___fstatat64 0 0% 74.84% 73ms 0.93% std::filesystem::create_directory 0 0% 74.84% 72ms 0.92% std::filesystem::status 6ms 0.076% 74.91% 70ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 51ms 0.65% 75.56% 69ms 0.88% std::num_put::do_put 17ms 0.22% 75.78% 68ms 0.87% boost::numeric::ublas::indexing_vector_assign 0 0% 75.78% 67ms 0.85% std::vector::vector (inline) 0 0% 75.78% 66ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 0 0% 75.78% 66ms 0.84% std::__new_allocator::destroy (inline) 0 0% 75.78% 66ms 0.84% std::allocator_traits::destroy (inline) 62ms 0.79% 76.57% 66ms 0.84% vertexsort 1ms 0.013% 76.58% 65ms 0.83% std::_Vector_base::_M_create_storage (inline) 0 0% 76.58% 65ms 0.83% std::_Vector_base::_Vector_base (inline) 45ms 0.57% 77.15% 63ms 0.8% boost::numeric::ublas::c_matrix::operator() 0 0% 77.15% 60ms 0.76% AbstractCentreBasedCellPopulation::CreateCellPair 58ms 0.74% 77.89% 58ms 0.74% Node::GetIndex 0 0% 77.89% 58ms 0.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.89% 58ms 0.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 58ms 0.74% 78.63% 58ms 0.74% counterclockwise 4ms 0.051% 78.68% 57ms 0.73% TetrahedralMesh::EdgeIterator::GetNodeA 57ms 0.73% 79.40% 57ms 0.73% [libstdc++.so.6.0.33] 54ms 0.69% 80.09% 56ms 0.71% boost::detail::shared_count::shared_count (inline) 13ms 0.17% 80.26% 55ms 0.7% Determinant (inline) 55ms 0.7% 80.96% 55ms 0.7% __memcpy_avx_unaligned_erms 22ms 0.28% 81.24% 52ms 0.66% AbstractTetrahedralMesh::GetElement 0 0% 81.24% 52ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 39ms 0.5% 81.73% 51ms 0.65% std::basic_streambuf::xsputn 1ms 0.013% 81.75% 50ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 49ms 0.62% 82.37% 49ms 0.62% std::ostream::sentry::sentry 0 0% 82.37% 47ms 0.6% BoundaryNodeWriter::Visit 0 0% 82.37% 46ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 46ms 0.59% 82.95% 46ms 0.59% [libchaste_mesh.so] 35ms 0.45% 83.40% 45ms 0.57% AbstractElement::GetNodeGlobalIndex 0 0% 83.40% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 15ms 0.19% 83.59% 44ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 83.60% 44ms 0.56% _IO_new_fclose 0 0% 83.60% 44ms 0.56% boost::numeric::ublas::norm_2 (inline) 13ms 0.17% 83.77% 44ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.77% 44ms 0.56% std::__basic_file::close 1ms 0.013% 83.78% 43ms 0.55% std::basic_filebuf::_M_allocate_internal_buffer 5ms 0.064% 83.84% 42ms 0.53% Inverse 42ms 0.53% 84.38% 42ms 0.53% Node::rGetLocation 42ms 0.53% 84.91% 42ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 84.91% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 5ms 0.064% 84.98% 40ms 0.51% Element::~Element 1ms 0.013% 84.99% 40ms 0.51% _IO_new_file_close_it