File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6639ms, 84.88% of 7822ms total Dropped 570 nodes (cum <= 39.11ms) flat flat% sum% cum cum% 0 0% 0% 7789ms 99.58% __libc_start_call_main 0 0% 0% 7789ms 99.58% __libc_start_main_impl 0 0% 0% 7789ms 99.58% _start 0 0% 0% 7774ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7774ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7774ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7774ms 99.39% main 0 0% 0% 7738ms 98.93% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7738ms 98.93% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7738ms 98.93% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7736ms 98.90% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3389ms 43.33% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.051% 2882ms 36.84% MeshBasedCellPopulation::Update 2ms 0.026% 0.077% 2864ms 36.61% AbstractCellPopulation::WriteResultsToFiles 2ms 0.026% 0.1% 1472ms 18.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.1% 1436ms 18.36% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.1% 1376ms 17.59% MutableMesh::ReMesh 1ms 0.013% 0.12% 1333ms 17.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.22% 1283ms 16.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.12% 0.33% 1231ms 15.74% MeshBasedCellPopulation::SpringIterator::operator++ 118ms 1.51% 1.84% 1020ms 13.04% TetrahedralMesh::EdgeIterator::operator++ 426ms 5.45% 7.29% 962ms 12.30% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 7.33% 907ms 11.60% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.064% 7.39% 891ms 11.39% CellPopulationElementWriter::Visit 4ms 0.051% 7.44% 874ms 11.17% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.18% 7.62% 871ms 11.14% CellPropertyCollection::GetPropertiesType (inline) 284ms 3.63% 11.25% 858ms 10.97% __dynamic_cast 27ms 0.35% 11.60% 762ms 9.74% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.038% 11.63% 754ms 9.64% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.077% 11.71% 732ms 9.36% TetrahedralMesh::ImportFromMesher 39ms 0.5% 12.21% 715ms 9.14% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.25% 673ms 8.60% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.26% 592ms 7.57% std::ostream::operator<< (inline) 89ms 1.14% 13.40% 590ms 7.54% std::ostream::_M_insert 36ms 0.46% 13.86% 574ms 7.34% operator new 52ms 0.66% 14.52% 557ms 7.12% std::map::operator[] (partial-inline) 23ms 0.29% 14.82% 555ms 7.10% std::_Rb_tree::find (inline) 178ms 2.28% 17.09% 522ms 6.67% __GI___libc_malloc 6ms 0.077% 17.17% 517ms 6.61% Cell::GetCellProliferativeType 9ms 0.12% 17.28% 512ms 6.55% std::set::insert (inline) 29ms 0.37% 17.66% 509ms 6.51% std::__new_allocator::allocate (inline) 0 0% 17.66% 505ms 6.46% std::allocator_traits::allocate (inline) 5ms 0.064% 17.72% 503ms 6.43% std::_Rb_tree::_M_insert_unique 0 0% 17.72% 495ms 6.33% std::set::count (inline) 4ms 0.051% 17.77% 493ms 6.30% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 17.77% 492ms 6.29% triangulate 4ms 0.051% 17.82% 489ms 6.25% AbstractCellBasedSimulation::DoCellBirth 0 0% 17.82% 457ms 5.84% std::_Rb_tree::lower_bound (inline) 0 0% 17.82% 457ms 5.84% std::map::lower_bound (inline) 449ms 5.74% 23.56% 449ms 5.74% __strcmp_avx2 29ms 0.37% 23.93% 436ms 5.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 23.93% 420ms 5.37% std::_Rb_tree::_M_create_node (inline) 0 0% 23.93% 417ms 5.33% delaunay 1ms 0.013% 23.95% 415ms 5.31% divconqdelaunay 195ms 2.49% 26.44% 405ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.44% 405ms 5.18% std::set::~set (inline) 99ms 1.27% 27.70% 396ms 5.06% std::_Rb_tree::_M_erase 0 0% 27.70% 395ms 5.05% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.70% 389ms 4.97% std::_Rb_tree::_M_get_node (inline) 5ms 0.064% 27.77% 376ms 4.81% Cell::GetMutationState 2ms 0.026% 27.79% 370ms 4.73% NodeLocationWriter::Visit 16ms 0.2% 28.00% 369ms 4.72% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.089% 28.09% 360ms 4.60% std::less::operator() (inline) 353ms 4.51% 32.60% 353ms 4.51% std::operator< (inline) 3ms 0.038% 32.64% 337ms 4.31% std::set::set (inline) 26ms 0.33% 32.97% 328ms 4.19% std::num_put::_M_insert_float 0 0% 32.97% 327ms 4.18% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 32.97% 325ms 4.15% AbstractCellBasedWriter::OpenOutputFileForAppend 325ms 4.15% 37.13% 325ms 4.15% std::_Rb_tree::_S_right (inline) 0 0% 37.13% 323ms 4.13% OutputFileHandler::OpenOutputFile 19ms 0.24% 37.37% 321ms 4.10% std::_Rb_tree::_M_insert_ (inline) 41ms 0.52% 37.89% 318ms 4.07% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 37.91% 317ms 4.05% MeshBasedCellPopulation::GetDampingConstant 107ms 1.37% 39.27% 317ms 4.05% __GI___libc_free 5ms 0.064% 39.34% 316ms 4.04% Cell::ReadyToDivide 4ms 0.051% 39.39% 315ms 4.03% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.077% 39.47% 299ms 3.82% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.038% 39.50% 290ms 3.71% Element::Element 0 0% 39.50% 275ms 3.52% std::_Rb_tree::_M_drop_node (inline) 12ms 0.15% 39.66% 275ms 3.52% std::__new_allocator::deallocate (inline) 0 0% 39.66% 274ms 3.50% std::allocator_traits::deallocate (inline) 78ms 1% 40.65% 273ms 3.49% std::_Rb_tree::_M_clone_node (inline) 180ms 2.30% 42.96% 271ms 3.46% _int_malloc 5ms 0.064% 43.02% 256ms 3.27% std::__cxx11::collate::do_transform 1ms 0.013% 43.03% 243ms 3.11% ___vsnprintf 1ms 0.013% 43.05% 242ms 3.09% __vsnprintf_internal (inline) 7ms 0.089% 43.13% 241ms 3.08% AbstractCellProperty::IsType (inline) 27ms 0.35% 43.48% 238ms 3.04% __printf_buffer 9ms 0.12% 43.59% 236ms 3.02% CellPropertyCollection::HasProperty 0 0% 43.59% 235ms 3.00% Cell::HasCellProperty (inline) 0 0% 43.59% 233ms 2.98% CellProliferativeTypesWriter::VisitCell 0 0% 43.59% 231ms 2.95% std::_Rb_tree::_M_put_node (inline) 10ms 0.13% 43.72% 219ms 2.80% divconqrecurse 16ms 0.2% 43.93% 214ms 2.74% TetrahedralMesh::Clear 184ms 2.35% 46.28% 210ms 2.68% _int_free 3ms 0.038% 46.32% 208ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.1% 46.42% 204ms 2.61% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 64ms 0.82% 47.24% 204ms 2.61% mergehulls 10ms 0.13% 47.37% 196ms 2.51% __printf_fp_l_buffer 0 0% 47.37% 196ms 2.51% __printf_fp_spec (inline) 1ms 0.013% 47.38% 193ms 2.47% Element::RegisterWithNodes (inline) 2ms 0.026% 47.40% 187ms 2.39% Node::AddElement 8ms 0.1% 47.51% 186ms 2.38% MeshBasedCellPopulation::SpringsEnd (inline) 58ms 0.74% 48.25% 177ms 2.26% std::_Rb_tree::_M_get_insert_unique_pos (inline) 94ms 1.20% 49.45% 175ms 2.24% __printf_fp_buffer_1 46ms 0.59% 50.04% 169ms 2.16% AbstractCellProperty::IsSame 45ms 0.58% 50.61% 162ms 2.07% TetrahedralMesh::EdgesEnd (partial-inline) 6ms 0.077% 50.69% 162ms 2.07% boost::numeric::ublas::vector_assign (inline) 0 0% 50.69% 162ms 2.07% std::basic_ofstream::basic_ofstream (inline) 8ms 0.1% 50.79% 158ms 2.02% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 50.81% 157ms 2.01% std::basic_filebuf::open 0 0% 50.81% 157ms 2.01% std::basic_ofstream::open (inline) 5ms 0.064% 50.87% 155ms 1.98% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 50.88% 149ms 1.90% OutputFileHandler::OutputFileHandler 0 0% 50.88% 148ms 1.89% OutputFileHandler::CommonConstructor 21ms 0.27% 51.15% 145ms 1.85% AbstractCellPopulation::Iterator::IsRealCell (inline) 57ms 0.73% 51.88% 145ms 1.85% std::__ostream_insert 2ms 0.026% 51.90% 144ms 1.84% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.90% 143ms 1.83% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 51.92% 135ms 1.73% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.92% 133ms 1.70% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 51.93% 133ms 1.70% std::filesystem::permissions 132ms 1.69% 53.62% 132ms 1.69% __GI_fchmodat 0 0% 53.62% 125ms 1.60% AbstractCellPopulation::CloseRoundRobinWritersFiles 17ms 0.22% 53.84% 125ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 53.84% 125ms 1.60% _IO_new_fopen 0 0% 53.84% 125ms 1.60% __fopen_internal (inline) 3ms 0.038% 53.87% 125ms 1.60% std::basic_filebuf::close 0 0% 53.87% 124ms 1.59% AbstractCellBasedWriter::CloseFile 5ms 0.064% 53.94% 124ms 1.59% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.038% 53.98% 124ms 1.59% Node::~Node 2ms 0.026% 54.00% 124ms 1.59% _IO_new_file_fopen 0 0% 54.00% 124ms 1.59% std::basic_ofstream::close (inline) 17ms 0.22% 54.22% 123ms 1.57% AbstractTetrahedralElement::RefreshJacobian 0 0% 54.22% 123ms 1.57% std::__basic_file::open 36ms 0.46% 54.68% 123ms 1.57% std::type_info::operator== (inline) 0 0% 54.68% 122ms 1.56% __GI__IO_file_open 1ms 0.013% 54.69% 122ms 1.56% std::operator<< (inline) 6ms 0.077% 54.77% 120ms 1.53% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 36ms 0.46% 55.23% 119ms 1.52% std::num_put::_M_insert_int 27ms 0.35% 55.57% 118ms 1.51% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 55.59% 117ms 1.50% std::_Vector_base::_M_allocate (inline) 12ms 0.15% 55.74% 115ms 1.47% std::_Rb_tree_const_iterator::operator++ (inline) 72ms 0.92% 56.66% 111ms 1.42% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 10ms 0.13% 56.79% 111ms 1.42% boost::detail::shared_count::~shared_count (inline) 0 0% 56.79% 111ms 1.42% boost::shared_ptr::~shared_ptr (inline) 5ms 0.064% 56.85% 110ms 1.41% std::vector::push_back (inline) 109ms 1.39% 58.25% 109ms 1.39% std::_Rb_tree_insert_and_rebalance 2ms 0.026% 58.27% 107ms 1.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.038% 58.31% 107ms 1.37% alternateaxes 106ms 1.36% 59.67% 106ms 1.36% std::_Rb_tree_increment 104ms 1.33% 60.99% 104ms 1.33% __libc_open64 8ms 0.1% 61.10% 104ms 1.33% std::vector::_M_realloc_insert 96ms 1.23% 62.32% 104ms 1.33% vertexmedian 1ms 0.013% 62.34% 103ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.026% 62.36% 97ms 1.24% AbstractCellPopulation::GetLocationIndexUsingCell 96ms 1.23% 63.59% 97ms 1.24% boost::detail::sp_counted_base::release 96ms 1.23% 64.82% 96ms 1.23% [libchaste_cell_based.so] 37ms 0.47% 65.29% 90ms 1.15% boost::shared_ptr::shared_ptr (inline) 2ms 0.026% 65.32% 89ms 1.14% std::basic_filebuf::overflow 61ms 0.78% 66.10% 89ms 1.14% std::basic_filebuf::xsputn 88ms 1.13% 67.22% 88ms 1.13% incircle 0 0% 67.22% 88ms 1.13% std::basic_filebuf::_M_terminate_output 1ms 0.013% 67.23% 86ms 1.10% std::basic_filebuf::_M_convert_to_external 85ms 1.09% 68.32% 85ms 1.09% __GI___libc_write 0 0% 68.32% 85ms 1.09% std::__basic_file::xsputn 31ms 0.4% 68.72% 83ms 1.06% AbstractElement::GetNodeLocation 1ms 0.013% 68.73% 77ms 0.98% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 76ms 0.97% 69.70% 76ms 0.97% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 69.71% 76ms 0.97% std::filesystem::create_directory 59ms 0.75% 70.47% 75ms 0.96% malloc_consolidate 65ms 0.83% 71.30% 73ms 0.93% vertexsort 72ms 0.92% 72.22% 72ms 0.92% __GI___fstatat64 0 0% 72.22% 72ms 0.92% std::filesystem::status 53ms 0.68% 72.90% 71ms 0.91% std::basic_streambuf::xsputn 0 0% 72.90% 70ms 0.89% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 58ms 0.74% 73.64% 69ms 0.88% AbstractElement::GetNodeGlobalIndex 0 0% 73.64% 67ms 0.86% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 73.64% 66ms 0.84% Cell::GetCellId 66ms 0.84% 74.48% 66ms 0.84% Node::GetIndex 64ms 0.82% 75.30% 64ms 0.82% std::vector::size (inline) 3ms 0.038% 75.34% 61ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 75.34% 61ms 0.78% tcache_get (inline) 61ms 0.78% 76.12% 61ms 0.78% tcache_get_n (inline) 4ms 0.051% 76.17% 58ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.17% 57ms 0.73% std::map::find (inline) 31ms 0.4% 76.57% 56ms 0.72% boost::numeric::ublas::c_matrix::operator() (partial-inline) 7ms 0.089% 76.66% 55ms 0.7% CellPropertyCollection::AddProperty 55ms 0.7% 77.36% 55ms 0.7% __memcpy_avx_unaligned_erms 0 0% 77.36% 55ms 0.7% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.36% 55ms 0.7% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 77.37% 53ms 0.68% Node::ClearAppliedForce 3ms 0.038% 77.41% 53ms 0.68% Node::ConstructNodeAttributes (inline) 49ms 0.63% 78.04% 53ms 0.68% boost::detail::shared_count::shared_count (inline) 53ms 0.68% 78.71% 53ms 0.68% boost::numeric::ublas::c_vector::operator() (partial-inline) 52ms 0.66% 79.38% 52ms 0.66% [libchaste_mesh.so] 50ms 0.64% 80.02% 50ms 0.64% [libstdc++.so.6.0.33] 49ms 0.63% 80.64% 49ms 0.63% counterclockwise 25ms 0.32% 80.96% 48ms 0.61% AbstractTetrahedralMesh::GetElement 0 0% 80.96% 48ms 0.61% BoundaryNodeWriter::Visit 3ms 0.038% 81.00% 48ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 47ms 0.6% 81.60% 47ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 81.60% 46ms 0.59% std::vector::vector (inline) 45ms 0.58% 82.18% 45ms 0.58% Node::rGetLocation 32ms 0.41% 82.59% 45ms 0.58% std::num_put::do_put 44ms 0.56% 83.15% 44ms 0.56% Node::IsDeleted 44ms 0.56% 83.71% 44ms 0.56% boost::numeric::ublas::same_impl_ex 0 0% 83.71% 44ms 0.56% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.038% 83.75% 44ms 0.56% std::_Vector_base::_M_deallocate (inline) 0 0% 83.75% 44ms 0.56% std::__new_allocator::destroy (inline) 0 0% 83.75% 44ms 0.56% std::allocator_traits::destroy (inline) 0 0% 83.75% 43ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 83.75% 43ms 0.55% CellPropertyCollection::~CellPropertyCollection (inline) 15ms 0.19% 83.94% 42ms 0.54% Determinant (inline) 29ms 0.37% 84.31% 42ms 0.54% hack_digit 0 0% 84.31% 42ms 0.54% std::_Vector_base::_Vector_base (inline) 3ms 0.038% 84.35% 41ms 0.52% NodeAttributes::NodeAttributes 41ms 0.52% 84.88% 41ms 0.52% std::ostream::sentry::sentry 0 0% 84.88% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline)