File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6459ms, 84.93% of 7605ms total Dropped 603 nodes (cum <= 38.02ms) flat flat% sum% cum cum% 0 0% 0% 7570ms 99.54% __libc_start_call_main 0 0% 0% 7570ms 99.54% __libc_start_main_impl 0 0% 0% 7570ms 99.54% _start 0 0% 0% 7556ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7556ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7556ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7556ms 99.36% main 0 0% 0% 7517ms 98.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7517ms 98.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7517ms 98.84% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7514ms 98.80% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3210ms 42.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.026% 2741ms 36.04% MeshBasedCellPopulation::Update 1ms 0.013% 0.039% 2718ms 35.74% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.039% 1579ms 20.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.053% 1443ms 18.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.039% 0.092% 1384ms 18.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.11% 1344ms 17.67% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.11% 1339ms 17.61% MutableMesh::ReMesh 17ms 0.22% 0.33% 1176ms 15.46% MeshBasedCellPopulation::SpringIterator::operator++ 426ms 5.60% 5.93% 978ms 12.86% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.053% 5.98% 951ms 12.50% AbstractTwoBodyInteractionForce::AddForceContribution 97ms 1.28% 7.26% 951ms 12.50% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.013% 7.27% 932ms 12.26% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.14% 7.42% 916ms 12.04% CellPropertyCollection::GetPropertiesType (inline) 271ms 3.56% 10.98% 912ms 11.99% __dynamic_cast 4ms 0.053% 11.03% 877ms 11.53% CellPopulationElementWriter::Visit 45ms 0.59% 11.62% 835ms 10.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.026% 11.65% 786ms 10.34% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.29% 11.94% 736ms 9.68% AbstractCellPopulation::GetCellUsingLocationIndex 13ms 0.17% 12.11% 718ms 9.44% TetrahedralMesh::ImportFromMesher 7ms 0.092% 12.20% 703ms 9.24% AbstractCellProperty::IsSubType (inline) 64ms 0.84% 13.04% 601ms 7.90% std::map::operator[] (partial-inline) 88ms 1.16% 14.20% 599ms 7.88% std::ostream::_M_insert 0 0% 14.20% 599ms 7.88% std::ostream::operator<< (inline) 44ms 0.58% 14.78% 547ms 7.19% operator new 536ms 7.05% 21.83% 536ms 7.05% __strcmp_avx2 16ms 0.21% 22.04% 521ms 6.85% std::_Rb_tree::find (inline) 6ms 0.079% 22.12% 520ms 6.84% Cell::GetCellProliferativeType 2ms 0.026% 22.14% 512ms 6.73% LegacyCellProliferativeTypesWriter::VisitCell 174ms 2.29% 24.43% 491ms 6.46% __GI___libc_malloc 0 0% 24.43% 491ms 6.46% std::_Rb_tree::lower_bound (inline) 0 0% 24.43% 491ms 6.46% std::map::lower_bound (inline) 36ms 0.47% 24.90% 488ms 6.42% std::__new_allocator::allocate (inline) 0 0% 24.90% 483ms 6.35% std::allocator_traits::allocate (inline) 0 0% 24.90% 479ms 6.30% std::set::count (inline) 190ms 2.50% 27.40% 468ms 6.15% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.092% 27.50% 467ms 6.14% std::set::insert (inline) 9ms 0.12% 27.61% 460ms 6.05% std::_Rb_tree::_M_insert_unique 2ms 0.026% 27.64% 456ms 6.00% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 27.65% 452ms 5.94% triangulate 0 0% 27.65% 398ms 5.23% std::_Rb_tree::_M_create_node (inline) 0 0% 27.65% 397ms 5.22% Cell::GetMutationState 28ms 0.37% 28.02% 395ms 5.19% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.02% 394ms 5.18% delaunay 0 0% 28.02% 394ms 5.18% divconqdelaunay 1ms 0.013% 28.03% 380ms 5.00% NodeLocationWriter::Visit 0 0% 28.03% 373ms 4.90% std::set::~set (inline) 0 0% 28.03% 372ms 4.89% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.03% 365ms 4.80% std::_Rb_tree::_M_get_node (inline) 85ms 1.12% 29.15% 363ms 4.77% std::_Rb_tree::_M_erase 9ms 0.12% 29.27% 352ms 4.63% std::less::operator() (inline) 2ms 0.026% 29.30% 351ms 4.62% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 29.30% 351ms 4.62% MeshBasedCellPopulation::GetDampingConstant 348ms 4.58% 33.87% 348ms 4.58% std::_Rb_tree::_S_right (inline) 343ms 4.51% 38.38% 343ms 4.51% std::operator< (inline) 19ms 0.25% 38.63% 325ms 4.27% std::_Rb_tree::_Rb_tree (partial-inline) 24ms 0.32% 38.95% 322ms 4.23% std::num_put::_M_insert_float 4ms 0.053% 39.00% 311ms 4.09% Cell::ReadyToDivide 3ms 0.039% 39.04% 298ms 3.92% std::set::set (inline) 2ms 0.026% 39.07% 293ms 3.85% Element::Element 8ms 0.11% 39.17% 288ms 3.79% AbstractCellPopulation::IsCellAttachedToLocationIndex 96ms 1.26% 40.43% 287ms 3.77% __GI___libc_free 31ms 0.41% 40.84% 282ms 3.71% std::_Rb_tree::_M_copy (inline) 15ms 0.2% 41.04% 280ms 3.68% std::_Rb_tree::_M_insert_ (inline) 5ms 0.066% 41.10% 266ms 3.50% AbstractCellProperty::IsType (inline) 166ms 2.18% 43.29% 260ms 3.42% _int_malloc 3ms 0.039% 43.33% 259ms 3.41% std::__cxx11::collate::do_transform 0 0% 43.33% 258ms 3.39% Cell::HasCellProperty (inline) 5ms 0.066% 43.39% 258ms 3.39% CellPropertyCollection::HasProperty 7ms 0.092% 43.48% 258ms 3.39% std::__new_allocator::deallocate (inline) 0 0% 43.48% 255ms 3.35% std::allocator_traits::deallocate (inline) 1ms 0.013% 43.50% 249ms 3.27% ___vsnprintf 1ms 0.013% 43.51% 248ms 3.26% __vsnprintf_internal (inline) 11ms 0.14% 43.66% 248ms 3.26% divconqrecurse 68ms 0.89% 44.55% 247ms 3.25% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.55% 246ms 3.23% std::_Rb_tree::_M_drop_node (inline) 2ms 0.026% 44.58% 245ms 3.22% CellProliferativeTypesWriter::VisitCell 36ms 0.47% 45.05% 239ms 3.14% __printf_buffer 60ms 0.79% 45.84% 232ms 3.05% mergehulls 16ms 0.21% 46.05% 211ms 2.77% TetrahedralMesh::Clear 0 0% 46.05% 209ms 2.75% std::_Rb_tree::_M_put_node (inline) 1ms 0.013% 46.06% 206ms 2.71% AbstractPhaseBasedCellCycleModel::ReadyToDivide 10ms 0.13% 46.19% 203ms 2.67% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.14% 46.34% 190ms 2.50% __printf_fp_l_buffer 0 0% 46.34% 190ms 2.50% __printf_fp_spec (inline) 170ms 2.24% 48.57% 190ms 2.50% _int_free 43ms 0.57% 49.14% 184ms 2.42% AbstractCellProperty::IsSame 4ms 0.053% 49.19% 183ms 2.41% Element::RegisterWithNodes (inline) 6ms 0.079% 49.27% 182ms 2.39% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.039% 49.31% 178ms 2.34% Node::AddElement 83ms 1.09% 50.40% 172ms 2.26% __printf_fp_buffer_1 62ms 0.82% 51.22% 171ms 2.25% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 51.22% 170ms 2.24% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.22% 170ms 2.24% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 51.23% 168ms 2.21% OutputFileHandler::OpenOutputFile 0 0% 51.23% 163ms 2.14% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.23% 160ms 2.10% std::basic_ofstream::open (inline) 17ms 0.22% 51.45% 159ms 2.09% AbstractTetrahedralElement::CalculateJacobian 42ms 0.55% 52.01% 159ms 2.09% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.026% 52.03% 159ms 2.09% std::basic_filebuf::open 5ms 0.066% 52.10% 150ms 1.97% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 52.11% 146ms 1.92% TetrahedralMesh::RefreshJacobianCachedData 34ms 0.45% 52.56% 145ms 1.91% std::num_put::_M_insert_int 5ms 0.066% 52.62% 142ms 1.87% boost::numeric::ublas::c_vector::c_vector (inline) 22ms 0.29% 52.91% 141ms 1.85% std::type_info::operator== (inline) 0 0% 52.91% 136ms 1.79% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.026% 52.94% 136ms 1.79% OutputFileHandler::OutputFileHandler 0 0% 52.94% 134ms 1.76% AbstractCellBasedWriter::CloseFile 0 0% 52.94% 134ms 1.76% OutputFileHandler::CommonConstructor 1ms 0.013% 52.95% 134ms 1.76% std::basic_ofstream::close (inline) 11ms 0.14% 53.10% 133ms 1.75% Node::~Node 0 0% 53.10% 133ms 1.75% std::basic_filebuf::close 8ms 0.11% 53.20% 131ms 1.72% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 53.20% 131ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 56ms 0.74% 53.94% 129ms 1.70% std::__ostream_insert 14ms 0.18% 54.12% 125ms 1.64% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.12% 123ms 1.62% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.14% 54.27% 123ms 1.62% std::_Rb_tree_const_iterator::operator++ (inline) 17ms 0.22% 54.49% 118ms 1.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 54.49% 118ms 1.55% std::_Vector_base::_M_allocate (inline) 117ms 1.54% 56.03% 117ms 1.54% std::_Rb_tree_increment 1ms 0.013% 56.04% 116ms 1.53% std::__basic_file::open 0 0% 56.04% 115ms 1.51% _IO_new_fopen 1ms 0.013% 56.06% 115ms 1.51% __fopen_internal (inline) 5ms 0.066% 56.12% 114ms 1.50% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 56.13% 113ms 1.49% _IO_new_file_fopen 2ms 0.026% 56.16% 112ms 1.47% __GI__IO_file_open 111ms 1.46% 57.62% 111ms 1.46% incircle 31ms 0.41% 58.03% 110ms 1.45% boost::numeric::ublas::indexing_vector_assign 46ms 0.6% 58.63% 108ms 1.42% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 58.65% 107ms 1.41% std::operator<< (inline) 5ms 0.066% 58.71% 107ms 1.41% std::vector::push_back (inline) 4ms 0.053% 58.76% 105ms 1.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 17ms 0.22% 58.99% 105ms 1.38% AbstractTetrahedralElement::RefreshJacobian 10ms 0.13% 59.12% 102ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 59.12% 102ms 1.34% boost::shared_ptr::~shared_ptr (inline) 83ms 1.09% 60.21% 101ms 1.33% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.039% 60.25% 101ms 1.33% std::vector::_M_realloc_insert 99ms 1.30% 61.55% 99ms 1.30% __libc_open64 0 0% 61.55% 97ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 61.56% 92ms 1.21% std::basic_filebuf::_M_terminate_output 1ms 0.013% 61.58% 91ms 1.20% std::basic_filebuf::overflow 90ms 1.18% 62.76% 90ms 1.18% [libchaste_cell_based.so] 88ms 1.16% 63.92% 90ms 1.18% boost::detail::sp_counted_base::release 1ms 0.013% 63.93% 90ms 1.18% std::basic_filebuf::_M_convert_to_external 89ms 1.17% 65.10% 89ms 1.17% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 65.12% 88ms 1.16% std::__basic_file::xsputn 86ms 1.13% 66.25% 87ms 1.14% __GI___libc_write 2ms 0.026% 66.27% 87ms 1.14% alternateaxes 76ms 1% 67.27% 85ms 1.12% vertexmedian 3ms 0.039% 67.31% 83ms 1.09% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.31% 80ms 1.05% Cell::GetCellId 63ms 0.83% 68.14% 78ms 1.03% malloc_consolidate 77ms 1.01% 69.15% 77ms 1.01% std::_Rb_tree_insert_and_rebalance 63ms 0.83% 69.98% 76ms 1% AbstractElement::GetNodeGlobalIndex 34ms 0.45% 70.43% 76ms 1% AbstractElement::GetNodeLocation 47ms 0.62% 71.05% 74ms 0.97% std::basic_streambuf::xsputn 4ms 0.053% 71.10% 72ms 0.95% std::filesystem::status 8ms 0.11% 71.20% 69ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 69ms 0.91% 72.11% 69ms 0.91% __GI___fstatat64 67ms 0.88% 72.99% 67ms 0.88% __memcpy_avx_unaligned_erms 0 0% 72.99% 67ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.99% 67ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 34ms 0.45% 73.44% 63ms 0.83% std::basic_filebuf::xsputn 7ms 0.092% 73.53% 62ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeA 60ms 0.79% 74.32% 62ms 0.82% boost::detail::shared_count::shared_count (inline) 0 0% 74.32% 62ms 0.82% std::filesystem::create_directory 5ms 0.066% 74.39% 60ms 0.79% CellPropertyCollection::AddProperty 58ms 0.76% 75.15% 58ms 0.76% [libstdc++.so.6.0.33] 40ms 0.53% 75.67% 58ms 0.76% boost::numeric::ublas::c_matrix::operator() 57ms 0.75% 76.42% 57ms 0.75% boost::shared_ptr::operator-> (inline) 29ms 0.38% 76.80% 56ms 0.74% AbstractCellCycleModel::GetAge 2ms 0.026% 76.83% 56ms 0.74% Node::ConstructNodeAttributes (inline) 56ms 0.74% 77.57% 56ms 0.74% counterclockwise 20ms 0.26% 77.83% 55ms 0.72% Determinant (inline) 55ms 0.72% 78.55% 55ms 0.72% Node::GetIndex 55ms 0.72% 79.28% 55ms 0.72% [libchaste_mesh.so] 55ms 0.72% 80.00% 55ms 0.72% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 80.00% 54ms 0.71% Node::ClearAppliedForce 43ms 0.57% 80.57% 53ms 0.7% std::num_put::do_put 28ms 0.37% 80.93% 52ms 0.68% AbstractTetrahedralMesh::GetElement 47ms 0.62% 81.55% 52ms 0.68% vertexsort 35ms 0.46% 82.01% 51ms 0.67% hack_digit 0 0% 82.01% 51ms 0.67% tcache_get (inline) 51ms 0.67% 82.68% 51ms 0.67% tcache_get_n (inline) 49ms 0.64% 83.33% 49ms 0.64% std::vector::size (inline) 0 0% 83.33% 49ms 0.64% std::vector::vector (inline) 0 0% 83.33% 48ms 0.63% boost::numeric::ublas::norm_2 (inline) 11ms 0.14% 83.47% 48ms 0.63% boost::numeric::ublas::vector_norm_2::apply (inline) 5ms 0.066% 83.54% 48ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 83.54% 47ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 83.54% 46ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.013% 83.55% 46ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 46ms 0.6% 84.16% 46ms 0.6% std::ostream::sentry::sentry 8ms 0.11% 84.26% 45ms 0.59% Inverse 0 0% 84.26% 45ms 0.59% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 84.27% 44ms 0.58% std::_Vector_base::_M_create_storage (inline) 0 0% 84.27% 43ms 0.57% BoundaryNodeWriter::Visit 43ms 0.57% 84.84% 43ms 0.57% Node::IsDeleted 4ms 0.053% 84.89% 42ms 0.55% NodeAttributes::NodeAttributes 2ms 0.026% 84.92% 41ms 0.54% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 84.92% 40ms 0.53% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 84.92% 40ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.92% 39ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.013% 84.93% 39ms 0.51% std::__basic_file::close