File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6844ms, 84.86% of 8065ms total Dropped 568 nodes (cum <= 40.33ms) flat flat% sum% cum cum% 0 0% 0% 8031ms 99.58% __libc_start_call_main 0 0% 0% 8031ms 99.58% __libc_start_main_impl 0 0% 0% 8031ms 99.58% _start 0 0% 0% 8015ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8015ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8015ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8015ms 99.38% main 0 0% 0% 7973ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7973ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7973ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 7970ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3434ms 42.58% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.037% 2990ms 37.07% MeshBasedCellPopulation::Update 1ms 0.012% 0.05% 2972ms 36.85% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.074% 1555ms 19.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.074% 1506ms 18.67% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.087% 1436ms 17.81% MutableMesh::ReMesh 2ms 0.025% 0.11% 1411ms 17.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.099% 0.21% 1350ms 16.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.17% 0.38% 1310ms 16.24% MeshBasedCellPopulation::SpringIterator::operator++ 111ms 1.38% 1.76% 1068ms 13.24% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 1.80% 992ms 12.30% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 437ms 5.42% 7.22% 955ms 11.84% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.012% 7.23% 949ms 11.77% AbstractTwoBodyInteractionForce::AddForceContribution 285ms 3.53% 10.76% 940ms 11.66% __dynamic_cast 9ms 0.11% 10.87% 919ms 11.39% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.05% 10.92% 875ms 10.85% CellPopulationElementWriter::Visit 42ms 0.52% 11.44% 842ms 10.44% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 27ms 0.33% 11.78% 804ms 9.97% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.89% 802ms 9.94% MeshBasedCellPopulation::AcceptCellWriter 0 0% 11.89% 738ms 9.15% AbstractCellProperty::IsSubType (inline) 15ms 0.19% 12.08% 710ms 8.80% TetrahedralMesh::ImportFromMesher 0 0% 12.08% 590ms 7.32% std::ostream::operator<< (inline) 97ms 1.20% 13.28% 588ms 7.29% std::ostream::_M_insert 38ms 0.47% 13.75% 581ms 7.20% operator new 44ms 0.55% 14.30% 574ms 7.12% std::map::operator[] (partial-inline) 1ms 0.012% 14.31% 568ms 7.04% triangulate 3ms 0.037% 14.35% 566ms 7.02% Cell::GetCellProliferativeType 185ms 2.29% 16.64% 544ms 6.75% __GI___libc_malloc 6ms 0.074% 16.71% 537ms 6.66% std::set::insert (inline) 12ms 0.15% 16.86% 531ms 6.58% std::_Rb_tree::_M_insert_unique 507ms 6.29% 23.15% 507ms 6.29% __strcmp_avx2 20ms 0.25% 23.40% 507ms 6.29% std::_Rb_tree::find (inline) 2ms 0.025% 23.42% 504ms 6.25% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.42% 500ms 6.20% delaunay 31ms 0.38% 23.81% 500ms 6.20% std::__new_allocator::allocate (inline) 1ms 0.012% 23.82% 499ms 6.19% divconqdelaunay 0 0% 23.82% 499ms 6.19% std::allocator_traits::allocate (inline) 0 0% 23.82% 487ms 6.04% std::_Rb_tree::lower_bound (inline) 0 0% 23.82% 487ms 6.04% std::map::lower_bound (inline) 0 0% 23.82% 481ms 5.96% std::set::count (inline) 226ms 2.80% 26.62% 456ms 5.65% __cxxabiv1::__si_class_type_info::__do_dyncast 49ms 0.61% 27.23% 450ms 5.58% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.025% 27.25% 436ms 5.41% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.25% 420ms 5.21% std::set::~set (inline) 0 0% 27.25% 410ms 5.08% std::_Rb_tree::_M_create_node (inline) 0 0% 27.25% 394ms 4.89% std::_Rb_tree::_Alloc_node::operator() (inline) 84ms 1.04% 28.30% 394ms 4.89% std::_Rb_tree::_M_erase 24ms 0.3% 28.59% 391ms 4.85% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.59% 368ms 4.56% std::_Rb_tree::_M_get_node (inline) 10ms 0.12% 28.72% 368ms 4.56% std::set::set (inline) 1ms 0.012% 28.73% 361ms 4.48% NodeLocationWriter::Visit 2ms 0.025% 28.75% 360ms 4.46% Cell::GetMutationState 6ms 0.074% 28.83% 359ms 4.45% std::less::operator() (inline) 353ms 4.38% 33.21% 353ms 4.38% std::operator< (inline) 1ms 0.012% 33.22% 330ms 4.09% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.22% 328ms 4.07% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.22% 327ms 4.05% OutputFileHandler::OpenOutputFile 21ms 0.26% 33.48% 326ms 4.04% std::num_put::_M_insert_float 9ms 0.11% 33.59% 325ms 4.03% AbstractCellPopulation::IsCellAttachedToLocationIndex 38ms 0.47% 34.06% 325ms 4.03% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 34.09% 313ms 3.88% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 34.11% 309ms 3.83% AbstractCentreBasedCellPopulation::GetDampingConstant 18ms 0.22% 34.33% 306ms 3.79% std::_Rb_tree::_M_insert_ (inline) 8ms 0.099% 34.43% 304ms 3.77% Cell::ReadyToDivide 299ms 3.71% 38.14% 299ms 3.71% std::_Rb_tree::_S_right (inline) 189ms 2.34% 40.48% 296ms 3.67% _int_malloc 89ms 1.10% 41.59% 293ms 3.63% __GI___libc_free 0 0% 41.59% 293ms 3.63% std::_Rb_tree::_M_drop_node (inline) 2ms 0.025% 41.61% 286ms 3.55% Element::Element 86ms 1.07% 42.68% 276ms 3.42% std::_Rb_tree::_M_clone_node (inline) 16ms 0.2% 42.88% 272ms 3.37% divconqrecurse 11ms 0.14% 43.01% 264ms 3.27% std::__cxx11::collate::do_transform 3ms 0.037% 43.05% 258ms 3.20% std::__new_allocator::deallocate (inline) 0 0% 43.05% 254ms 3.15% std::allocator_traits::deallocate (inline) 2ms 0.025% 43.08% 253ms 3.14% CellProliferativeTypesWriter::VisitCell 1ms 0.012% 43.09% 242ms 3.00% ___vsnprintf 71ms 0.88% 43.97% 242ms 3.00% mergehulls 0 0% 43.97% 241ms 2.99% __vsnprintf_internal (inline) 31ms 0.38% 44.35% 239ms 2.96% __printf_buffer 0 0% 44.35% 231ms 2.86% std::_Rb_tree::_M_put_node (inline) 11ms 0.14% 44.49% 218ms 2.70% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.012% 44.50% 214ms 2.65% AbstractCellProperty::IsType (inline) 77ms 0.95% 45.46% 213ms 2.64% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.025% 45.48% 210ms 2.60% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.48% 210ms 2.60% Cell::HasCellProperty (inline) 1ms 0.012% 45.49% 210ms 2.60% CellPropertyCollection::HasProperty 6ms 0.074% 45.57% 204ms 2.53% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 174ms 2.16% 47.72% 204ms 2.53% _int_free 13ms 0.16% 47.89% 190ms 2.36% TetrahedralMesh::Clear 5ms 0.062% 47.95% 190ms 2.36% __printf_fp_l_buffer 0 0% 47.95% 190ms 2.36% __printf_fp_spec (inline) 97ms 1.20% 49.15% 181ms 2.24% __printf_fp_buffer_1 14ms 0.17% 49.32% 180ms 2.23% AbstractTetrahedralElement::CalculateJacobian 6ms 0.074% 49.40% 179ms 2.22% Element::RegisterWithNodes (inline) 36ms 0.45% 49.85% 176ms 2.18% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 49.85% 173ms 2.15% std::basic_ofstream::basic_ofstream (inline) 1ms 0.012% 49.86% 172ms 2.13% OutputFileHandler::CommonConstructor 0 0% 49.86% 172ms 2.13% OutputFileHandler::OutputFileHandler 1ms 0.012% 49.87% 170ms 2.11% Node::AddElement 0 0% 49.87% 170ms 2.11% std::basic_filebuf::open 0 0% 49.87% 170ms 2.11% std::basic_ofstream::open (inline) 0 0% 49.87% 165ms 2.05% OutputFileHandler::MakeFoldersAndReturnFullPath 26ms 0.32% 50.19% 160ms 1.98% AbstractCellProperty::IsSame 1ms 0.012% 50.20% 152ms 1.88% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.012% 50.22% 151ms 1.87% alternateaxes 0 0% 50.22% 150ms 1.86% AbstractCellBasedWriter::CloseFile 0 0% 50.22% 150ms 1.86% std::basic_filebuf::close 0 0% 50.22% 150ms 1.86% std::basic_ofstream::close (inline) 140ms 1.74% 51.95% 149ms 1.85% vertexmedian 13ms 0.16% 52.11% 144ms 1.79% boost::detail::shared_count::~shared_count (inline) 0 0% 52.11% 144ms 1.79% boost::shared_ptr::~shared_ptr (inline) 0 0% 52.11% 142ms 1.76% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.025% 52.14% 140ms 1.74% boost::numeric::ublas::vector_assign (inline) 13ms 0.16% 52.30% 138ms 1.71% MeshBasedCellPopulation::SpringIterator::SpringIterator 63ms 0.78% 53.08% 137ms 1.70% boost::shared_ptr::shared_ptr (inline) 49ms 0.61% 53.69% 137ms 1.70% std::__ostream_insert 8ms 0.099% 53.79% 136ms 1.69% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.062% 53.85% 135ms 1.67% boost::numeric::ublas::c_vector::c_vector (inline) 31ms 0.38% 54.23% 134ms 1.66% std::type_info::operator== (inline) 1ms 0.012% 54.25% 132ms 1.64% std::_Vector_base::_M_allocate (inline) 2ms 0.025% 54.27% 130ms 1.61% std::__basic_file::open 1ms 0.012% 54.28% 127ms 1.57% _IO_new_fopen 127ms 1.57% 55.86% 127ms 1.57% incircle 0 0% 55.86% 126ms 1.56% __fopen_internal (inline) 122ms 1.51% 57.37% 126ms 1.56% boost::detail::sp_counted_base::release 85ms 1.05% 58.43% 125ms 1.55% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 58.43% 124ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.012% 58.44% 124ms 1.54% _IO_new_file_fopen 1ms 0.012% 58.45% 124ms 1.54% std::filesystem::permissions 0 0% 58.45% 122ms 1.51% __GI__IO_file_open 122ms 1.51% 59.96% 122ms 1.51% __GI_fchmodat 14ms 0.17% 60.14% 119ms 1.48% AbstractTetrahedralElement::RefreshJacobian 12ms 0.15% 60.29% 119ms 1.48% std::vector::push_back (inline) 8ms 0.099% 60.38% 116ms 1.44% Node::~Node 4ms 0.05% 60.43% 114ms 1.41% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.062% 60.50% 110ms 1.36% std::_Rb_tree_const_iterator::operator++ (inline) 107ms 1.33% 61.82% 109ms 1.35% __libc_open64 1ms 0.012% 61.84% 108ms 1.34% std::basic_filebuf::overflow 1ms 0.012% 61.85% 108ms 1.34% std::operator<< (inline) 0 0% 61.85% 107ms 1.33% std::basic_filebuf::_M_convert_to_external 0 0% 61.85% 107ms 1.33% std::basic_filebuf::_M_terminate_output 105ms 1.30% 63.15% 106ms 1.31% __GI___libc_write 106ms 1.31% 64.46% 106ms 1.31% std::_Rb_tree_increment 0 0% 64.46% 106ms 1.31% std::__basic_file::xsputn 14ms 0.17% 64.64% 105ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 25ms 0.31% 64.95% 104ms 1.29% std::num_put::_M_insert_int 102ms 1.26% 66.21% 102ms 1.26% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.012% 66.22% 101ms 1.25% AbstractCellPopulation::Iterator::operator++ (inline) 6ms 0.074% 66.30% 101ms 1.25% std::vector::_M_realloc_insert 32ms 0.4% 66.70% 99ms 1.23% boost::numeric::ublas::indexing_vector_assign 95ms 1.18% 67.87% 95ms 1.18% [libchaste_cell_based.so] 64ms 0.79% 68.67% 95ms 1.18% std::basic_filebuf::xsputn 0 0% 68.67% 92ms 1.14% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 68.68% 92ms 1.14% std::filesystem::create_directory 36ms 0.45% 69.13% 91ms 1.13% AbstractElement::GetNodeLocation 91ms 1.13% 70.25% 91ms 1.13% std::_Rb_tree_insert_and_rebalance 60ms 0.74% 71.00% 87ms 1.08% malloc_consolidate 0 0% 71.00% 83ms 1.03% Cell::GetCellId 0 0% 71.00% 75ms 0.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.00% 75ms 0.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.05% 71.05% 75ms 0.93% std::filesystem::status 2ms 0.025% 71.07% 74ms 0.92% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 74ms 0.92% 71.99% 74ms 0.92% boost::detail::shared_count::shared_count (inline) 6ms 0.074% 72.06% 73ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 72ms 0.89% 72.96% 72ms 0.89% std::vector::size (inline) 71ms 0.88% 73.84% 71ms 0.88% __GI___fstatat64 4ms 0.05% 73.89% 70ms 0.87% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 59ms 0.73% 74.62% 68ms 0.84% vertexsort 65ms 0.81% 75.42% 65ms 0.81% __memcpy_avx_unaligned_erms 46ms 0.57% 76.00% 64ms 0.79% AbstractElement::GetNodeGlobalIndex 9ms 0.11% 76.11% 64ms 0.79% CellPropertyCollection::AddProperty 32ms 0.4% 76.50% 62ms 0.77% AbstractTetrahedralMesh::GetElement 0 0% 76.50% 62ms 0.77% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.50% 62ms 0.77% std::__new_allocator::destroy (inline) 0 0% 76.50% 62ms 0.77% std::allocator_traits::destroy (inline) 60ms 0.74% 77.25% 60ms 0.74% Node::GetIndex 2ms 0.025% 77.27% 60ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 39ms 0.48% 77.76% 60ms 0.74% boost::numeric::ublas::c_matrix::operator() (partial-inline) 20ms 0.25% 78.00% 59ms 0.73% Determinant (inline) 45ms 0.56% 78.56% 59ms 0.73% std::num_put::do_put 0 0% 78.56% 58ms 0.72% tcache_get (inline) 58ms 0.72% 79.28% 58ms 0.72% tcache_get_n (inline) 4ms 0.05% 79.33% 57ms 0.71% Node::ConstructNodeAttributes (inline) 1ms 0.012% 79.34% 56ms 0.69% AbstractCentreBasedCellPopulation::CreateCellPair 56ms 0.69% 80.04% 56ms 0.69% __GI___mkdir 0 0% 80.04% 55ms 0.68% boost::numeric::ublas::norm_2 (inline) 17ms 0.21% 80.25% 55ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.25% 53ms 0.66% Node::ClearAppliedForce 53ms 0.66% 80.91% 53ms 0.66% [libchaste_mesh.so] 35ms 0.43% 81.34% 53ms 0.66% std::basic_streambuf::xsputn 1ms 0.012% 81.35% 52ms 0.64% BoundaryNodeWriter::Visit 0 0% 81.35% 51ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.025% 81.38% 50ms 0.62% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.6% 81.97% 48ms 0.6% boost::numeric::ublas::c_vector::operator() 48ms 0.6% 82.57% 48ms 0.6% counterclockwise 0 0% 82.57% 47ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 82.57% 47ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 39ms 0.48% 83.05% 47ms 0.58% hack_digit 0 0% 83.05% 47ms 0.58% std::vector::vector (inline) 0 0% 83.05% 46ms 0.57% std::_Vector_base::_Vector_base (inline) 14ms 0.17% 83.22% 44ms 0.55% AbstractTetrahedralMesh::GetNumAllElements 44ms 0.55% 83.77% 44ms 0.55% Node::rGetLocation 0 0% 83.77% 44ms 0.55% std::_Vector_base::_M_create_storage (inline) 0 0% 83.77% 44ms 0.55% std::__new_allocator::construct (inline) 0 0% 83.77% 44ms 0.55% std::allocator_traits::construct (inline) 5ms 0.062% 83.83% 43ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 42ms 0.52% 84.35% 42ms 0.52% [libstdc++.so.6.0.33] 0 0% 84.35% 42ms 0.52% std::_Rb_tree::_M_construct_node (inline) 41ms 0.51% 84.86% 41ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 84.86% 41ms 0.51% std::__basic_file::close