File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6584ms, 84.27% of 7813ms total Dropped 556 nodes (cum <= 39.06ms) flat flat% sum% cum cum% 0 0% 0% 7778ms 99.55% __libc_start_call_main 0 0% 0% 7778ms 99.55% __libc_start_main_impl 0 0% 0% 7778ms 99.55% _start 0 0% 0% 7764ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7764ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7764ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7764ms 99.37% main 0 0% 0% 7728ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7728ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7728ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7724ms 98.86% AbstractCellBasedSimulation::Solve 0 0% 0% 3300ms 42.24% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.026% 2913ms 37.28% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.064% 2863ms 36.64% MeshBasedCellPopulation::Update 1ms 0.013% 0.077% 1502ms 19.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.077% 1423ms 18.21% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.09% 1382ms 17.69% MutableMesh::ReMesh 1ms 0.013% 0.1% 1348ms 17.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.077% 0.18% 1284ms 16.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 32ms 0.41% 0.59% 1233ms 15.78% MeshBasedCellPopulation::SpringIterator::operator++ 114ms 1.46% 2.05% 984ms 12.59% TetrahedralMesh::EdgeIterator::operator++ 403ms 5.16% 7.21% 955ms 12.22% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.026% 7.23% 916ms 11.72% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 7.23% 915ms 11.71% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.064% 7.30% 892ms 11.42% CellPopulationElementWriter::Visit 252ms 3.23% 10.52% 887ms 11.35% __dynamic_cast 11ms 0.14% 10.66% 869ms 11.12% CellPropertyCollection::GetPropertiesType (inline) 32ms 0.41% 11.07% 788ms 10.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.064% 11.14% 773ms 9.89% MeshBasedCellPopulation::AcceptCellWriter 32ms 0.41% 11.54% 734ms 9.39% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.051% 11.60% 694ms 8.88% AbstractCellProperty::IsSubType (inline) 18ms 0.23% 11.83% 694ms 8.88% TetrahedralMesh::ImportFromMesher 1ms 0.013% 11.84% 618ms 7.91% std::ostream::operator<< (inline) 92ms 1.18% 13.02% 616ms 7.88% std::ostream::_M_insert 45ms 0.58% 13.59% 571ms 7.31% std::map::operator[] (partial-inline) 24ms 0.31% 13.90% 545ms 6.98% std::_Rb_tree::find (inline) 39ms 0.5% 14.40% 531ms 6.80% operator new 12ms 0.15% 14.55% 522ms 6.68% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.026% 14.58% 522ms 6.68% triangulate 5ms 0.064% 14.64% 509ms 6.51% Cell::GetCellProliferativeType 503ms 6.44% 21.08% 503ms 6.44% __strcmp_avx2 44ms 0.56% 21.64% 503ms 6.44% std::__new_allocator::allocate (inline) 0 0% 21.64% 501ms 6.41% std::allocator_traits::allocate (inline) 0 0% 21.64% 498ms 6.37% std::set::count (inline) 171ms 2.19% 23.83% 487ms 6.23% __GI___libc_malloc 7ms 0.09% 23.92% 482ms 6.17% std::set::insert (inline) 13ms 0.17% 24.09% 475ms 6.08% std::_Rb_tree::_M_insert_unique 204ms 2.61% 26.70% 472ms 6.04% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.70% 470ms 6.02% std::_Rb_tree::lower_bound (inline) 0 0% 26.70% 470ms 6.02% std::map::lower_bound (inline) 0 0% 26.70% 450ms 5.76% delaunay 1ms 0.013% 26.71% 449ms 5.75% divconqdelaunay 0 0% 26.71% 427ms 5.47% std::_Rb_tree::_M_create_node (inline) 3ms 0.038% 26.75% 415ms 5.31% AbstractCellBasedSimulation::DoCellBirth 33ms 0.42% 27.17% 398ms 5.09% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.17% 393ms 5.03% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.026% 27.20% 388ms 4.97% NodeLocationWriter::Visit 0 0% 27.20% 388ms 4.97% std::_Rb_tree::_M_get_node (inline) 4ms 0.051% 27.25% 380ms 4.86% Cell::GetMutationState 21ms 0.27% 27.52% 380ms 4.86% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.52% 379ms 4.85% std::set::~set (inline) 7ms 0.09% 27.61% 373ms 4.77% std::less::operator() (inline) 366ms 4.68% 32.29% 366ms 4.68% std::operator< (inline) 75ms 0.96% 33.25% 362ms 4.63% std::_Rb_tree::_M_erase 3ms 0.038% 33.29% 351ms 4.49% std::set::set (inline) 25ms 0.32% 33.61% 346ms 4.43% std::num_put::_M_insert_float 0 0% 33.61% 330ms 4.22% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.026% 33.64% 328ms 4.20% AbstractCellBasedWriter::OpenOutputFileForAppend 323ms 4.13% 37.77% 323ms 4.13% std::_Rb_tree::_S_right (inline) 1ms 0.013% 37.78% 318ms 4.07% OutputFileHandler::OpenOutputFile 38ms 0.49% 38.27% 312ms 3.99% std::_Rb_tree::_M_copy (inline) 6ms 0.077% 38.35% 305ms 3.90% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 38.36% 305ms 3.90% Element::Element 139ms 1.78% 40.14% 302ms 3.87% __GI___libc_free 16ms 0.2% 40.34% 299ms 3.83% std::_Rb_tree::_M_insert_ (inline) 2ms 0.026% 40.37% 298ms 3.81% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 40.37% 298ms 3.81% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 40.41% 296ms 3.79% Cell::ReadyToDivide 73ms 0.93% 41.34% 270ms 3.46% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.34% 262ms 3.35% std::_Rb_tree::_M_drop_node (inline) 7ms 0.09% 41.43% 260ms 3.33% std::__cxx11::collate::do_transform 15ms 0.19% 41.62% 255ms 3.26% divconqrecurse 164ms 2.10% 43.72% 254ms 3.25% _int_malloc 7ms 0.09% 43.81% 251ms 3.21% std::__new_allocator::deallocate (inline) 0 0% 43.81% 248ms 3.17% ___vsnprintf 1ms 0.013% 43.82% 248ms 3.17% __vsnprintf_internal (inline) 0 0% 43.82% 247ms 3.16% std::allocator_traits::deallocate (inline) 26ms 0.33% 44.16% 243ms 3.11% __printf_buffer 77ms 0.99% 45.14% 235ms 3.01% mergehulls 0 0% 45.14% 226ms 2.89% Cell::HasCellProperty (inline) 4ms 0.051% 45.19% 226ms 2.89% CellPropertyCollection::HasProperty 2ms 0.026% 45.22% 222ms 2.84% CellProliferativeTypesWriter::VisitCell 4ms 0.051% 45.27% 213ms 2.73% AbstractCellProperty::IsType (inline) 0 0% 45.27% 203ms 2.60% std::_Rb_tree::_M_put_node (inline) 6ms 0.077% 45.35% 197ms 2.52% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 45.49% 197ms 2.52% TetrahedralMesh::Clear 5ms 0.064% 45.55% 195ms 2.50% Element::RegisterWithNodes (inline) 2ms 0.026% 45.58% 193ms 2.47% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 45.59% 189ms 2.42% __printf_fp_spec (inline) 8ms 0.1% 45.69% 188ms 2.41% __printf_fp_l_buffer 4ms 0.051% 45.74% 186ms 2.38% Node::AddElement 5ms 0.064% 45.81% 185ms 2.37% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 86ms 1.10% 46.91% 168ms 2.15% __printf_fp_buffer_1 13ms 0.17% 47.08% 164ms 2.10% AbstractTetrahedralElement::CalculateJacobian 136ms 1.74% 48.82% 163ms 2.09% _int_free 59ms 0.76% 49.57% 163ms 2.09% std::_Rb_tree::_M_get_insert_unique_pos (inline) 47ms 0.6% 50.17% 161ms 2.06% TetrahedralMesh::EdgesEnd (partial-inline) 41ms 0.52% 50.70% 159ms 2.04% AbstractCellProperty::IsSame 0 0% 50.70% 158ms 2.02% OutputFileHandler::CommonConstructor 0 0% 50.70% 158ms 2.02% OutputFileHandler::OutputFileHandler 1ms 0.013% 50.71% 151ms 1.93% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 50.71% 148ms 1.89% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.71% 147ms 1.88% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.71% 144ms 1.84% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.71% 144ms 1.84% std::basic_ofstream::open (inline) 0 0% 50.71% 143ms 1.83% AbstractCellBasedWriter::CloseFile 2ms 0.026% 50.74% 143ms 1.83% boost::numeric::ublas::vector_assign (inline) 2ms 0.026% 50.76% 143ms 1.83% std::basic_filebuf::close 1ms 0.013% 50.77% 143ms 1.83% std::basic_filebuf::open 0 0% 50.77% 143ms 1.83% std::basic_ofstream::close (inline) 2ms 0.026% 50.80% 142ms 1.82% std::filesystem::permissions 0 0% 50.80% 141ms 1.80% FilesystemPermissions::SetFilePermissions (inline) 138ms 1.77% 52.57% 138ms 1.77% __GI_fchmodat 5ms 0.064% 52.63% 137ms 1.75% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.1% 52.73% 134ms 1.72% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.24% 52.98% 131ms 1.68% MeshBasedCellPopulation::SpringIterator::SpringIterator 24ms 0.31% 53.28% 131ms 1.68% std::num_put::_M_insert_int 22ms 0.28% 53.56% 122ms 1.56% AbstractTetrahedralElement::RefreshJacobian 12ms 0.15% 53.72% 120ms 1.54% std::_Rb_tree_const_iterator::operator++ (inline) 51ms 0.65% 54.37% 118ms 1.51% std::__ostream_insert 23ms 0.29% 54.67% 118ms 1.51% std::type_info::operator== (inline) 117ms 1.50% 56.16% 117ms 1.50% std::_Rb_tree_increment 7ms 0.09% 56.25% 115ms 1.47% boost::detail::shared_count::~shared_count (inline) 0 0% 56.25% 115ms 1.47% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 56.27% 114ms 1.46% std::_Vector_base::_M_allocate (inline) 6ms 0.077% 56.34% 113ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.026% 56.37% 112ms 1.43% Node::~Node 34ms 0.44% 56.80% 112ms 1.43% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 56.82% 110ms 1.41% alternateaxes 2ms 0.026% 56.84% 109ms 1.40% _IO_new_file_fopen 0 0% 56.84% 109ms 1.40% _IO_new_fopen 0 0% 56.84% 109ms 1.40% __fopen_internal (inline) 49ms 0.63% 57.47% 109ms 1.40% boost::shared_ptr::shared_ptr (inline) 0 0% 57.47% 109ms 1.40% std::__basic_file::open 101ms 1.29% 58.76% 109ms 1.40% vertexmedian 61ms 0.78% 59.54% 108ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 4ms 0.051% 59.59% 108ms 1.38% std::operator<< (inline) 12ms 0.15% 59.75% 107ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.038% 59.78% 106ms 1.36% __GI__IO_file_open 3ms 0.038% 59.82% 106ms 1.36% std::vector::push_back (inline) 0 0% 59.82% 102ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 59.84% 102ms 1.31% std::basic_filebuf::overflow 99ms 1.27% 61.10% 101ms 1.29% boost::detail::sp_counted_base::release 101ms 1.29% 62.40% 101ms 1.29% incircle 1ms 0.013% 62.41% 101ms 1.29% std::basic_filebuf::_M_convert_to_external 0 0% 62.41% 101ms 1.29% std::basic_filebuf::_M_terminate_output 100ms 1.28% 63.69% 100ms 1.28% __GI___libc_write 0 0% 63.69% 100ms 1.28% std::__basic_file::xsputn 7ms 0.09% 63.78% 98ms 1.25% std::vector::_M_realloc_insert 96ms 1.23% 65.01% 96ms 1.23% std::_Rb_tree_insert_and_rebalance 94ms 1.20% 66.21% 94ms 1.20% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 92ms 1.18% 67.39% 92ms 1.18% __libc_open64 3ms 0.038% 67.43% 91ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 90ms 1.15% 68.58% 90ms 1.15% [libchaste_cell_based.so] 60ms 0.77% 69.35% 85ms 1.09% std::basic_streambuf::xsputn 0 0% 69.35% 84ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.73% 70.08% 83ms 1.06% std::basic_filebuf::xsputn 32ms 0.41% 70.49% 78ms 1% AbstractElement::GetNodeLocation 0 0% 70.49% 77ms 0.99% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.49% 77ms 0.99% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 70.50% 76ms 0.97% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.50% 75ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.96% 71.46% 75ms 0.96% __GI___fstatat64 0 0% 71.46% 74ms 0.95% std::filesystem::create_directory 0 0% 71.46% 74ms 0.95% std::filesystem::status 62ms 0.79% 72.25% 74ms 0.95% vertexsort 56ms 0.72% 72.97% 72ms 0.92% malloc_consolidate 3ms 0.038% 73.01% 68ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeB 67ms 0.86% 73.86% 67ms 0.86% Node::GetIndex 6ms 0.077% 73.94% 66ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 63ms 0.81% 74.75% 63ms 0.81% __memcpy_avx_unaligned_erms 30ms 0.38% 75.13% 62ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 75.13% 61ms 0.78% boost::numeric::ublas::norm_2 (inline) 20ms 0.26% 75.39% 61ms 0.78% boost::numeric::ublas::vector_norm_2::apply (inline) 60ms 0.77% 76.16% 60ms 0.77% boost::detail::shared_count::shared_count (inline) 0 0% 76.16% 59ms 0.76% Cell::GetCellId 0 0% 76.16% 59ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.16% 59ms 0.76% std::__new_allocator::destroy (inline) 0 0% 76.16% 59ms 0.76% std::allocator_traits::destroy (inline) 57ms 0.73% 76.88% 57ms 0.73% counterclockwise 6ms 0.077% 76.96% 56ms 0.72% CellPropertyCollection::AddProperty 2ms 0.026% 76.99% 56ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 0 0% 76.99% 56ms 0.72% tcache_get (inline) 56ms 0.72% 77.70% 56ms 0.72% tcache_get_n (inline) 30ms 0.38% 78.09% 55ms 0.7% AbstractTetrahedralMesh::GetElement 43ms 0.55% 78.64% 55ms 0.7% std::num_put::do_put 0 0% 78.64% 55ms 0.7% std::vector::vector (inline) 54ms 0.69% 79.33% 54ms 0.69% std::vector::size (inline) 45ms 0.58% 79.91% 53ms 0.68% AbstractElement::GetNodeGlobalIndex 52ms 0.67% 80.57% 52ms 0.67% [libchaste_mesh.so] 0 0% 80.57% 49ms 0.63% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 80.58% 48ms 0.61% std::_Vector_base::_M_create_storage (inline) 7ms 0.09% 80.67% 48ms 0.61% std::_Vector_base::_M_deallocate (inline) 0 0% 80.67% 46ms 0.59% BoundaryNodeWriter::Visit 32ms 0.41% 81.08% 46ms 0.59% hack_digit 45ms 0.58% 81.66% 45ms 0.58% [libstdc++.so.6.0.33] 20ms 0.26% 81.91% 44ms 0.56% AbstractCellCycleModel::GetAge 0 0% 81.91% 44ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 44ms 0.56% 82.48% 44ms 0.56% boost::numeric::ublas::c_vector::operator() 2ms 0.026% 82.50% 44ms 0.56% std::__new_allocator::construct (inline) 0 0% 82.50% 44ms 0.56% std::allocator_traits::construct (inline) 0 0% 82.50% 44ms 0.56% std::map::find (inline) 17ms 0.22% 82.72% 43ms 0.55% Determinant (inline) 0 0% 82.72% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 6ms 0.077% 82.80% 43ms 0.55% Node::ConstructNodeAttributes (inline) 43ms 0.55% 83.35% 43ms 0.55% Node::IsDeleted 0 0% 83.35% 43ms 0.55% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.013% 83.36% 43ms 0.55% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 83.36% 42ms 0.54% AbstractCentreBasedCellPopulation::CreateCellPair 6ms 0.077% 83.44% 42ms 0.54% Element::~Element 42ms 0.54% 83.98% 42ms 0.54% std::_Rb_tree_header::_M_reset (inline) 19ms 0.24% 84.22% 41ms 0.52% AbstractTetrahedralMesh::GetNumAllElements 0 0% 84.22% 41ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.051% 84.27% 41ms 0.52% Inverse