File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6651ms, 84.40% of 7880ms total Dropped 581 nodes (cum <= 39.40ms) flat flat% sum% cum cum% 0 0% 0% 7844ms 99.54% __libc_start_call_main 0 0% 0% 7844ms 99.54% __libc_start_main_impl 0 0% 0% 7844ms 99.54% _start 0 0% 0% 7830ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7830ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7830ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7830ms 99.37% main 0 0% 0% 7795ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7795ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7795ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7791ms 98.87% AbstractCellBasedSimulation::Solve 0 0% 0% 3345ms 42.45% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.051% 0.051% 2906ms 36.88% MeshBasedCellPopulation::Update 2ms 0.025% 0.076% 2862ms 36.32% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.076% 1570ms 19.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.089% 1429ms 18.13% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.089% 1415ms 17.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.089% 1411ms 17.91% MutableMesh::ReMesh 11ms 0.14% 0.23% 1353ms 17.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 23ms 0.29% 0.52% 1258ms 15.96% MeshBasedCellPopulation::SpringIterator::operator++ 120ms 1.52% 2.04% 1011ms 12.83% TetrahedralMesh::EdgeIterator::operator++ 437ms 5.55% 7.59% 967ms 12.27% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.076% 7.66% 913ms 11.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 7ms 0.089% 7.75% 908ms 11.52% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.16% 7.92% 895ms 11.36% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.076% 7.99% 866ms 10.99% CellPopulationElementWriter::Visit 277ms 3.52% 11.51% 832ms 10.56% __dynamic_cast 36ms 0.46% 11.97% 800ms 10.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.038% 12.01% 768ms 9.75% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.36% 12.36% 725ms 9.20% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.51% 709ms 9.00% TetrahedralMesh::ImportFromMesher 4ms 0.051% 12.56% 678ms 8.60% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 12.59% 612ms 7.77% std::ostream::operator<< (inline) 91ms 1.15% 13.74% 610ms 7.74% std::ostream::_M_insert 56ms 0.71% 14.45% 607ms 7.70% std::map::operator[] (partial-inline) 48ms 0.61% 15.06% 555ms 7.04% operator new 2ms 0.025% 15.09% 541ms 6.87% triangulate 7ms 0.089% 15.18% 533ms 6.76% std::set::insert (inline) 11ms 0.14% 15.32% 527ms 6.69% std::_Rb_tree::_M_insert_unique 22ms 0.28% 15.60% 521ms 6.61% std::_Rb_tree::find (inline) 169ms 2.14% 17.74% 501ms 6.36% __GI___libc_malloc 43ms 0.55% 18.29% 501ms 6.36% std::__new_allocator::allocate (inline) 0 0% 18.29% 496ms 6.29% std::_Rb_tree::lower_bound (inline) 0 0% 18.29% 496ms 6.29% std::map::lower_bound (inline) 0 0% 18.29% 495ms 6.28% std::allocator_traits::allocate (inline) 0 0% 18.29% 486ms 6.17% delaunay 2ms 0.025% 18.31% 486ms 6.17% divconqdelaunay 2ms 0.025% 18.34% 476ms 6.04% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.038% 18.38% 472ms 5.99% Cell::GetCellProliferativeType 0 0% 18.38% 465ms 5.90% std::set::count (inline) 0 0% 18.38% 432ms 5.48% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 18.39% 424ms 5.38% AbstractCellBasedSimulation::DoCellBirth 423ms 5.37% 23.76% 423ms 5.37% __strcmp_avx2 213ms 2.70% 26.46% 422ms 5.36% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.076% 26.54% 408ms 5.18% Cell::GetMutationState 31ms 0.39% 26.93% 408ms 5.18% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.93% 407ms 5.16% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.025% 26.95% 394ms 5.00% NodeLocationWriter::Visit 0 0% 26.95% 385ms 4.89% std::_Rb_tree::_M_get_node (inline) 0 0% 26.95% 383ms 4.86% std::set::~set (inline) 87ms 1.10% 28.06% 373ms 4.73% std::_Rb_tree::_M_erase 11ms 0.14% 28.20% 353ms 4.48% std::less::operator() (inline) 17ms 0.22% 28.41% 350ms 4.44% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 28.43% 349ms 4.43% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 28.43% 349ms 4.43% MeshBasedCellPopulation::GetDampingConstant 342ms 4.34% 32.77% 342ms 4.34% std::operator< (inline) 26ms 0.33% 33.10% 341ms 4.33% std::num_put::_M_insert_float 22ms 0.28% 33.38% 338ms 4.29% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 33.41% 326ms 4.14% std::set::set (inline) 320ms 4.06% 37.47% 320ms 4.06% std::_Rb_tree::_S_right (inline) 0 0% 37.47% 317ms 4.02% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.47% 316ms 4.01% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.47% 313ms 3.97% OutputFileHandler::OpenOutputFile 99ms 1.26% 38.73% 306ms 3.88% __GI___libc_free 26ms 0.33% 39.06% 301ms 3.82% std::_Rb_tree::_M_copy (inline) 6ms 0.076% 39.14% 284ms 3.60% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.063% 39.20% 279ms 3.54% Cell::ReadyToDivide 9ms 0.11% 39.31% 272ms 3.45% divconqrecurse 89ms 1.13% 40.44% 269ms 3.41% std::_Rb_tree::_M_clone_node (inline) 6ms 0.076% 40.52% 268ms 3.40% Element::Element 0 0% 40.52% 266ms 3.38% std::_Rb_tree::_M_drop_node (inline) 4ms 0.051% 40.57% 266ms 3.38% std::__cxx11::collate::do_transform 7ms 0.089% 40.66% 261ms 3.31% std::__new_allocator::deallocate (inline) 0 0% 40.66% 257ms 3.26% std::allocator_traits::deallocate (inline) 6ms 0.076% 40.74% 256ms 3.25% CellProliferativeTypesWriter::VisitCell 69ms 0.88% 41.61% 256ms 3.25% mergehulls 6ms 0.076% 41.69% 253ms 3.21% ___vsnprintf 165ms 2.09% 43.78% 250ms 3.17% _int_malloc 3ms 0.038% 43.82% 249ms 3.16% AbstractCellProperty::IsType (inline) 9ms 0.11% 43.93% 248ms 3.15% CellPropertyCollection::HasProperty 0 0% 43.93% 247ms 3.13% __vsnprintf_internal (inline) 0 0% 43.93% 245ms 3.11% Cell::HasCellProperty (inline) 44ms 0.56% 44.49% 240ms 3.05% __printf_buffer 25ms 0.32% 44.81% 221ms 2.80% TetrahedralMesh::Clear 0 0% 44.81% 212ms 2.69% std::_Rb_tree::_M_put_node (inline) 176ms 2.23% 47.04% 207ms 2.63% _int_free 8ms 0.1% 47.14% 200ms 2.54% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.025% 47.17% 182ms 2.31% __printf_fp_spec (inline) 44ms 0.56% 47.73% 180ms 2.28% AbstractCellProperty::IsSame 9ms 0.11% 47.84% 180ms 2.28% __printf_fp_l_buffer 60ms 0.76% 48.60% 179ms 2.27% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.063% 48.67% 176ms 2.23% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.038% 48.71% 175ms 2.22% Element::RegisterWithNodes (inline) 11ms 0.14% 48.85% 170ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 48.85% 170ms 2.16% Node::AddElement 89ms 1.13% 49.97% 160ms 2.03% __printf_fp_buffer_1 41ms 0.52% 50.49% 158ms 2.01% TetrahedralMesh::EdgesEnd (partial-inline) 63ms 0.8% 51.29% 158ms 2.01% std::__ostream_insert 0 0% 51.29% 148ms 1.88% std::basic_ofstream::basic_ofstream (inline) 7ms 0.089% 51.38% 145ms 1.84% AbstractTetrahedralElement::CalculateJacobian 2ms 0.025% 51.41% 144ms 1.83% std::basic_filebuf::open 0 0% 51.41% 144ms 1.83% std::basic_ofstream::open (inline) 0 0% 51.41% 143ms 1.81% AbstractCellPopulation::CloseRoundRobinWritersFiles 6ms 0.076% 51.48% 143ms 1.81% boost::numeric::ublas::vector_assign (inline) 0 0% 51.48% 142ms 1.80% OutputFileHandler::CommonConstructor 0 0% 51.48% 142ms 1.80% OutputFileHandler::OutputFileHandler 2ms 0.025% 51.51% 140ms 1.78% AbstractCellBasedWriter::CloseFile 0 0% 51.51% 140ms 1.78% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.51% 138ms 1.75% OutputFileHandler::MakeFoldersAndReturnFullPath 7ms 0.089% 51.60% 138ms 1.75% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 51.62% 138ms 1.75% std::basic_ofstream::close (inline) 2ms 0.025% 51.65% 136ms 1.73% alternateaxes 1ms 0.013% 51.66% 136ms 1.73% std::basic_filebuf::close 33ms 0.42% 52.08% 136ms 1.73% std::type_info::operator== (inline) 119ms 1.51% 53.59% 133ms 1.69% vertexmedian 2ms 0.025% 53.62% 132ms 1.68% std::operator<< (inline) 5ms 0.063% 53.68% 131ms 1.66% AbstractTetrahedralElement::CalculateInverseJacobian 28ms 0.36% 54.04% 131ms 1.66% MeshBasedCellPopulation::SpringIterator::SpringIterator 15ms 0.19% 54.23% 128ms 1.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.23% 128ms 1.62% FilesystemPermissions::SetFilePermissions (inline) 127ms 1.61% 55.84% 127ms 1.61% __GI_fchmodat 0 0% 55.84% 127ms 1.61% std::filesystem::permissions 0 0% 55.84% 126ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.063% 55.90% 126ms 1.60% Node::~Node 42ms 0.53% 56.43% 125ms 1.59% std::num_put::_M_insert_int 15ms 0.19% 56.62% 119ms 1.51% boost::detail::shared_count::~shared_count (inline) 0 0% 56.62% 119ms 1.51% boost::shared_ptr::~shared_ptr (inline) 3ms 0.038% 56.66% 113ms 1.43% std::__basic_file::open 0 0% 56.66% 111ms 1.41% _IO_new_fopen 0 0% 56.66% 111ms 1.41% __fopen_internal (inline) 1ms 0.013% 56.68% 111ms 1.41% std::_Vector_base::_M_allocate (inline) 108ms 1.37% 58.05% 108ms 1.37% incircle 108ms 1.37% 59.42% 108ms 1.37% std::_Rb_tree_increment 1ms 0.013% 59.43% 106ms 1.35% _IO_new_file_fopen 0 0% 59.43% 105ms 1.33% __GI__IO_file_open 24ms 0.3% 59.73% 105ms 1.33% boost::numeric::ublas::indexing_vector_assign 5ms 0.063% 59.80% 105ms 1.33% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 59.82% 105ms 1.33% std::vector::push_back (inline) 11ms 0.14% 59.96% 104ms 1.32% AbstractTetrahedralElement::RefreshJacobian 2ms 0.025% 59.99% 103ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 102ms 1.29% 61.28% 102ms 1.29% __GI___libc_write 101ms 1.28% 62.56% 102ms 1.29% boost::detail::sp_counted_base::release 0 0% 62.56% 102ms 1.29% std::__basic_file::xsputn 0 0% 62.56% 102ms 1.29% std::basic_filebuf::_M_convert_to_external 0 0% 62.56% 102ms 1.29% std::basic_filebuf::_M_terminate_output 0 0% 62.56% 102ms 1.29% std::basic_filebuf::overflow 97ms 1.23% 63.79% 97ms 1.23% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 63.81% 96ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 62ms 0.79% 64.59% 96ms 1.22% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.063% 64.66% 95ms 1.21% std::vector::_M_realloc_insert 94ms 1.19% 65.85% 94ms 1.19% __libc_open64 61ms 0.77% 66.62% 94ms 1.19% std::basic_filebuf::xsputn 3ms 0.038% 66.66% 93ms 1.18% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 66.66% 87ms 1.10% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.66% 87ms 1.10% Cell::GetCellId 87ms 1.10% 67.77% 87ms 1.10% [libchaste_cell_based.so] 15ms 0.19% 67.96% 86ms 1.09% CellPropertyCollection::AddProperty 86ms 1.09% 69.05% 86ms 1.09% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 40ms 0.51% 69.56% 85ms 1.08% boost::shared_ptr::shared_ptr (inline) 77ms 0.98% 70.53% 77ms 0.98% __GI___fstatat64 1ms 0.013% 70.55% 76ms 0.96% std::filesystem::status 42ms 0.53% 71.08% 75ms 0.95% AbstractElement::GetNodeLocation 73ms 0.93% 72.01% 73ms 0.93% Node::GetIndex 73ms 0.93% 72.93% 73ms 0.93% counterclockwise 0 0% 72.93% 72ms 0.91% tcache_get (inline) 72ms 0.91% 73.85% 72ms 0.91% tcache_get_n (inline) 1ms 0.013% 73.86% 71ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 73.86% 70ms 0.89% std::filesystem::create_directory 52ms 0.66% 74.52% 69ms 0.88% malloc_consolidate 51ms 0.65% 75.16% 68ms 0.86% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 75.18% 68ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeA 54ms 0.69% 75.86% 68ms 0.86% std::basic_streambuf::xsputn 62ms 0.79% 76.65% 67ms 0.85% vertexsort 66ms 0.84% 77.49% 66ms 0.84% std::vector::size (inline) 0 0% 77.49% 65ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.49% 65ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 28ms 0.36% 77.84% 63ms 0.8% AbstractTetrahedralMesh::GetElement 63ms 0.8% 78.64% 63ms 0.8% [libchaste_mesh.so] 5ms 0.063% 78.71% 59ms 0.75% Node::ConstructNodeAttributes (inline) 59ms 0.75% 79.45% 59ms 0.75% __memcpy_avx_unaligned_erms 31ms 0.39% 79.85% 56ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 45ms 0.57% 80.42% 56ms 0.71% std::num_put::do_put 0 0% 80.42% 55ms 0.7% Node::ClearAppliedForce 5ms 0.063% 80.48% 55ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.48% 54ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.013% 80.49% 54ms 0.69% std::__new_allocator::construct (inline) 0 0% 80.49% 54ms 0.69% std::__new_allocator::destroy (inline) 0 0% 80.49% 54ms 0.69% std::allocator_traits::construct (inline) 0 0% 80.49% 54ms 0.69% std::allocator_traits::destroy (inline) 53ms 0.67% 81.17% 53ms 0.67% boost::numeric::ublas::c_vector::operator() (partial-inline) 52ms 0.66% 81.83% 52ms 0.66% Node::IsDeleted 52ms 0.66% 82.49% 52ms 0.66% boost::shared_ptr::operator-> (inline) 3ms 0.038% 82.53% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 82.54% 50ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 23ms 0.29% 82.83% 50ms 0.63% Determinant (inline) 0 0% 82.83% 50ms 0.63% std::map::find (inline) 0 0% 82.83% 47ms 0.6% boost::numeric::ublas::norm_2 (inline) 19ms 0.24% 83.07% 47ms 0.6% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.07% 47ms 0.6% std::_Rb_tree::_M_construct_node (inline) 0 0% 83.07% 46ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 83.08% 45ms 0.57% BoundaryNodeWriter::Visit 44ms 0.56% 83.64% 45ms 0.57% boost::detail::shared_count::shared_count (inline) 1ms 0.013% 83.65% 44ms 0.56% std::_Vector_base::_M_deallocate (inline) 0 0% 83.65% 44ms 0.56% std::vector::vector (inline) 17ms 0.22% 83.87% 43ms 0.55% AbstractCellCycleModel::GetAge 0 0% 83.87% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 28ms 0.36% 84.23% 43ms 0.55% hack_digit 0 0% 84.23% 43ms 0.55% std::_Vector_base::_Vector_base (inline) 10ms 0.13% 84.35% 41ms 0.52% Inverse 4ms 0.051% 84.40% 40ms 0.51% NodeAttributes::NodeAttributes 0 0% 84.40% 40ms 0.51% std::_Vector_base::_M_create_storage (inline)