File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6749ms, 83.76% of 8058ms total Dropped 570 nodes (cum <= 40.29ms) flat flat% sum% cum cum% 0 0% 0% 8024ms 99.58% __libc_start_call_main 0 0% 0% 8024ms 99.58% __libc_start_main_impl 0 0% 0% 8024ms 99.58% _start 0 0% 0% 8008ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8008ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8008ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8008ms 99.38% main 0 0% 0% 7966ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7966ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7966ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7963ms 98.82% AbstractCellBasedSimulation::Solve 2ms 0.025% 0.025% 3453ms 42.85% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.037% 2987ms 37.07% MeshBasedCellPopulation::Update 0 0% 0.037% 2963ms 36.77% AbstractCellPopulation::WriteResultsToFiles 3ms 0.037% 0.074% 1542ms 19.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.087% 1476ms 18.32% MutableMesh::ReMesh 0 0% 0.087% 1460ms 18.12% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.099% 1389ms 17.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.037% 0.14% 1341ms 16.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.37% 1246ms 15.46% MeshBasedCellPopulation::SpringIterator::operator++ 103ms 1.28% 1.65% 991ms 12.30% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 1.69% 966ms 11.99% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.074% 1.76% 962ms 11.94% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 256ms 3.18% 4.94% 948ms 11.76% __dynamic_cast 398ms 4.94% 9.88% 932ms 11.57% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.087% 9.97% 916ms 11.37% CellPopulationElementWriter::Visit 7ms 0.087% 10.05% 879ms 10.91% CellPropertyCollection::GetPropertiesType (inline) 59ms 0.73% 10.78% 865ms 10.73% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.074% 10.86% 794ms 9.85% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.43% 11.29% 766ms 9.51% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.34% 733ms 9.10% TetrahedralMesh::ImportFromMesher 1ms 0.012% 11.36% 717ms 8.90% AbstractCellProperty::IsSubType (inline) 0 0% 11.36% 602ms 7.47% std::ostream::operator<< (inline) 100ms 1.24% 12.60% 597ms 7.41% std::ostream::_M_insert 39ms 0.48% 13.08% 584ms 7.25% operator new 59ms 0.73% 13.81% 580ms 7.20% std::map::operator[] (partial-inline) 1ms 0.012% 13.82% 570ms 7.07% triangulate 562ms 6.97% 20.80% 562ms 6.97% __strcmp_avx2 184ms 2.28% 23.08% 535ms 6.64% __GI___libc_malloc 10ms 0.12% 23.21% 527ms 6.54% std::set::insert (inline) 7ms 0.087% 23.29% 522ms 6.48% Cell::GetCellProliferativeType 10ms 0.12% 23.42% 517ms 6.42% std::_Rb_tree::_M_insert_unique 24ms 0.3% 23.72% 511ms 6.34% std::__new_allocator::allocate (inline) 26ms 0.32% 24.04% 509ms 6.32% std::_Rb_tree::find (inline) 0 0% 24.04% 506ms 6.28% std::allocator_traits::allocate (inline) 1ms 0.012% 24.05% 501ms 6.22% delaunay 232ms 2.88% 26.93% 500ms 6.21% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.012% 26.94% 500ms 6.21% divconqdelaunay 4ms 0.05% 26.99% 488ms 6.06% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.99% 477ms 5.92% std::_Rb_tree::lower_bound (inline) 0 0% 26.99% 477ms 5.92% std::map::lower_bound (inline) 0 0% 26.99% 449ms 5.57% std::set::count (inline) 4ms 0.05% 27.04% 447ms 5.55% AbstractCellBasedSimulation::DoCellBirth 44ms 0.55% 27.59% 423ms 5.25% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.59% 400ms 4.96% std::_Rb_tree::_M_create_node (inline) 0 0% 27.59% 395ms 4.90% std::set::~set (inline) 0 0% 27.59% 383ms 4.75% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.025% 27.61% 374ms 4.64% NodeLocationWriter::Visit 94ms 1.17% 28.78% 373ms 4.63% std::_Rb_tree::_M_erase 0 0% 28.78% 367ms 4.55% std::_Rb_tree::_M_get_node (inline) 11ms 0.14% 28.92% 359ms 4.46% std::less::operator() (inline) 23ms 0.29% 29.20% 356ms 4.42% std::_Rb_tree::_Rb_tree (partial-inline) 348ms 4.32% 33.52% 348ms 4.32% std::operator< (inline) 5ms 0.062% 33.58% 346ms 4.29% Cell::GetMutationState 0 0% 33.58% 319ms 3.96% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.58% 318ms 3.95% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.58% 317ms 3.93% OutputFileHandler::OpenOutputFile 317ms 3.93% 37.52% 317ms 3.93% std::_Rb_tree::_S_right (inline) 1ms 0.012% 37.53% 315ms 3.91% std::set::set (inline) 25ms 0.31% 37.84% 311ms 3.86% std::num_put::_M_insert_float 7ms 0.087% 37.93% 307ms 3.81% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.062% 37.99% 305ms 3.79% Element::Element 22ms 0.27% 38.26% 305ms 3.79% std::_Rb_tree::_M_insert_ (inline) 30ms 0.37% 38.63% 301ms 3.74% std::_Rb_tree::_M_copy (inline) 4ms 0.05% 38.68% 298ms 3.70% Cell::ReadyToDivide 2ms 0.025% 38.71% 297ms 3.69% MeshBasedCellPopulation::GetDampingConstant 7ms 0.087% 38.79% 294ms 3.65% AbstractCentreBasedCellPopulation::GetDampingConstant 178ms 2.21% 41.00% 287ms 3.56% _int_malloc 6ms 0.074% 41.08% 283ms 3.51% divconqrecurse 89ms 1.10% 42.18% 276ms 3.43% __GI___libc_free 62ms 0.77% 42.95% 271ms 3.36% mergehulls 4ms 0.05% 43.00% 263ms 3.26% CellProliferativeTypesWriter::VisitCell 80ms 0.99% 43.99% 263ms 3.26% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.99% 255ms 3.16% std::_Rb_tree::_M_drop_node (inline) 13ms 0.16% 44.15% 249ms 3.09% std::__cxx11::collate::do_transform 11ms 0.14% 44.29% 240ms 2.98% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.12% 44.42% 240ms 2.98% std::__new_allocator::deallocate (inline) 1ms 0.012% 44.43% 239ms 2.97% AbstractCellProperty::IsType (inline) 0 0% 44.43% 234ms 2.90% Cell::HasCellProperty (inline) 4ms 0.05% 44.48% 234ms 2.90% CellPropertyCollection::HasProperty 0 0% 44.48% 234ms 2.90% std::allocator_traits::deallocate (inline) 2ms 0.025% 44.50% 231ms 2.87% ___vsnprintf 26ms 0.32% 44.83% 229ms 2.84% __printf_buffer 0 0% 44.83% 229ms 2.84% __vsnprintf_internal (inline) 3ms 0.037% 44.86% 215ms 2.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.11% 44.97% 209ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.099% 45.07% 208ms 2.58% Element::RegisterWithNodes (inline) 15ms 0.19% 45.26% 206ms 2.56% TetrahedralMesh::Clear 71ms 0.88% 46.14% 202ms 2.51% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.037% 46.18% 197ms 2.44% Node::AddElement 0 0% 46.18% 197ms 2.44% std::_Rb_tree::_M_put_node (inline) 33ms 0.41% 46.59% 190ms 2.36% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.05% 46.64% 190ms 2.36% __printf_fp_l_buffer 0 0% 46.64% 190ms 2.36% __printf_fp_spec (inline) 42ms 0.52% 47.16% 188ms 2.33% AbstractCellProperty::IsSame 153ms 1.90% 49.06% 185ms 2.30% _int_free 97ms 1.20% 50.26% 181ms 2.25% __printf_fp_buffer_1 0 0% 50.26% 168ms 2.08% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.26% 165ms 2.05% OutputFileHandler::CommonConstructor 0 0% 50.26% 165ms 2.05% OutputFileHandler::OutputFileHandler 0 0% 50.26% 163ms 2.02% std::basic_filebuf::open 0 0% 50.26% 163ms 2.02% std::basic_ofstream::open (inline) 0 0% 50.26% 160ms 1.99% OutputFileHandler::MakeFoldersAndReturnFullPath 22ms 0.27% 50.53% 157ms 1.95% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.025% 50.56% 154ms 1.91% AbstractCellBasedWriter::CloseFile 0 0% 50.56% 154ms 1.91% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.56% 154ms 1.91% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.012% 50.57% 152ms 1.89% std::basic_filebuf::close 0 0% 50.57% 152ms 1.89% std::basic_ofstream::close (inline) 128ms 1.59% 52.16% 151ms 1.87% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 149ms 1.85% 54.01% 149ms 1.85% incircle 7ms 0.087% 54.10% 147ms 1.82% AbstractTetrahedralElement::CalculateJacobian 32ms 0.4% 54.49% 146ms 1.81% std::type_info::operator== (inline) 4ms 0.05% 54.54% 144ms 1.79% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.11% 54.65% 141ms 1.75% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.05% 54.70% 140ms 1.74% boost::numeric::ublas::vector_assign (inline) 0 0% 54.70% 139ms 1.72% std::_Vector_base::_M_allocate (inline) 15ms 0.19% 54.89% 136ms 1.69% boost::detail::shared_count::~shared_count (inline) 0 0% 54.89% 136ms 1.69% boost::shared_ptr::~shared_ptr (inline) 46ms 0.57% 55.46% 135ms 1.68% std::__ostream_insert 0 0% 55.46% 128ms 1.59% std::__basic_file::open 0 0% 55.46% 126ms 1.56% FilesystemPermissions::SetFilePermissions (inline) 0 0% 55.46% 125ms 1.55% _IO_new_fopen 125ms 1.55% 57.01% 125ms 1.55% __GI_fchmodat 0 0% 57.01% 125ms 1.55% __fopen_internal (inline) 0 0% 57.01% 125ms 1.55% std::filesystem::permissions 5ms 0.062% 57.07% 123ms 1.53% Node::~Node 2ms 0.025% 57.10% 123ms 1.53% _IO_new_file_fopen 1ms 0.012% 57.11% 122ms 1.51% alternateaxes 32ms 0.4% 57.51% 121ms 1.50% std::num_put::_M_insert_int 2ms 0.025% 57.53% 119ms 1.48% __GI__IO_file_open 108ms 1.34% 58.87% 118ms 1.46% vertexmedian 9ms 0.11% 58.98% 117ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 117ms 1.45% 60.44% 117ms 1.45% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.037% 60.47% 114ms 1.41% std::vector::push_back (inline) 0 0% 60.47% 112ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.15% 60.62% 110ms 1.37% AbstractTetrahedralElement::RefreshJacobian 0 0% 60.62% 110ms 1.37% std::operator<< (inline) 63ms 0.78% 61.40% 109ms 1.35% boost::shared_ptr::shared_ptr (inline) 100ms 1.24% 62.65% 108ms 1.34% boost::detail::sp_counted_base::release 9ms 0.11% 62.76% 108ms 1.34% std::vector::_M_realloc_insert 0 0% 62.76% 107ms 1.33% std::basic_filebuf::_M_terminate_output 1ms 0.012% 62.77% 107ms 1.33% std::basic_filebuf::overflow 0 0% 62.77% 105ms 1.30% std::__basic_file::xsputn 0 0% 62.77% 105ms 1.30% std::basic_filebuf::_M_convert_to_external 104ms 1.29% 64.06% 104ms 1.29% __GI___libc_write 6ms 0.074% 64.14% 99ms 1.23% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.05% 64.18% 98ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 31ms 0.38% 64.57% 95ms 1.18% boost::numeric::ublas::indexing_vector_assign 1ms 0.012% 64.58% 94ms 1.17% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 93ms 1.15% 65.74% 93ms 1.15% [libchaste_cell_based.so] 93ms 1.15% 66.89% 93ms 1.15% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 66.91% 93ms 1.15% std::filesystem::create_directory 92ms 1.14% 68.06% 92ms 1.14% __libc_open64 74ms 0.92% 68.97% 91ms 1.13% malloc_consolidate 7ms 0.087% 69.06% 89ms 1.10% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.06% 88ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 88ms 1.09% 70.15% 88ms 1.09% std::_Rb_tree_increment 0 0% 70.15% 86ms 1.07% Cell::GetCellId 2ms 0.025% 70.18% 86ms 1.07% std::filesystem::status 84ms 1.04% 71.22% 84ms 1.04% __GI___fstatat64 3ms 0.037% 71.26% 83ms 1.03% AbstractCellPopulation::GetLocationIndexUsingCell 70ms 0.87% 72.13% 83ms 1.03% vertexsort 33ms 0.41% 72.54% 82ms 1.02% AbstractElement::GetNodeLocation 78ms 0.97% 73.50% 78ms 0.97% Node::GetIndex 44ms 0.55% 74.05% 77ms 0.96% std::basic_filebuf::xsputn 1ms 0.012% 74.06% 73ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 6ms 0.074% 74.14% 71ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 44ms 0.55% 74.68% 69ms 0.86% std::basic_streambuf::xsputn 0 0% 74.68% 64ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.68% 64ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 52ms 0.65% 75.33% 63ms 0.78% AbstractElement::GetNodeGlobalIndex 63ms 0.78% 76.11% 63ms 0.78% __memcpy_avx_unaligned_erms 0 0% 76.11% 61ms 0.76% std::vector::vector (inline) 2ms 0.025% 76.14% 60ms 0.74% Node::ConstructNodeAttributes (inline) 60ms 0.74% 76.88% 60ms 0.74% std::vector::size (inline) 54ms 0.67% 77.55% 59ms 0.73% std::num_put::do_put 0 0% 77.55% 58ms 0.72% Node::ClearAppliedForce 58ms 0.72% 78.27% 58ms 0.72% counterclockwise 0 0% 78.27% 58ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.27% 58ms 0.72% std::__new_allocator::destroy (inline) 0 0% 78.27% 58ms 0.72% std::allocator_traits::destroy (inline) 57ms 0.71% 78.98% 57ms 0.71% [libstdc++.so.6.0.33] 0 0% 78.98% 56ms 0.69% tcache_get (inline) 56ms 0.69% 79.67% 56ms 0.69% tcache_get_n (inline) 32ms 0.4% 80.07% 54ms 0.67% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 80.07% 54ms 0.67% std::map::find (inline) 53ms 0.66% 80.73% 53ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 80.73% 53ms 0.66% std::_Vector_base::_Vector_base (inline) 4ms 0.05% 80.78% 51ms 0.63% CellPropertyCollection::AddProperty 1ms 0.012% 80.79% 51ms 0.63% std::_Vector_base::_M_create_storage (inline) 1ms 0.012% 80.80% 50ms 0.62% AbstractCentreBasedCellPopulation::IsMarkedSpring 29ms 0.36% 81.16% 50ms 0.62% hack_digit 5ms 0.062% 81.22% 48ms 0.6% NodeAttributes::NodeAttributes 0 0% 81.22% 48ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 48ms 0.6% 81.82% 48ms 0.6% boost::numeric::ublas::c_vector::operator() (partial-inline) 47ms 0.58% 82.40% 47ms 0.58% [libchaste_mesh.so] 0 0% 82.40% 47ms 0.58% boost::numeric::ublas::norm_2 (inline) 10ms 0.12% 82.53% 47ms 0.58% boost::numeric::ublas::vector_norm_2::apply (inline) 20ms 0.25% 82.77% 46ms 0.57% AbstractTetrahedralMesh::GetElement 41ms 0.51% 83.28% 46ms 0.57% boost::detail::shared_count::shared_count (inline) 1ms 0.012% 83.30% 45ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 83.30% 44ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.05% 83.35% 44ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.35% 42ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.35% 42ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 6ms 0.074% 83.42% 42ms 0.52% std::_Vector_base::_M_deallocate (inline) 0 0% 83.42% 42ms 0.52% std::map::map (inline) 15ms 0.19% 83.61% 41ms 0.51% Determinant (inline) 12ms 0.15% 83.76% 41ms 0.51% Inverse