File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6469ms, 83.96% of 7705ms total Dropped 567 nodes (cum <= 38.52ms) flat flat% sum% cum cum% 0 0% 0% 7670ms 99.55% __libc_start_main_impl 0 0% 0% 7670ms 99.55% _start 0 0% 0% 7669ms 99.53% __libc_start_call_main 0 0% 0% 7655ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7655ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7655ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7655ms 99.35% main 0 0% 0% 7619ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7619ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7619ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7616ms 98.84% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3358ms 43.58% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.026% 2848ms 36.96% MeshBasedCellPopulation::Update 0 0% 0.026% 2829ms 36.72% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.039% 1434ms 18.61% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.039% 0.078% 1420ms 18.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.091% 1366ms 17.73% MutableMesh::ReMesh 2ms 0.026% 0.12% 1296ms 16.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.078% 0.19% 1239ms 16.08% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.039% 0.23% 1234ms 16.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 114ms 1.48% 1.71% 1014ms 13.16% TetrahedralMesh::EdgeIterator::operator++ 442ms 5.74% 7.45% 928ms 12.04% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.052% 7.50% 918ms 11.91% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.63% 913ms 11.85% CellPopulationElementWriter::Visit 5ms 0.065% 7.70% 883ms 11.46% CellPropertyCollection::GetPropertiesType (inline) 271ms 3.52% 11.21% 872ms 11.32% __dynamic_cast 5ms 0.065% 11.28% 816ms 10.59% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.039% 11.32% 752ms 9.76% MeshBasedCellPopulation::AcceptCellWriter 31ms 0.4% 11.72% 716ms 9.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 24ms 0.31% 12.03% 702ms 9.11% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.065% 12.10% 695ms 9.02% AbstractCellProperty::IsSubType (inline) 9ms 0.12% 12.21% 693ms 8.99% TetrahedralMesh::ImportFromMesher 2ms 0.026% 12.24% 588ms 7.63% std::ostream::operator<< (inline) 81ms 1.05% 13.29% 586ms 7.61% std::ostream::_M_insert 52ms 0.67% 13.96% 551ms 7.15% operator new 47ms 0.61% 14.57% 546ms 7.09% std::map::operator[] (partial-inline) 6ms 0.078% 14.65% 526ms 6.83% Cell::GetCellProliferativeType 7ms 0.091% 14.74% 525ms 6.81% std::set::insert (inline) 5ms 0.065% 14.81% 518ms 6.72% std::_Rb_tree::_M_insert_unique 3ms 0.039% 14.85% 517ms 6.71% triangulate 22ms 0.29% 15.13% 507ms 6.58% std::_Rb_tree::find (inline) 39ms 0.51% 15.64% 507ms 6.58% std::__new_allocator::allocate (inline) 0 0% 15.64% 503ms 6.53% std::allocator_traits::allocate (inline) 498ms 6.46% 22.10% 498ms 6.46% __strcmp_avx2 192ms 2.49% 24.59% 491ms 6.37% __GI___libc_malloc 5ms 0.065% 24.66% 487ms 6.32% AbstractCellBasedSimulation::DoCellBirth 7ms 0.091% 24.75% 478ms 6.20% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.75% 470ms 6.10% std::set::count (inline) 0 0% 24.75% 460ms 5.97% std::_Rb_tree::lower_bound (inline) 0 0% 24.75% 460ms 5.97% std::map::lower_bound (inline) 0 0% 24.75% 452ms 5.87% delaunay 1ms 0.013% 24.76% 451ms 5.85% divconqdelaunay 192ms 2.49% 27.26% 440ms 5.71% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.26% 428ms 5.55% std::_Rb_tree::_M_create_node (inline) 0 0% 27.26% 406ms 5.27% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.26% 392ms 5.09% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 27.27% 383ms 4.97% Cell::GetMutationState 32ms 0.42% 27.68% 377ms 4.89% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.14% 27.83% 371ms 4.82% std::less::operator() (inline) 2ms 0.026% 27.85% 361ms 4.69% NodeLocationWriter::Visit 360ms 4.67% 32.52% 360ms 4.67% std::operator< (inline) 0 0% 32.52% 353ms 4.58% std::set::~set (inline) 18ms 0.23% 32.76% 351ms 4.56% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.1% 32.86% 347ms 4.50% Cell::ReadyToDivide 69ms 0.9% 33.76% 339ms 4.40% std::_Rb_tree::_M_erase 1ms 0.013% 33.77% 330ms 4.28% MeshBasedCellPopulation::GetDampingConstant 3ms 0.039% 33.81% 329ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.026% 33.84% 324ms 4.21% std::set::set (inline) 25ms 0.32% 34.16% 320ms 4.15% std::num_put::_M_insert_float 15ms 0.19% 34.35% 311ms 4.04% std::_Rb_tree::_M_insert_ (inline) 95ms 1.23% 35.59% 293ms 3.80% __GI___libc_free 32ms 0.42% 36.00% 293ms 3.80% std::_Rb_tree::_M_copy (inline) 4ms 0.052% 36.05% 290ms 3.76% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.065% 36.12% 288ms 3.74% Element::Element 1ms 0.013% 36.13% 276ms 3.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 36.15% 275ms 3.57% AbstractCellBasedWriter::OpenOutputFileForAppend 270ms 3.50% 39.65% 270ms 3.50% std::_Rb_tree::_S_right (inline) 0 0% 39.65% 268ms 3.48% OutputFileHandler::OpenOutputFile 69ms 0.9% 40.55% 256ms 3.32% std::_Rb_tree::_M_clone_node (inline) 9ms 0.12% 40.66% 254ms 3.30% divconqrecurse 4ms 0.052% 40.71% 254ms 3.30% std::__cxx11::collate::do_transform 2ms 0.026% 40.74% 250ms 3.24% AbstractCellProperty::IsType (inline) 0 0% 40.74% 250ms 3.24% std::_Rb_tree::_M_drop_node (inline) 0 0% 40.74% 247ms 3.21% Cell::HasCellProperty (inline) 5ms 0.065% 40.80% 247ms 3.21% CellPropertyCollection::HasProperty 11ms 0.14% 40.95% 243ms 3.15% std::__new_allocator::deallocate (inline) 0 0% 40.95% 241ms 3.13% ___vsnprintf 0 0% 40.95% 241ms 3.13% __vsnprintf_internal (inline) 0 0% 40.95% 239ms 3.10% std::allocator_traits::deallocate (inline) 3ms 0.039% 40.99% 238ms 3.09% CellProliferativeTypesWriter::VisitCell 69ms 0.9% 41.88% 237ms 3.08% mergehulls 37ms 0.48% 42.36% 234ms 3.04% __printf_buffer 163ms 2.12% 44.48% 233ms 3.02% _int_malloc 2ms 0.026% 44.50% 218ms 2.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 44.65% 213ms 2.76% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 57ms 0.74% 45.39% 202ms 2.62% std::_Rb_tree::_M_get_insert_unique_pos (inline) 167ms 2.17% 47.55% 198ms 2.57% _int_free 0 0% 47.55% 198ms 2.57% std::_Rb_tree::_M_put_node (inline) 23ms 0.3% 47.85% 196ms 2.54% TetrahedralMesh::Clear 6ms 0.078% 47.93% 194ms 2.52% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.052% 47.98% 189ms 2.45% Element::RegisterWithNodes (inline) 52ms 0.67% 48.66% 188ms 2.44% AbstractCellProperty::IsSame 4ms 0.052% 48.71% 181ms 2.35% Node::AddElement 6ms 0.078% 48.79% 178ms 2.31% __printf_fp_l_buffer 0 0% 48.79% 178ms 2.31% __printf_fp_spec (inline) 91ms 1.18% 49.97% 163ms 2.12% __printf_fp_buffer_1 32ms 0.42% 50.38% 162ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.38% 151ms 1.96% OutputFileHandler::CommonConstructor 0 0% 50.38% 151ms 1.96% OutputFileHandler::OutputFileHandler 0 0% 50.38% 149ms 1.93% OutputFileHandler::MakeFoldersAndReturnFullPath 69ms 0.9% 51.28% 148ms 1.92% std::__ostream_insert 1ms 0.013% 51.29% 144ms 1.87% boost::numeric::ublas::vector_assign (inline) 5ms 0.065% 51.36% 137ms 1.78% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 51.36% 137ms 1.78% std::basic_ofstream::basic_ofstream (inline) 11ms 0.14% 51.50% 136ms 1.77% AbstractTetrahedralElement::CalculateJacobian 34ms 0.44% 51.94% 136ms 1.77% std::type_info::operator== (inline) 0 0% 51.94% 133ms 1.73% AbstractCellBasedWriter::CloseFile 0 0% 51.94% 133ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.94% 133ms 1.73% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.94% 133ms 1.73% std::basic_filebuf::close 0 0% 51.94% 133ms 1.73% std::basic_ofstream::close (inline) 3ms 0.039% 51.98% 130ms 1.69% std::basic_filebuf::open 0 0% 51.98% 130ms 1.69% std::basic_ofstream::open (inline) 33ms 0.43% 52.41% 130ms 1.69% std::num_put::_M_insert_int 22ms 0.29% 52.69% 124ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.026% 52.72% 122ms 1.58% std::operator<< (inline) 4ms 0.052% 52.77% 121ms 1.57% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.77% 120ms 1.56% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.14% 52.91% 118ms 1.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.039% 52.95% 118ms 1.53% alternateaxes 79ms 1.03% 53.98% 116ms 1.51% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 102ms 1.32% 55.30% 115ms 1.49% vertexmedian 0 0% 55.30% 111ms 1.44% std::_Vector_base::_M_allocate (inline) 11ms 0.14% 55.44% 109ms 1.41% boost::detail::shared_count::~shared_count (inline) 32ms 0.42% 55.86% 109ms 1.41% boost::numeric::ublas::indexing_vector_assign 0 0% 55.86% 109ms 1.41% boost::shared_ptr::~shared_ptr (inline) 109ms 1.41% 57.27% 109ms 1.41% incircle 20ms 0.26% 57.53% 108ms 1.40% AbstractTetrahedralElement::RefreshJacobian 0 0% 57.53% 108ms 1.40% FilesystemPermissions::SetFilePermissions (inline) 108ms 1.40% 58.94% 108ms 1.40% __GI_fchmodat 0 0% 58.94% 108ms 1.40% std::filesystem::permissions 2ms 0.026% 58.96% 105ms 1.36% std::basic_filebuf::overflow 4ms 0.052% 59.01% 103ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 103ms 1.34% 60.35% 103ms 1.34% std::_Rb_tree_increment 1ms 0.013% 60.36% 103ms 1.34% std::basic_filebuf::_M_convert_to_external 0 0% 60.36% 103ms 1.34% std::basic_filebuf::_M_terminate_output 1ms 0.013% 60.38% 102ms 1.32% _IO_new_file_fopen 0 0% 60.38% 102ms 1.32% _IO_new_fopen 0 0% 60.38% 102ms 1.32% __fopen_internal (inline) 0 0% 60.38% 102ms 1.32% std::__basic_file::open 1ms 0.013% 60.39% 102ms 1.32% std::__basic_file::xsputn 5ms 0.065% 60.45% 101ms 1.31% std::vector::push_back (inline) 5ms 0.065% 60.52% 100ms 1.30% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 60.53% 99ms 1.28% __GI__IO_file_open 97ms 1.26% 61.79% 98ms 1.27% __GI___libc_write 9ms 0.12% 61.91% 96ms 1.25% Node::~Node 93ms 1.21% 63.11% 95ms 1.23% boost::detail::sp_counted_base::release 38ms 0.49% 63.61% 95ms 1.23% boost::shared_ptr::shared_ptr (inline) 7ms 0.091% 63.70% 93ms 1.21% std::vector::_M_realloc_insert 6ms 0.078% 63.78% 92ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 63.79% 90ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 90ms 1.17% 64.96% 90ms 1.17% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 88ms 1.14% 66.10% 90ms 1.17% __libc_open64 48ms 0.62% 66.72% 89ms 1.16% std::basic_filebuf::xsputn 16ms 0.21% 66.93% 88ms 1.14% TetrahedralMesh::EdgeIterator::GetNodeB 83ms 1.08% 68.01% 83ms 1.08% std::_Rb_tree_insert_and_rebalance 81ms 1.05% 69.06% 81ms 1.05% [libchaste_cell_based.so] 3ms 0.039% 69.10% 80ms 1.04% AbstractCellPopulation::GetLocationIndexUsingCell 38ms 0.49% 69.59% 79ms 1.03% AbstractElement::GetNodeLocation 77ms 1% 70.59% 77ms 1% Node::GetIndex 1ms 0.013% 70.60% 75ms 0.97% std::filesystem::status 74ms 0.96% 71.56% 74ms 0.96% __GI___fstatat64 1ms 0.013% 71.58% 73ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 67ms 0.87% 72.45% 73ms 0.95% vertexsort 2ms 0.026% 72.47% 72ms 0.93% std::filesystem::create_directory 56ms 0.73% 73.20% 71ms 0.92% AbstractElement::GetNodeGlobalIndex 53ms 0.69% 73.89% 68ms 0.88% std::num_put::do_put 11ms 0.14% 74.03% 67ms 0.87% CellPropertyCollection::AddProperty 64ms 0.83% 74.86% 64ms 0.83% [libchaste_mesh.so] 44ms 0.57% 75.43% 64ms 0.83% std::basic_streambuf::xsputn 64ms 0.83% 76.26% 64ms 0.83% std::vector::size (inline) 46ms 0.6% 76.86% 60ms 0.78% malloc_consolidate 1ms 0.013% 76.87% 59ms 0.77% Cell::GetCellId 58ms 0.75% 77.62% 58ms 0.75% counterclockwise 7ms 0.091% 77.72% 57ms 0.74% Node::ClearAppliedForce 55ms 0.71% 78.43% 57ms 0.74% boost::detail::shared_count::shared_count (inline) 0 0% 78.43% 57ms 0.74% tcache_get (inline) 57ms 0.74% 79.17% 57ms 0.74% tcache_get_n (inline) 0 0% 79.17% 54ms 0.7% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 79.17% 54ms 0.7% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 79.17% 54ms 0.7% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 31ms 0.4% 79.57% 52ms 0.67% AbstractTetrahedralMesh::GetElement 52ms 0.67% 80.25% 52ms 0.67% __memcpy_avx_unaligned_erms 52ms 0.67% 80.92% 52ms 0.67% boost::numeric::ublas::c_vector::operator() (partial-inline) 28ms 0.36% 81.28% 52ms 0.67% hack_digit 0 0% 81.28% 52ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.28% 52ms 0.67% std::__new_allocator::destroy (inline) 0 0% 81.28% 52ms 0.67% std::allocator_traits::destroy (inline) 0 0% 81.28% 50ms 0.65% Node::ConstructNodeAttributes (inline) 3ms 0.039% 81.32% 50ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 24ms 0.31% 81.64% 49ms 0.64% AbstractCellCycleModel::GetAge 0 0% 81.64% 47ms 0.61% std::vector::vector (inline) 7ms 0.091% 81.73% 46ms 0.6% std::_Vector_base::_M_deallocate (inline) 24ms 0.31% 82.04% 45ms 0.58% boost::numeric::ublas::c_matrix::operator() 45ms 0.58% 82.62% 45ms 0.58% boost::shared_ptr::operator-> (inline) 0 0% 82.62% 42ms 0.55% std::_Vector_base::_Vector_base (inline) 4ms 0.052% 82.67% 41ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 6ms 0.078% 82.75% 41ms 0.53% Inverse 0 0% 82.75% 41ms 0.53% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 0 0% 82.75% 41ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.53% 83.28% 41ms 0.53% [libstdc++.so.6.0.33] 0 0% 83.28% 40ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline) 40ms 0.52% 83.80% 40ms 0.52% Node::IsDeleted 4ms 0.052% 83.85% 40ms 0.52% NodeAttributes::NodeAttributes 0 0% 83.85% 40ms 0.52% std::_Vector_base::_M_create_storage (inline) 3ms 0.039% 83.89% 40ms 0.52% std::__new_allocator::construct (inline) 0 0% 83.89% 40ms 0.52% std::allocator_traits::construct (inline) 4ms 0.052% 83.95% 39ms 0.51% Element::~Element 0 0% 83.95% 39ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 83.96% 39ms 0.51% std::_Rb_tree::_M_emplace_hint_unique