File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6767ms, 84.69% of 7990ms total Dropped 597 nodes (cum <= 39.95ms) flat flat% sum% cum cum% 0 0% 0% 7955ms 99.56% __libc_start_call_main 0 0% 0% 7955ms 99.56% __libc_start_main_impl 0 0% 0% 7955ms 99.56% _start 0 0% 0% 7940ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7940ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7940ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7940ms 99.37% main 0 0% 0% 7903ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7903ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7903ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7899ms 98.86% AbstractCellBasedSimulation::Solve 0 0% 0% 3330ms 41.68% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.05% 0.05% 2936ms 36.75% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.05% 2843ms 35.58% MeshBasedCellPopulation::Update 1ms 0.013% 0.063% 1623ms 20.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.075% 1470ms 18.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.18% 1421ms 17.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.18% 1414ms 17.70% MutableMesh::ReMesh 2ms 0.025% 0.2% 1381ms 17.28% MeshBasedCellPopulation::UpdateNodePairs 22ms 0.28% 0.48% 1199ms 15.01% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.075% 0.55% 1004ms 12.57% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.075% 0.63% 1003ms 12.55% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 121ms 1.51% 2.14% 998ms 12.49% TetrahedralMesh::EdgeIterator::operator++ 431ms 5.39% 7.53% 968ms 12.12% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.13% 7.66% 923ms 11.55% CellPropertyCollection::GetPropertiesType (inline) 257ms 3.22% 10.88% 916ms 11.46% __dynamic_cast 40ms 0.5% 11.38% 890ms 11.14% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.075% 11.45% 888ms 11.11% CellPopulationElementWriter::Visit 2ms 0.025% 11.48% 824ms 10.31% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.28% 11.75% 797ms 9.97% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.80% 707ms 8.85% AbstractCellProperty::IsSubType (inline) 9ms 0.11% 11.91% 701ms 8.77% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.95% 605ms 7.57% std::ostream::operator<< (inline) 93ms 1.16% 13.12% 602ms 7.53% std::ostream::_M_insert 44ms 0.55% 13.67% 600ms 7.51% std::map::operator[] (partial-inline) 37ms 0.46% 14.13% 578ms 7.23% operator new 5ms 0.063% 14.19% 569ms 7.12% Cell::GetCellProliferativeType 1ms 0.013% 14.21% 549ms 6.87% triangulate 544ms 6.81% 21.01% 544ms 6.81% __strcmp_avx2 165ms 2.07% 23.08% 540ms 6.76% __GI___libc_malloc 37ms 0.46% 23.54% 530ms 6.63% std::__new_allocator::allocate (inline) 0 0% 23.54% 526ms 6.58% std::allocator_traits::allocate (inline) 23ms 0.29% 23.83% 515ms 6.45% std::_Rb_tree::find (inline) 4ms 0.05% 23.88% 503ms 6.30% std::set::insert (inline) 3ms 0.038% 23.92% 502ms 6.28% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.92% 501ms 6.27% std::_Rb_tree::lower_bound (inline) 0 0% 23.92% 501ms 6.27% std::map::lower_bound (inline) 16ms 0.2% 24.12% 499ms 6.25% std::_Rb_tree::_M_insert_unique 202ms 2.53% 26.65% 489ms 6.12% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.025% 26.67% 478ms 5.98% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.67% 477ms 5.97% std::set::count (inline) 0 0% 26.67% 475ms 5.94% delaunay 3ms 0.038% 26.71% 475ms 5.94% divconqdelaunay 0 0% 26.71% 454ms 5.68% std::_Rb_tree::_M_create_node (inline) 0 0% 26.71% 426ms 5.33% std::_Rb_tree::_Alloc_node::operator() (inline) 40ms 0.5% 27.21% 416ms 5.21% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.21% 415ms 5.19% std::_Rb_tree::_M_get_node (inline) 42ms 0.53% 27.73% 390ms 4.88% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 27.77% 381ms 4.77% std::set::set (inline) 1ms 0.013% 27.78% 364ms 4.56% Cell::GetMutationState 0 0% 27.78% 362ms 4.53% std::set::~set (inline) 10ms 0.13% 27.91% 358ms 4.48% std::less::operator() (inline) 1ms 0.013% 27.92% 357ms 4.47% NodeLocationWriter::Visit 348ms 4.36% 32.28% 348ms 4.36% std::operator< (inline) 72ms 0.9% 33.18% 346ms 4.33% std::_Rb_tree::_M_erase 41ms 0.51% 33.69% 342ms 4.28% std::_Rb_tree::_M_copy (inline) 10ms 0.13% 33.82% 339ms 4.24% Cell::ReadyToDivide 2ms 0.025% 33.84% 328ms 4.11% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 33.87% 325ms 4.07% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 33.87% 324ms 4.06% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.87% 322ms 4.03% AbstractCellBasedWriter::OpenOutputFileForAppend 321ms 4.02% 37.88% 321ms 4.02% std::_Rb_tree::_S_right (inline) 1ms 0.013% 37.90% 317ms 3.97% OutputFileHandler::OpenOutputFile 24ms 0.3% 38.20% 317ms 3.97% std::num_put::_M_insert_float 10ms 0.13% 38.32% 307ms 3.84% std::_Rb_tree::_M_insert_ (inline) 103ms 1.29% 39.61% 306ms 3.83% __GI___libc_free 2ms 0.025% 39.64% 297ms 3.72% CellProliferativeTypesWriter::VisitCell 79ms 0.99% 40.63% 295ms 3.69% std::_Rb_tree::_M_clone_node (inline) 189ms 2.37% 42.99% 290ms 3.63% _int_malloc 9ms 0.11% 43.10% 285ms 3.57% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 43.13% 283ms 3.54% Element::Element 0 0% 43.13% 265ms 3.32% Cell::HasCellProperty (inline) 4ms 0.05% 43.18% 265ms 3.32% CellPropertyCollection::HasProperty 2ms 0.025% 43.20% 264ms 3.30% AbstractCellProperty::IsType (inline) 9ms 0.11% 43.32% 262ms 3.28% divconqrecurse 4ms 0.05% 43.37% 251ms 3.14% std::__new_allocator::deallocate (inline) 0 0% 43.37% 250ms 3.13% std::allocator_traits::deallocate (inline) 4ms 0.05% 43.42% 247ms 3.09% std::__cxx11::collate::do_transform 0 0% 43.42% 246ms 3.08% std::_Rb_tree::_M_drop_node (inline) 68ms 0.85% 44.27% 242ms 3.03% mergehulls 1ms 0.013% 44.28% 233ms 2.92% ___vsnprintf 1ms 0.013% 44.29% 232ms 2.90% __vsnprintf_internal (inline) 29ms 0.36% 44.66% 228ms 2.85% __printf_buffer 10ms 0.13% 44.78% 210ms 2.63% AbstractPhaseBasedCellCycleModel::ReadyToDivide 49ms 0.61% 45.39% 209ms 2.62% AbstractCellProperty::IsSame 24ms 0.3% 45.69% 207ms 2.59% TetrahedralMesh::Clear 0 0% 45.69% 204ms 2.55% std::_Rb_tree::_M_put_node (inline) 175ms 2.19% 47.88% 202ms 2.53% _int_free 11ms 0.14% 48.02% 199ms 2.49% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.088% 48.11% 191ms 2.39% Element::RegisterWithNodes (inline) 5ms 0.063% 48.17% 184ms 2.30% Node::AddElement 6ms 0.075% 48.25% 183ms 2.29% __printf_fp_l_buffer 0 0% 48.25% 183ms 2.29% __printf_fp_spec (inline) 63ms 0.79% 49.04% 177ms 2.22% std::_Rb_tree::_M_get_insert_unique_pos (inline) 12ms 0.15% 49.19% 176ms 2.20% MeshBasedCellPopulation::SpringsEnd (inline) 86ms 1.08% 50.26% 169ms 2.12% __printf_fp_buffer_1 6ms 0.075% 50.34% 160ms 2.00% boost::numeric::ublas::vector_assign (inline) 0 0% 50.34% 160ms 2.00% std::basic_ofstream::basic_ofstream (inline) 38ms 0.48% 50.81% 160ms 2.00% std::type_info::operator== (inline) 1ms 0.013% 50.83% 156ms 1.95% std::basic_ofstream::open (inline) 0 0% 50.83% 155ms 1.94% std::basic_filebuf::open 6ms 0.075% 50.90% 153ms 1.91% AbstractTetrahedralElement::CalculateJacobian 4ms 0.05% 50.95% 151ms 1.89% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 50.95% 143ms 1.79% OutputFileHandler::CommonConstructor 0 0% 50.95% 143ms 1.79% OutputFileHandler::OutputFileHandler 34ms 0.43% 51.38% 142ms 1.78% std::num_put::_M_insert_int 1ms 0.013% 51.39% 140ms 1.75% TetrahedralMesh::RefreshJacobianCachedData 35ms 0.44% 51.83% 137ms 1.71% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.83% 136ms 1.70% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.83% 136ms 1.70% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.83% 135ms 1.69% AbstractCellBasedWriter::CloseFile 1ms 0.013% 51.84% 135ms 1.69% std::basic_ofstream::close (inline) 2ms 0.025% 51.86% 134ms 1.68% std::basic_filebuf::close 12ms 0.15% 52.02% 131ms 1.64% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.05% 52.07% 130ms 1.63% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.063% 52.13% 130ms 1.63% alternateaxes 61ms 0.76% 52.89% 129ms 1.61% std::__ostream_insert 4ms 0.05% 52.94% 127ms 1.59% std::vector::push_back (inline) 17ms 0.21% 53.15% 126ms 1.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 118ms 1.48% 54.63% 125ms 1.56% vertexmedian 0 0% 54.63% 123ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 26ms 0.33% 54.96% 123ms 1.54% boost::numeric::ublas::indexing_vector_assign 123ms 1.54% 56.50% 123ms 1.54% std::_Rb_tree_increment 1ms 0.013% 56.51% 123ms 1.54% std::__basic_file::open 1ms 0.013% 56.52% 123ms 1.54% std::filesystem::permissions 0 0% 56.52% 122ms 1.53% _IO_new_fopen 122ms 1.53% 58.05% 122ms 1.53% __GI_fchmodat 0 0% 58.05% 122ms 1.53% __fopen_internal (inline) 4ms 0.05% 58.10% 119ms 1.49% _IO_new_file_fopen 14ms 0.18% 58.27% 117ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.15% 58.42% 116ms 1.45% std::vector::_M_realloc_insert 0 0% 58.42% 114ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 14ms 0.18% 58.60% 113ms 1.41% AbstractTetrahedralElement::RefreshJacobian 4ms 0.05% 58.65% 112ms 1.40% __GI__IO_file_open 112ms 1.40% 60.05% 112ms 1.40% incircle 1ms 0.013% 60.06% 112ms 1.40% std::_Vector_base::_M_allocate (inline) 2ms 0.025% 60.09% 111ms 1.39% boost::detail::shared_count::~shared_count (inline) 0 0% 60.09% 111ms 1.39% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 60.11% 111ms 1.39% std::operator<< (inline) 3ms 0.038% 60.15% 110ms 1.38% Node::~Node 106ms 1.33% 61.48% 108ms 1.35% boost::detail::sp_counted_base::release 98ms 1.23% 62.70% 101ms 1.26% __libc_open64 48ms 0.6% 63.30% 100ms 1.25% boost::shared_ptr::shared_ptr (inline) 100ms 1.25% 64.56% 100ms 1.25% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 64.59% 98ms 1.23% AbstractTetrahedralElement::AbstractTetrahedralElement 64ms 0.8% 65.39% 95ms 1.19% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 65.39% 93ms 1.16% std::basic_filebuf::_M_terminate_output 1ms 0.013% 65.41% 93ms 1.16% std::basic_filebuf::overflow 1ms 0.013% 65.42% 92ms 1.15% std::basic_filebuf::_M_convert_to_external 0 0% 65.42% 91ms 1.14% std::__basic_file::xsputn 89ms 1.11% 66.53% 90ms 1.13% __GI___libc_write 0 0% 66.53% 89ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 38ms 0.48% 67.01% 89ms 1.11% AbstractElement::GetNodeLocation 57ms 0.71% 67.72% 87ms 1.09% std::basic_streambuf::xsputn 5ms 0.063% 67.78% 86ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 83ms 1.04% 68.82% 83ms 1.04% [libchaste_cell_based.so] 77ms 0.96% 69.79% 77ms 0.96% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 53ms 0.66% 70.45% 77ms 0.96% malloc_consolidate 71ms 0.89% 71.34% 76ms 0.95% vertexsort 48ms 0.6% 71.94% 74ms 0.93% std::basic_filebuf::xsputn 2ms 0.025% 71.96% 73ms 0.91% std::filesystem::status 0 0% 71.96% 72ms 0.9% tcache_get (inline) 72ms 0.9% 72.87% 72ms 0.9% tcache_get_n (inline) 71ms 0.89% 73.75% 71ms 0.89% __GI___fstatat64 2ms 0.025% 73.78% 70ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.78% 70ms 0.88% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 73.80% 70ms 0.88% std::filesystem::create_directory 1ms 0.013% 73.82% 69ms 0.86% Cell::GetCellId 69ms 0.86% 74.68% 69ms 0.86% Node::GetIndex 12ms 0.15% 74.83% 67ms 0.84% CellPropertyCollection::AddProperty 48ms 0.6% 75.43% 65ms 0.81% AbstractElement::GetNodeGlobalIndex 64ms 0.8% 76.23% 64ms 0.8% std::vector::size (inline) 63ms 0.79% 77.02% 63ms 0.79% __memcpy_avx_unaligned_erms 5ms 0.063% 77.08% 61ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.08% 61ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.08% 61ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 61ms 0.76% 77.85% 61ms 0.76% counterclockwise 39ms 0.49% 78.34% 60ms 0.75% boost::numeric::ublas::c_matrix::operator() (partial-inline) 59ms 0.74% 79.07% 59ms 0.74% boost::shared_ptr::operator-> (inline) 28ms 0.35% 79.42% 58ms 0.73% AbstractTetrahedralMesh::GetElement 3ms 0.038% 79.46% 57ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeB 57ms 0.71% 80.18% 57ms 0.71% [libstdc++.so.6.0.33] 5ms 0.063% 80.24% 55ms 0.69% Node::ConstructNodeAttributes (inline) 2ms 0.025% 80.26% 55ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 41ms 0.51% 80.78% 55ms 0.69% std::num_put::do_put 54ms 0.68% 81.45% 54ms 0.68% boost::numeric::ublas::c_vector::operator() 1ms 0.013% 81.46% 52ms 0.65% Node::ClearAppliedForce 49ms 0.61% 82.08% 52ms 0.65% boost::detail::shared_count::shared_count (inline) 50ms 0.63% 82.70% 50ms 0.63% Node::IsDeleted 16ms 0.2% 82.90% 49ms 0.61% Determinant (inline) 30ms 0.38% 83.28% 49ms 0.61% hack_digit 0 0% 83.28% 49ms 0.61% std::vector::vector (inline) 3ms 0.038% 83.32% 48ms 0.6% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 3ms 0.038% 83.35% 48ms 0.6% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 83.37% 45ms 0.56% Element::~Element 0 0% 83.37% 45ms 0.56% boost::numeric::ublas::norm_2 (inline) 10ms 0.13% 83.49% 45ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.49% 45ms 0.56% std::_Vector_base::_Vector_base (inline) 0 0% 83.49% 45ms 0.56% std::__new_allocator::construct (inline) 0 0% 83.49% 45ms 0.56% std::allocator_traits::construct (inline) 10ms 0.13% 83.62% 44ms 0.55% Inverse 44ms 0.55% 84.17% 44ms 0.55% Node::rGetLocation 0 0% 84.17% 43ms 0.54% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.17% 43ms 0.54% std::_Vector_base::_M_create_storage (inline) 42ms 0.53% 84.69% 42ms 0.53% [libchaste_mesh.so] 0 0% 84.69% 42ms 0.53% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.69% 42ms 0.53% std::__new_allocator::destroy (inline) 0 0% 84.69% 42ms 0.53% std::allocator_traits::destroy (inline) 0 0% 84.69% 41ms 0.51% BoundaryNodeWriter::Visit 0 0% 84.69% 40ms 0.5% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 84.69% 40ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.69% 40ms 0.5% std::map::map (inline)