File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4538ms, 85.88% of 5284ms total Dropped 474 nodes (cum <= 26.42ms) flat flat% sum% cum cum% 0 0% 0% 5259ms 99.53% __libc_start_call_main 0 0% 0% 5259ms 99.53% __libc_start_main_impl 0 0% 0% 5259ms 99.53% _start 0 0% 0% 5246ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5246ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5246ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5246ms 99.28% main 0 0% 0% 5211ms 98.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5211ms 98.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5211ms 98.62% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 5208ms 98.56% AbstractCellBasedSimulation::Solve 0 0% 0% 2496ms 47.24% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.019% 0.019% 2202ms 41.67% MeshBasedCellPopulation::Update 1ms 0.019% 0.038% 1710ms 32.36% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1111ms 21.03% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.038% 1049ms 19.85% MutableMesh::ReMesh 1ms 0.019% 0.057% 997ms 18.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.38% 0.44% 988ms 18.70% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.038% 0.47% 889ms 16.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.019% 0.49% 859ms 16.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 77ms 1.46% 1.95% 808ms 15.29% TetrahedralMesh::EdgeIterator::operator++ 308ms 5.83% 7.78% 671ms 12.70% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.13% 7.91% 661ms 12.51% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.057% 7.97% 621ms 11.75% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.13% 8.10% 576ms 10.90% CellPopulationElementWriter::Visit 10ms 0.19% 8.29% 565ms 10.69% AbstractCellPopulation::GetCellUsingLocationIndex 18ms 0.34% 8.63% 559ms 10.58% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 135ms 2.55% 11.18% 541ms 10.24% __dynamic_cast 11ms 0.21% 11.39% 529ms 10.01% MeshBasedCellPopulation::AcceptCellWriter 1ms 0.019% 11.41% 520ms 9.84% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.11% 11.53% 494ms 9.35% TetrahedralMesh::ImportFromMesher 35ms 0.66% 12.19% 466ms 8.82% operator new 0 0% 12.19% 439ms 8.31% triangulate 3ms 0.057% 12.24% 432ms 8.18% std::set::insert (inline) 153ms 2.90% 15.14% 429ms 8.12% __GI___libc_malloc 5ms 0.095% 15.23% 429ms 8.12% std::_Rb_tree::_M_insert_unique 4ms 0.076% 15.31% 428ms 8.10% AbstractCellProperty::IsSubType (inline) 66ms 1.25% 16.56% 428ms 8.10% std::_Rb_tree::~_Rb_tree (inline) 0 0% 16.56% 408ms 7.72% std::set::~set (inline) 7ms 0.13% 16.69% 399ms 7.55% std::_Rb_tree::find (inline) 11ms 0.21% 16.90% 385ms 7.29% std::__new_allocator::allocate (inline) 0 0% 16.90% 382ms 7.23% delaunay 1ms 0.019% 16.92% 382ms 7.23% divconqdelaunay 0 0% 16.92% 381ms 7.21% std::allocator_traits::allocate (inline) 0 0% 16.92% 377ms 7.13% std::set::count (inline) 39ms 0.74% 17.66% 367ms 6.95% std::map::operator[] (partial-inline) 0 0% 17.66% 366ms 6.93% std::ostream::operator<< (inline) 52ms 0.98% 18.64% 365ms 6.91% std::ostream::_M_insert 37ms 0.7% 19.34% 359ms 6.79% std::_Rb_tree::_M_erase 2ms 0.038% 19.38% 341ms 6.45% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 19.38% 337ms 6.38% Cell::GetCellProliferativeType 0 0% 19.38% 317ms 6.00% std::_Rb_tree::_M_drop_node (inline) 0 0% 19.38% 313ms 5.92% std::_Rb_tree::_M_create_node (inline) 0 0% 19.38% 304ms 5.75% std::_Rb_tree::_M_get_node (inline) 0 0% 19.38% 302ms 5.72% std::_Rb_tree::lower_bound (inline) 0 0% 19.38% 302ms 5.72% std::map::lower_bound (inline) 0 0% 19.38% 299ms 5.66% std::_Rb_tree::_Alloc_node::operator() (inline) 296ms 5.60% 24.98% 296ms 5.60% __strcmp_evex 1ms 0.019% 25.00% 289ms 5.47% AbstractCellBasedSimulation::DoCellBirth 141ms 2.67% 27.67% 279ms 5.28% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.038% 27.71% 277ms 5.24% boost::detail::shared_count::~shared_count (inline) 0 0% 27.71% 277ms 5.24% boost::shared_ptr::~shared_ptr (inline) 33ms 0.62% 28.33% 275ms 5.20% std::_Rb_tree::_M_insert_ (inline) 267ms 5.05% 33.38% 269ms 5.09% boost::detail::sp_counted_base::release 16ms 0.3% 33.69% 244ms 4.62% std::_Rb_tree::_Rb_tree (partial-inline) 61ms 1.15% 34.84% 239ms 4.52% __GI___libc_free 5ms 0.095% 34.94% 232ms 4.39% Cell::GetMutationState 0 0% 34.94% 229ms 4.33% NodeLocationWriter::Visit 4ms 0.076% 35.01% 225ms 4.26% Element::Element 1ms 0.019% 35.03% 224ms 4.24% std::set::set (inline) 14ms 0.26% 35.30% 221ms 4.18% std::_Rb_tree::_M_copy (inline) 150ms 2.84% 38.13% 220ms 4.16% _int_malloc 4ms 0.076% 38.21% 220ms 4.16% std::__new_allocator::deallocate (inline) 217ms 4.11% 42.32% 217ms 4.11% std::_Rb_tree::_S_right (inline) 0 0% 42.32% 214ms 4.05% std::allocator_traits::deallocate (inline) 16ms 0.3% 42.62% 205ms 3.88% std::num_put::_M_insert_float 10ms 0.19% 42.81% 203ms 3.84% divconqrecurse 78ms 1.48% 44.28% 200ms 3.79% std::_Rb_tree::_M_clone_node (inline) 9ms 0.17% 44.45% 198ms 3.75% std::less::operator() (inline) 1ms 0.019% 44.47% 194ms 3.67% AbstractCellPopulation::IsCellAttachedToLocationIndex 189ms 3.58% 48.05% 189ms 3.58% std::operator< (inline) 0 0% 48.05% 184ms 3.48% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 48.05% 184ms 3.48% MeshBasedCellPopulation::GetDampingConstant 52ms 0.98% 49.03% 184ms 3.48% mergehulls 0 0% 49.03% 182ms 3.44% Cell::ReadyToDivide 155ms 2.93% 51.97% 178ms 3.37% _int_free 0 0% 51.97% 176ms 3.33% std::_Rb_tree::_M_put_node (inline) 5ms 0.095% 52.06% 173ms 3.27% std::__cxx11::collate::do_transform 0 0% 52.06% 164ms 3.10% ___vsnprintf 0 0% 52.06% 164ms 3.10% __vsnprintf_internal (inline) 3ms 0.057% 52.12% 163ms 3.08% Element::RegisterWithNodes (inline) 18ms 0.34% 52.46% 161ms 3.05% __printf_buffer 4ms 0.076% 52.54% 157ms 2.97% Node::AddElement 154ms 2.91% 55.45% 154ms 2.91% [libchaste_cell_based.so] 56ms 1.06% 56.51% 149ms 2.82% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 56.51% 147ms 2.78% CellProliferativeTypesWriter::VisitCell 0 0% 56.51% 141ms 2.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 56.51% 141ms 2.67% std::__new_allocator::destroy (inline) 0 0% 56.51% 141ms 2.67% std::allocator_traits::destroy (inline) 1ms 0.019% 56.53% 140ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.076% 56.60% 137ms 2.59% AbstractCellProperty::IsType (inline) 5ms 0.095% 56.70% 135ms 2.55% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.13% 56.83% 135ms 2.55% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.019% 56.85% 133ms 2.52% CellPropertyCollection::HasProperty 0 0% 56.85% 132ms 2.50% Cell::HasCellProperty (inline) 1ms 0.019% 56.87% 130ms 2.46% __printf_fp_spec (inline) 7ms 0.13% 57.00% 129ms 2.44% __printf_fp_l_buffer 1ms 0.019% 57.02% 127ms 2.40% OutputFileHandler::OpenOutputFile 0 0% 57.02% 126ms 2.38% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 57.02% 126ms 2.38% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.038% 57.06% 119ms 2.25% alternateaxes 54ms 1.02% 58.08% 116ms 2.20% __printf_fp_buffer_1 105ms 1.99% 60.07% 116ms 2.20% vertexmedian 9ms 0.17% 60.24% 113ms 2.14% AbstractTetrahedralElement::CalculateJacobian 1ms 0.019% 60.26% 112ms 2.12% TetrahedralMesh::Clear 0 0% 60.26% 108ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 107ms 2.02% 62.28% 107ms 2.02% [libchaste_mesh.so] 2ms 0.038% 62.32% 104ms 1.97% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.019% 62.34% 91ms 1.72% boost::numeric::ublas::vector_assign (inline) 13ms 0.25% 62.59% 89ms 1.68% AbstractCellProperty::IsSame 13ms 0.25% 62.83% 88ms 1.67% TetrahedralMesh::EdgesEnd (partial-inline) 13ms 0.25% 63.08% 87ms 1.65% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.095% 63.17% 85ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.019% 63.19% 85ms 1.61% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 63.19% 84ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.17% 63.36% 82ms 1.55% AbstractTetrahedralElement::RefreshJacobian 82ms 1.55% 64.91% 82ms 1.55% incircle 30ms 0.57% 65.48% 82ms 1.55% std::__ostream_insert 23ms 0.44% 65.92% 79ms 1.50% std::num_put::_M_insert_int 2ms 0.038% 65.95% 79ms 1.50% std::vector::push_back (inline) 1ms 0.019% 65.97% 78ms 1.48% std::_Vector_base::_M_allocate (inline) 62ms 1.17% 67.15% 76ms 1.44% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 8ms 0.15% 67.30% 76ms 1.44% std::type_info::operator== (inline) 0 0% 67.30% 72ms 1.36% std::basic_ofstream::basic_ofstream (inline) 4ms 0.076% 67.37% 72ms 1.36% std::vector::_M_realloc_insert 5ms 0.095% 67.47% 69ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 68ms 1.29% 68.75% 68ms 1.29% std::_Rb_tree_insert_and_rebalance 0 0% 68.75% 68ms 1.29% std::basic_ofstream::open (inline) 0 0% 68.75% 66ms 1.25% std::basic_filebuf::open 0 0% 68.75% 64ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 64ms 1.21% 69.97% 64ms 1.21% [libstdc++.so.6.0.33] 17ms 0.32% 70.29% 64ms 1.21% boost::numeric::ublas::indexing_vector_assign 0 0% 70.29% 64ms 1.21% std::operator<< (inline) 28ms 0.53% 70.82% 63ms 1.19% AbstractElement::GetNodeLocation 1ms 0.019% 70.84% 63ms 1.19% Node::~Node 2ms 0.038% 70.87% 59ms 1.12% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 70.87% 59ms 1.12% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.019% 70.89% 58ms 1.10% Cell::GetCellId 43ms 0.81% 71.71% 58ms 1.10% malloc_consolidate 54ms 1.02% 72.73% 54ms 1.02% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.057% 72.79% 53ms 1.00% AbstractCellPopulation::GetLocationIndexUsingCell 50ms 0.95% 73.73% 53ms 1.00% vertexsort 1ms 0.019% 73.75% 50ms 0.95% CellPropertyCollection::AddProperty 50ms 0.95% 74.70% 50ms 0.95% std::_Rb_tree::_S_left (inline) 5ms 0.095% 74.79% 50ms 0.95% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 74.79% 50ms 0.95% tcache_get (inline) 50ms 0.95% 75.74% 50ms 0.95% tcache_get_n (inline) 1ms 0.019% 75.76% 47ms 0.89% Node::ConstructNodeAttributes (inline) 47ms 0.89% 76.65% 47ms 0.89% std::_Rb_tree_increment 25ms 0.47% 77.12% 47ms 0.89% std::basic_streambuf::xsputn 0 0% 77.12% 46ms 0.87% Node::ClearAppliedForce 45ms 0.85% 77.97% 45ms 0.85% counterclockwise 44ms 0.83% 78.80% 44ms 0.83% Node::GetIndex 43ms 0.81% 79.62% 43ms 0.81% std::vector::size (inline) 0 0% 79.62% 42ms 0.79% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 79.62% 42ms 0.79% OutputFileHandler::CommonConstructor 0 0% 79.62% 42ms 0.79% OutputFileHandler::OutputFileHandler 0 0% 79.62% 41ms 0.78% std::basic_filebuf::close 0 0% 79.62% 41ms 0.78% std::basic_ofstream::close (inline) 0 0% 79.62% 40ms 0.76% AbstractCellBasedWriter::CloseFile 5ms 0.095% 79.71% 40ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 79.71% 40ms 0.76% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 26ms 0.49% 80.20% 39ms 0.74% writeedges 18ms 0.34% 80.55% 38ms 0.72% AbstractElement::GetNodeGlobalIndex 0 0% 80.55% 38ms 0.72% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.057% 80.60% 38ms 0.72% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.019% 80.62% 37ms 0.7% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.62% 37ms 0.7% _IO_new_fopen 0 0% 80.62% 37ms 0.7% __fopen_internal (inline) 23ms 0.44% 81.06% 37ms 0.7% hack_digit 28ms 0.53% 81.59% 36ms 0.68% CellPropertyCollection::GetProperty 20ms 0.38% 81.96% 36ms 0.68% boost::shared_ptr::shared_ptr (inline) 0 0% 81.96% 36ms 0.68% std::__basic_file::open 0 0% 81.96% 35ms 0.66% _IO_new_file_fopen 0 0% 81.96% 35ms 0.66% __GI__IO_file_open 35ms 0.66% 82.63% 35ms 0.66% __memcpy_avx512_unaligned_erms 18ms 0.34% 82.97% 35ms 0.66% std::basic_filebuf::xsputn 23ms 0.44% 83.40% 34ms 0.64% AbstractTetrahedralMesh::GetElement 11ms 0.21% 83.61% 34ms 0.64% Determinant (inline) 0 0% 83.61% 34ms 0.64% FilesystemPermissions::SetFilePermissions (inline) 0 0% 83.61% 34ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 33ms 0.62% 84.24% 34ms 0.64% __GI___libc_write 34ms 0.64% 84.88% 34ms 0.64% __GI_fchmodat 0 0% 84.88% 34ms 0.64% std::__basic_file::xsputn 0 0% 84.88% 34ms 0.64% std::basic_filebuf::_M_convert_to_external 0 0% 84.88% 34ms 0.64% std::basic_filebuf::_M_terminate_output 0 0% 84.88% 34ms 0.64% std::basic_filebuf::overflow 0 0% 84.88% 34ms 0.64% std::filesystem::permissions 26ms 0.49% 85.37% 34ms 0.64% std::num_put::do_put 0 0% 85.37% 33ms 0.62% std::_Vector_base::_M_deallocate (inline) 0 0% 85.37% 32ms 0.61% CxxTest::RealWorldDescription::setUp 0 0% 85.37% 32ms 0.61% PMPI_Init_thread 0 0% 85.37% 32ms 0.61% PetscInitialize 0 0% 85.37% 32ms 0.61% PetscSetup::setUpWorld 0 0% 85.37% 32ms 0.61% PetscSetupUtils::CommonSetup 0 0% 85.37% 32ms 0.61% PetscSetupUtils::InitialisePetsc 0 0% 85.37% 32ms 0.61% ompi_mpi_init 0 0% 85.37% 32ms 0.61% std::vector::vector (inline) 25ms 0.47% 85.84% 31ms 0.59% boost::numeric::ublas::c_matrix::operator() 0 0% 85.84% 30ms 0.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 85.84% 30ms 0.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 85.84% 30ms 0.57% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 85.84% 29ms 0.55% _dl_init 0 0% 85.84% 29ms 0.55% call_init (inline) 0 0% 85.84% 27ms 0.51% 2ms 0.038% 85.88% 27ms 0.51% Inverse 0 0% 85.88% 27ms 0.51% NodeAttributes::NodeAttributes 0 0% 85.88% 27ms 0.51% std::_Vector_base::_Vector_base (inline) 0 0% 85.88% 27ms 0.51% std::map::map (inline)