File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6781ms, 85.79% of 7904ms total Dropped 603 nodes (cum <= 39.52ms) flat flat% sum% cum cum% 0 0% 0% 7865ms 99.51% __libc_start_call_main 0 0% 0% 7865ms 99.51% __libc_start_main_impl 0 0% 0% 7865ms 99.51% _start 0 0% 0% 7847ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7847ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7847ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7847ms 99.28% main 0 0% 0% 7799ms 98.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7799ms 98.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7799ms 98.67% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7795ms 98.62% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3399ms 43.00% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2932ms 37.10% MeshBasedCellPopulation::Update 0 0% 0.013% 2831ms 35.82% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.013% 1559ms 19.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 1467ms 18.56% MutableMesh::ReMesh 0 0% 0.013% 1408ms 17.81% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.013% 1407ms 17.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.038% 0.051% 1346ms 17.03% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.19% 0.24% 1203ms 15.22% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.43% 1.67% 998ms 12.63% TetrahedralMesh::EdgeIterator::operator++ 250ms 3.16% 4.83% 943ms 11.93% __dynamic_cast 3ms 0.038% 4.87% 935ms 11.83% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.013% 4.88% 921ms 11.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 454ms 5.74% 10.63% 916ms 11.59% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.076% 10.70% 903ms 11.42% CellPropertyCollection::GetPropertiesType (inline) 12ms 0.15% 10.86% 835ms 10.56% CellPopulationElementWriter::Visit 38ms 0.48% 11.34% 827ms 10.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 7ms 0.089% 11.42% 783ms 9.91% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.038% 11.46% 739ms 9.35% AbstractCellProperty::IsSubType (inline) 32ms 0.4% 11.87% 734ms 9.29% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 11.96% 721ms 9.12% TetrahedralMesh::ImportFromMesher 27ms 0.34% 12.30% 613ms 7.76% operator new 592ms 7.49% 19.79% 592ms 7.49% __strcmp_avx2 4ms 0.051% 19.84% 588ms 7.44% triangulate 197ms 2.49% 22.33% 577ms 7.30% __GI___libc_malloc 64ms 0.81% 23.14% 563ms 7.12% std::map::operator[] (partial-inline) 0 0% 23.14% 554ms 7.01% std::ostream::operator<< (inline) 85ms 1.08% 24.22% 553ms 7.00% std::ostream::_M_insert 21ms 0.27% 24.48% 541ms 6.84% std::__new_allocator::allocate (inline) 0 0% 24.48% 535ms 6.77% std::allocator_traits::allocate (inline) 7ms 0.089% 24.57% 535ms 6.77% std::set::insert (inline) 6ms 0.076% 24.65% 532ms 6.73% Cell::GetCellProliferativeType 7ms 0.089% 24.73% 528ms 6.68% std::_Rb_tree::_M_insert_unique 8ms 0.1% 24.84% 516ms 6.53% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.013% 24.85% 509ms 6.44% delaunay 2ms 0.025% 24.87% 505ms 6.39% divconqdelaunay 22ms 0.28% 25.15% 505ms 6.39% std::_Rb_tree::find (inline) 206ms 2.61% 27.76% 494ms 6.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.76% 459ms 5.81% std::set::count (inline) 4ms 0.051% 27.81% 456ms 5.77% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.81% 452ms 5.72% std::_Rb_tree::lower_bound (inline) 0 0% 27.81% 452ms 5.72% std::map::lower_bound (inline) 0 0% 27.81% 447ms 5.66% std::_Rb_tree::_M_create_node (inline) 31ms 0.39% 28.20% 431ms 5.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.20% 424ms 5.36% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.20% 418ms 5.29% std::_Rb_tree::_M_get_node (inline) 0 0% 28.20% 413ms 5.23% std::set::~set (inline) 84ms 1.06% 29.26% 397ms 5.02% std::_Rb_tree::_M_erase 6ms 0.076% 29.34% 387ms 4.90% Cell::GetMutationState 32ms 0.4% 29.74% 374ms 4.73% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.74% 362ms 4.58% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 29.74% 362ms 4.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 29.74% 359ms 4.54% OutputFileHandler::OpenOutputFile 0 0% 29.74% 337ms 4.26% NodeLocationWriter::Visit 5ms 0.063% 29.81% 332ms 4.20% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 29.86% 329ms 4.16% std::set::set (inline) 7ms 0.089% 29.95% 327ms 4.14% AbstractCentreBasedCellPopulation::GetDampingConstant 24ms 0.3% 30.25% 323ms 4.09% std::_Rb_tree::_M_insert_ (inline) 7ms 0.089% 30.34% 321ms 4.06% std::less::operator() (inline) 314ms 3.97% 34.31% 314ms 3.97% std::operator< (inline) 3ms 0.038% 34.35% 313ms 3.96% Element::Element 92ms 1.16% 35.51% 312ms 3.95% __GI___libc_free 30ms 0.38% 35.89% 307ms 3.88% std::_Rb_tree::_M_copy (inline) 7ms 0.089% 35.98% 303ms 3.83% Cell::ReadyToDivide 195ms 2.47% 38.45% 294ms 3.72% _int_malloc 0 0% 38.45% 289ms 3.66% std::_Rb_tree::_M_drop_node (inline) 15ms 0.19% 38.64% 285ms 3.61% std::__new_allocator::deallocate (inline) 24ms 0.3% 38.94% 285ms 3.61% std::num_put::_M_insert_float 0 0% 38.94% 283ms 3.58% std::allocator_traits::deallocate (inline) 279ms 3.53% 42.47% 279ms 3.53% std::_Rb_tree::_S_right (inline) 12ms 0.15% 42.62% 277ms 3.50% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.22% 42.84% 275ms 3.48% divconqrecurse 70ms 0.89% 43.72% 274ms 3.47% std::_Rb_tree::_M_clone_node (inline) 73ms 0.92% 44.65% 251ms 3.18% mergehulls 0 0% 44.65% 238ms 3.01% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 44.67% 237ms 3.00% AbstractCellProperty::IsType (inline) 8ms 0.1% 44.77% 235ms 2.97% CellPropertyCollection::HasProperty 10ms 0.13% 44.90% 235ms 2.97% std::__cxx11::collate::do_transform 1ms 0.013% 44.91% 234ms 2.96% CellProliferativeTypesWriter::VisitCell 0 0% 44.91% 231ms 2.92% Cell::HasCellProperty (inline) 187ms 2.37% 47.28% 220ms 2.78% _int_free 3ms 0.038% 47.32% 218ms 2.76% ___vsnprintf 0 0% 47.32% 215ms 2.72% __vsnprintf_internal (inline) 24ms 0.3% 47.62% 207ms 2.62% __printf_buffer 10ms 0.13% 47.75% 206ms 2.61% Element::RegisterWithNodes (inline) 7ms 0.089% 47.84% 203ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 72ms 0.91% 48.75% 198ms 2.51% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.051% 48.80% 196ms 2.48% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 48.84% 194ms 2.45% Node::AddElement 5ms 0.063% 48.90% 192ms 2.43% TetrahedralMesh::Clear 4ms 0.051% 48.95% 186ms 2.35% MeshBasedCellPopulation::SpringsEnd (inline) 40ms 0.51% 49.46% 182ms 2.30% AbstractCellProperty::IsSame 0 0% 49.46% 173ms 2.19% std::basic_ofstream::basic_ofstream (inline) 15ms 0.19% 49.65% 172ms 2.18% AbstractTetrahedralElement::CalculateJacobian 34ms 0.43% 50.08% 166ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 50.09% 166ms 2.10% std::basic_filebuf::open 0 0% 50.09% 166ms 2.10% std::basic_ofstream::open (inline) 5ms 0.063% 50.15% 164ms 2.07% __printf_fp_l_buffer 0 0% 50.15% 164ms 2.07% __printf_fp_spec (inline) 0 0% 50.15% 159ms 2.01% AbstractCellBasedWriter::CloseFile 0 0% 50.15% 159ms 2.01% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 50.16% 159ms 2.01% std::basic_ofstream::close (inline) 0 0% 50.16% 158ms 2.00% std::basic_filebuf::close 0 0% 50.16% 152ms 1.92% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 50.19% 152ms 1.92% std::filesystem::permissions 150ms 1.90% 52.09% 150ms 1.90% __GI_fchmodat 91ms 1.15% 53.24% 148ms 1.87% __printf_fp_buffer_1 1ms 0.013% 53.25% 147ms 1.86% OutputFileHandler::OutputFileHandler 1ms 0.013% 53.26% 146ms 1.85% OutputFileHandler::CommonConstructor 0 0% 53.26% 143ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.063% 53.33% 143ms 1.81% alternateaxes 0 0% 53.33% 142ms 1.80% TetrahedralMesh::RefreshJacobianCachedData 25ms 0.32% 53.64% 142ms 1.80% std::type_info::operator== (inline) 12ms 0.15% 53.80% 139ms 1.76% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.025% 53.82% 139ms 1.76% boost::numeric::ublas::vector_assign (inline) 132ms 1.67% 55.49% 138ms 1.75% vertexmedian 6ms 0.076% 55.57% 135ms 1.71% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 55.58% 133ms 1.68% std::__basic_file::open 0 0% 55.58% 132ms 1.67% _IO_new_file_fopen 0 0% 55.58% 132ms 1.67% _IO_new_fopen 0 0% 55.58% 132ms 1.67% __fopen_internal (inline) 82ms 1.04% 56.62% 131ms 1.66% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 56.63% 129ms 1.63% __GI__IO_file_open 127ms 1.61% 58.24% 127ms 1.61% incircle 13ms 0.16% 58.40% 126ms 1.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 58.41% 125ms 1.58% Node::~Node 24ms 0.3% 58.72% 122ms 1.54% AbstractTetrahedralElement::RefreshJacobian 20ms 0.25% 58.97% 120ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 117ms 1.48% 60.45% 118ms 1.49% __libc_open64 32ms 0.4% 60.86% 118ms 1.49% std::num_put::_M_insert_int 0 0% 60.86% 117ms 1.48% std::_Vector_base::_M_allocate (inline) 0 0% 60.86% 116ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.15% 61.01% 116ms 1.47% boost::detail::shared_count::~shared_count (inline) 0 0% 61.01% 116ms 1.47% boost::shared_ptr::~shared_ptr (inline) 3ms 0.038% 61.05% 112ms 1.42% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.076% 61.12% 111ms 1.40% std::vector::push_back (inline) 34ms 0.43% 61.55% 110ms 1.39% std::__ostream_insert 1ms 0.013% 61.56% 108ms 1.37% std::basic_filebuf::_M_terminate_output 31ms 0.39% 61.96% 107ms 1.35% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 61.98% 107ms 1.35% std::basic_filebuf::overflow 1ms 0.013% 61.99% 105ms 1.33% std::basic_filebuf::_M_convert_to_external 102ms 1.29% 63.28% 103ms 1.30% __GI___libc_write 0 0% 63.28% 103ms 1.30% std::__basic_file::xsputn 13ms 0.16% 63.45% 100ms 1.27% std::vector::_M_realloc_insert 4ms 0.051% 63.50% 97ms 1.23% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.063% 63.56% 95ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 91ms 1.15% 64.71% 95ms 1.20% boost::detail::sp_counted_base::release 95ms 1.20% 65.92% 95ms 1.20% std::_Rb_tree_increment 44ms 0.56% 66.47% 94ms 1.19% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 66.51% 91ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 66.51% 90ms 1.14% std::operator<< (inline) 88ms 1.11% 67.62% 88ms 1.11% std::_Rb_tree_insert_and_rebalance 84ms 1.06% 68.69% 84ms 1.06% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 67ms 0.85% 69.53% 83ms 1.05% malloc_consolidate 3ms 0.038% 69.57% 81ms 1.02% Cell::GetCellId 81ms 1.02% 70.60% 81ms 1.02% [libchaste_cell_based.so] 0 0% 70.60% 76ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.60% 75ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.60% 75ms 0.95% std::filesystem::create_directory 0 0% 70.60% 75ms 0.95% tcache_get (inline) 75ms 0.95% 71.55% 75ms 0.95% tcache_get_n (inline) 70ms 0.89% 72.43% 75ms 0.95% vertexsort 32ms 0.4% 72.84% 74ms 0.94% AbstractElement::GetNodeLocation 1ms 0.013% 72.85% 74ms 0.94% std::filesystem::status 72ms 0.91% 73.76% 72ms 0.91% __GI___fstatat64 49ms 0.62% 74.38% 72ms 0.91% std::basic_filebuf::xsputn 69ms 0.87% 75.25% 69ms 0.87% std::vector::size (inline) 6ms 0.076% 75.33% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 75.33% 66ms 0.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.33% 66ms 0.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 57ms 0.72% 76.05% 66ms 0.84% std::num_put::do_put 10ms 0.13% 76.18% 61ms 0.77% CellPropertyCollection::AddProperty 0 0% 76.18% 61ms 0.77% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 36ms 0.46% 76.63% 61ms 0.77% boost::numeric::ublas::c_matrix::operator() (partial-inline) 43ms 0.54% 77.18% 60ms 0.76% AbstractElement::GetNodeGlobalIndex 6ms 0.076% 77.25% 60ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeA 60ms 0.76% 78.01% 60ms 0.76% [libchaste_mesh.so] 0 0% 78.01% 58ms 0.73% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 78.01% 58ms 0.73% std::vector::vector (inline) 0 0% 78.01% 56ms 0.71% boost::numeric::ublas::norm_2 (inline) 13ms 0.16% 78.18% 56ms 0.71% boost::numeric::ublas::vector_norm_2::apply (inline) 55ms 0.7% 78.87% 55ms 0.7% Node::GetIndex 0 0% 78.87% 55ms 0.7% std::_Vector_base::_Vector_base (inline) 0 0% 78.87% 54ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 78.87% 53ms 0.67% std::_Vector_base::_M_create_storage (inline) 0 0% 78.87% 51ms 0.65% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.87% 51ms 0.65% std::__new_allocator::destroy (inline) 0 0% 78.87% 51ms 0.65% std::allocator_traits::destroy (inline) 1ms 0.013% 78.88% 50ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 17ms 0.22% 79.10% 50ms 0.63% Determinant (inline) 50ms 0.63% 79.73% 50ms 0.63% counterclockwise 6ms 0.076% 79.81% 50ms 0.63% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 79.82% 49ms 0.62% Node::ClearAppliedForce 45ms 0.57% 80.39% 49ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 80.39% 49ms 0.62% std::map::map (inline) 0 0% 80.39% 48ms 0.61% Node::ConstructNodeAttributes (inline) 3ms 0.038% 80.43% 48ms 0.61% _IO_new_fclose 1ms 0.013% 80.44% 48ms 0.61% std::__basic_file::close 48ms 0.61% 81.05% 48ms 0.61% std::ostream::sentry::sentry 0 0% 81.05% 47ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 21ms 0.27% 81.31% 45ms 0.57% AbstractTetrahedralMesh::GetElement 32ms 0.4% 81.72% 45ms 0.57% std::basic_streambuf::xsputn 15ms 0.19% 81.91% 44ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 0 0% 81.91% 44ms 0.56% CxxTest::RealWorldDescription::setUp 0 0% 81.91% 44ms 0.56% PetscSetup::setUpWorld 0 0% 81.91% 44ms 0.56% PetscSetupUtils::CommonSetup 44ms 0.56% 82.46% 44ms 0.56% __GI___mkdir 0 0% 82.46% 44ms 0.56% _dl_init 0 0% 82.46% 44ms 0.56% call_init (inline) 0 0% 82.46% 43ms 0.54% PMPI_Init_thread 0 0% 82.46% 43ms 0.54% PetscInitialize 0 0% 82.46% 43ms 0.54% PetscSetupUtils::InitialisePetsc 0 0% 82.46% 43ms 0.54% ompi_mpi_init 38ms 0.48% 82.95% 43ms 0.54% writeedges 21ms 0.27% 83.21% 42ms 0.53% AbstractCellCycleModel::GetAge 42ms 0.53% 83.74% 42ms 0.53% Node::rGetLocation 0 0% 83.74% 42ms 0.53% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 2ms 0.025% 83.77% 42ms 0.53% _IO_new_file_close_it 0 0% 83.77% 41ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.77% 40ms 0.51% BoundaryNodeWriter::Visit 40ms 0.51% 84.27% 40ms 0.51% __GI___close_nocancel 40ms 0.51% 84.78% 40ms 0.51% boost::numeric::ublas::c_vector::operator() 40ms 0.51% 85.29% 40ms 0.51% boost::numeric::ublas::same_impl_ex 40ms 0.51% 85.79% 40ms 0.51% boost::shared_ptr::operator-> (inline)