File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 3931ms, 84.21% of 4668ms total Dropped 449 nodes (cum <= 23.34ms) flat flat% sum% cum cum% 0 0% 0% 4641ms 99.42% __libc_start_call_main 0 0% 0% 4641ms 99.42% __libc_start_main_impl 0 0% 0% 4641ms 99.42% _start 0 0% 0% 4628ms 99.14% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4628ms 99.14% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4628ms 99.14% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4628ms 99.14% main 0 0% 0% 4591ms 98.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4591ms 98.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4591ms 98.35% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4589ms 98.31% AbstractCellBasedSimulation::Solve 0 0% 0% 2030ms 43.49% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.021% 0.021% 1757ms 37.64% MeshBasedCellPopulation::Update 0 0% 0.021% 1654ms 35.43% AbstractCellPopulation::WriteResultsToFiles 1ms 0.021% 0.043% 900ms 19.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 0.064% 871ms 18.66% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.064% 861ms 18.44% MutableMesh::ReMesh 0 0% 0.064% 801ms 17.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.064% 780ms 16.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.32% 0.39% 758ms 16.24% MeshBasedCellPopulation::SpringIterator::operator++ 74ms 1.59% 1.97% 634ms 13.58% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.021% 1.99% 573ms 12.28% AbstractTwoBodyInteractionForce::AddForceContribution 37ms 0.79% 2.78% 532ms 11.40% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 3ms 0.064% 2.85% 512ms 10.97% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.21% 3.06% 508ms 10.88% CellPopulationElementWriter::Visit 253ms 5.42% 8.48% 504ms 10.80% std::_Rb_tree::_M_lower_bound (inline) 22ms 0.47% 8.95% 455ms 9.75% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.064% 9.02% 421ms 9.02% TetrahedralMesh::ImportFromMesher 102ms 2.19% 11.20% 415ms 8.89% __dynamic_cast 8ms 0.17% 11.38% 408ms 8.74% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.11% 11.48% 398ms 8.53% CellPropertyCollection::GetPropertiesType (inline) 80ms 1.71% 13.20% 384ms 8.23% std::_Rb_tree::~_Rb_tree (inline) 24ms 0.51% 13.71% 380ms 8.14% operator new 0 0% 13.71% 366ms 7.84% std::set::~set (inline) 2ms 0.043% 13.75% 360ms 7.71% triangulate 150ms 3.21% 16.97% 352ms 7.54% __GI___libc_malloc 8ms 0.17% 17.14% 332ms 7.11% std::__new_allocator::allocate (inline) 0 0% 17.14% 329ms 7.05% delaunay 1ms 0.021% 17.16% 328ms 7.03% divconqdelaunay 0 0% 17.16% 327ms 7.01% std::allocator_traits::allocate (inline) 2ms 0.043% 17.20% 323ms 6.92% std::set::insert (inline) 0 0% 17.20% 322ms 6.90% AbstractCellProperty::IsSubType (inline) 4ms 0.086% 17.29% 321ms 6.88% std::_Rb_tree::_M_insert_unique 11ms 0.24% 17.52% 308ms 6.60% std::_Rb_tree::find (inline) 28ms 0.6% 18.12% 302ms 6.47% std::_Rb_tree::_M_erase 1ms 0.021% 18.14% 294ms 6.30% std::ostream::operator<< (inline) 7ms 0.15% 18.29% 292ms 6.26% boost::detail::shared_count::~shared_count (inline) 0 0% 18.29% 292ms 6.26% boost::shared_ptr::~shared_ptr (inline) 32ms 0.69% 18.98% 292ms 6.26% std::ostream::_M_insert 0 0% 18.98% 287ms 6.15% std::set::count (inline) 277ms 5.93% 24.91% 278ms 5.96% boost::detail::sp_counted_base::release 16ms 0.34% 25.26% 273ms 5.85% std::map::operator[] (partial-inline) 0 0% 25.26% 267ms 5.72% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.26% 265ms 5.68% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.26% 263ms 5.63% Cell::GetCellProliferativeType 1ms 0.021% 25.28% 259ms 5.55% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 25.28% 252ms 5.40% std::_Rb_tree::_M_create_node (inline) 0 0% 25.28% 244ms 5.23% std::_Rb_tree::_M_get_node (inline) 7ms 0.15% 25.43% 241ms 5.16% std::_Rb_tree::_Rb_tree (partial-inline) 135ms 2.89% 28.32% 232ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.32% 230ms 4.93% std::_Rb_tree::_Alloc_node::operator() (inline) 227ms 4.86% 33.18% 227ms 4.86% __strcmp_evex 1ms 0.021% 33.20% 227ms 4.86% std::set::set (inline) 0 0% 33.20% 225ms 4.82% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.20% 225ms 4.82% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.20% 223ms 4.78% OutputFileHandler::OpenOutputFile 0 0% 33.20% 217ms 4.65% std::_Rb_tree::lower_bound (inline) 0 0% 33.20% 217ms 4.65% std::map::lower_bound (inline) 25ms 0.54% 33.74% 212ms 4.54% std::_Rb_tree::_M_copy (inline) 31ms 0.66% 34.40% 210ms 4.50% __GI___libc_free 6ms 0.13% 34.53% 208ms 4.46% AbstractCellPopulation::IsCellAttachedToLocationIndex 32ms 0.69% 35.22% 206ms 4.41% std::_Rb_tree::_M_insert_ (inline) 9ms 0.19% 35.41% 203ms 4.35% std::less::operator() (inline) 194ms 4.16% 39.57% 194ms 4.16% std::operator< (inline) 1ms 0.021% 39.59% 188ms 4.03% NodeLocationWriter::Visit 85ms 1.82% 41.41% 187ms 4.01% std::_Rb_tree::_M_clone_node (inline) 7ms 0.15% 41.56% 183ms 3.92% std::__new_allocator::deallocate (inline) 0 0% 41.56% 181ms 3.88% std::allocator_traits::deallocate (inline) 6ms 0.13% 41.69% 180ms 3.86% divconqrecurse 166ms 3.56% 45.24% 179ms 3.83% _int_free 2ms 0.043% 45.29% 175ms 3.75% Cell::GetMutationState 10ms 0.21% 45.50% 175ms 3.75% std::num_put::_M_insert_float 44ms 0.94% 46.44% 171ms 3.66% mergehulls 2ms 0.043% 46.49% 163ms 3.49% Cell::ReadyToDivide 1ms 0.021% 46.51% 161ms 3.45% MeshBasedCellPopulation::GetDampingConstant 2ms 0.043% 46.55% 160ms 3.43% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.021% 46.57% 156ms 3.34% Element::Element 88ms 1.89% 48.46% 153ms 3.28% _int_malloc 1ms 0.021% 48.48% 144ms 3.08% std::__cxx11::collate::do_transform 0 0% 48.48% 140ms 3.00% std::_Rb_tree::_M_put_node (inline) 3ms 0.064% 48.54% 138ms 2.96% ___vsnprintf 1ms 0.021% 48.56% 135ms 2.89% __vsnprintf_internal (inline) 14ms 0.3% 48.86% 132ms 2.83% __printf_buffer 0 0% 48.86% 127ms 2.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 48.86% 127ms 2.72% std::__new_allocator::destroy (inline) 0 0% 48.86% 127ms 2.72% std::allocator_traits::destroy (inline) 3ms 0.064% 48.93% 125ms 2.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.17% 49.10% 121ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 49.10% 118ms 2.53% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.10% 117ms 2.51% std::basic_filebuf::open 0 0% 49.10% 117ms 2.51% std::basic_ofstream::open (inline) 2ms 0.043% 49.14% 115ms 2.46% CellProliferativeTypesWriter::VisitCell 4ms 0.086% 49.23% 115ms 2.46% CellPropertyCollection::HasProperty 2ms 0.043% 49.27% 115ms 2.46% TetrahedralMesh::Clear 0 0% 49.27% 113ms 2.42% Cell::HasCellProperty (inline) 3ms 0.064% 49.34% 112ms 2.40% AbstractCellProperty::IsType (inline) 44ms 0.94% 50.28% 111ms 2.38% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.021% 50.30% 110ms 2.36% __printf_fp_spec (inline) 0 0% 50.30% 109ms 2.34% __printf_fp_l_buffer 49ms 1.05% 51.35% 108ms 2.31% __printf_fp_buffer_1 108ms 2.31% 53.66% 108ms 2.31% std::_Rb_tree::_S_right (inline) 1ms 0.021% 53.68% 107ms 2.29% Element::RegisterWithNodes (inline) 1ms 0.021% 53.71% 102ms 2.19% Node::AddElement 0 0% 53.71% 98ms 2.10% AbstractCellBasedWriter::CloseFile 0 0% 53.71% 98ms 2.10% AbstractCellPopulation::CloseRoundRobinWritersFiles 7ms 0.15% 53.86% 98ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.043% 53.90% 98ms 2.10% std::__basic_file::open 1ms 0.021% 53.92% 98ms 2.10% std::basic_ofstream::close (inline) 0 0% 53.92% 97ms 2.08% std::basic_filebuf::close 0 0% 53.92% 96ms 2.06% _IO_new_fopen 1ms 0.021% 53.94% 96ms 2.06% __fopen_internal (inline) 3ms 0.064% 54.01% 95ms 2.04% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 54.01% 95ms 2.04% _IO_new_file_fopen 2ms 0.043% 54.05% 94ms 2.01% __GI__IO_file_open 0 0% 54.05% 89ms 1.91% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.021% 54.07% 89ms 1.91% std::filesystem::permissions 88ms 1.89% 55.96% 88ms 1.89% __GI_fchmodat 1ms 0.021% 55.98% 88ms 1.89% alternateaxes 83ms 1.78% 57.75% 87ms 1.86% vertexmedian 14ms 0.3% 58.05% 84ms 1.80% AbstractCellProperty::IsSame 0 0% 58.05% 83ms 1.78% std::_Vector_base::_M_allocate (inline) 0 0% 58.05% 82ms 1.76% OutputFileHandler::CommonConstructor 0 0% 58.05% 82ms 1.76% OutputFileHandler::OutputFileHandler 7ms 0.15% 58.20% 81ms 1.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 80ms 1.71% 59.92% 81ms 1.74% __libc_open64 0 0% 59.92% 81ms 1.74% std::vector::push_back (inline) 0 0% 59.92% 80ms 1.71% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 59.92% 80ms 1.71% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.021% 59.94% 79ms 1.69% std::basic_filebuf::overflow 44ms 0.94% 60.88% 78ms 1.67% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 78ms 1.67% 62.55% 78ms 1.67% incircle 0 0% 62.55% 78ms 1.67% std::basic_filebuf::_M_convert_to_external 0 0% 62.55% 78ms 1.67% std::basic_filebuf::_M_terminate_output 5ms 0.11% 62.66% 78ms 1.67% std::vector::_M_realloc_insert 77ms 1.65% 64.31% 77ms 1.65% __GI___libc_write 0 0% 64.31% 77ms 1.65% std::__basic_file::xsputn 75ms 1.61% 65.92% 75ms 1.61% std::vector::size (inline) 19ms 0.41% 66.32% 73ms 1.56% std::num_put::_M_insert_int 8ms 0.17% 66.50% 70ms 1.50% std::type_info::operator== (inline) 7ms 0.15% 66.65% 66ms 1.41% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 66.65% 64ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.064% 66.71% 63ms 1.35% AbstractTetrahedralElement::CalculateJacobian 3ms 0.064% 66.77% 60ms 1.29% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.34% 67.12% 58ms 1.24% std::__ostream_insert 0 0% 67.12% 57ms 1.22% Node::~Node 0 0% 67.12% 56ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 46ms 0.99% 68.10% 56ms 1.20% vertexsort 55ms 1.18% 69.28% 55ms 1.18% [libchaste_cell_based.so] 4ms 0.086% 69.37% 54ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.064% 69.43% 54ms 1.16% boost::numeric::ublas::vector_assign (inline) 41ms 0.88% 70.31% 53ms 1.14% malloc_consolidate 1ms 0.021% 70.33% 52ms 1.11% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 70.33% 51ms 1.09% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 51ms 1.09% 71.42% 51ms 1.09% [libstdc++.so.6.0.33] 51ms 1.09% 72.51% 51ms 1.09% std::_Rb_tree_insert_and_rebalance 0 0% 72.51% 51ms 1.09% std::filesystem::create_directory 1ms 0.021% 72.54% 50ms 1.07% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 72.54% 50ms 1.07% CellPropertyCollection::~CellPropertyCollection (inline) 48ms 1.03% 73.56% 48ms 1.03% counterclockwise 30ms 0.64% 74.21% 48ms 1.03% std::basic_filebuf::xsputn 4ms 0.086% 74.29% 46ms 0.99% CellPropertyCollection::AddProperty 1ms 0.021% 74.31% 46ms 0.99% std::operator<< (inline) 0 0% 74.31% 43ms 0.92% Cell::GetCellId 7ms 0.15% 74.46% 42ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeA 3ms 0.064% 74.53% 42ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.021% 74.55% 42ms 0.9% std::_Vector_base::_M_deallocate (inline) 7ms 0.15% 74.70% 41ms 0.88% AbstractTetrahedralElement::RefreshJacobian 40ms 0.86% 75.56% 40ms 0.86% [libchaste_mesh.so] 3ms 0.064% 75.62% 40ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.62% 40ms 0.86% std::vector::vector (inline) 0 0% 75.62% 39ms 0.84% tcache_get (inline) 39ms 0.84% 76.46% 39ms 0.84% tcache_get_n (inline) 37ms 0.79% 77.25% 37ms 0.79% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 28ms 0.6% 77.85% 37ms 0.79% boost::shared_ptr::shared_ptr (inline) 0 0% 77.85% 37ms 0.79% std::_Vector_base::_Vector_base (inline) 0 0% 77.85% 35ms 0.75% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.54% 78.38% 35ms 0.75% AbstractElement::GetNodeGlobalIndex 0 0% 78.38% 35ms 0.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.38% 35ms 0.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.021% 78.41% 35ms 0.75% std::_Vector_base::_M_create_storage (inline) 2ms 0.043% 78.45% 34ms 0.73% std::filesystem::status 3ms 0.064% 78.51% 33ms 0.71% AbstractTetrahedralMesh::GetNumAllElements 0 0% 78.51% 33ms 0.71% CxxTest::RealWorldDescription::setUp 0 0% 78.51% 33ms 0.71% PetscInitialize 0 0% 78.51% 33ms 0.71% PetscSetup::setUpWorld 0 0% 78.51% 33ms 0.71% PetscSetupUtils::CommonSetup 0 0% 78.51% 33ms 0.71% PetscSetupUtils::InitialisePetsc 0 0% 78.51% 33ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 27ms 0.58% 79.09% 33ms 0.71% std::basic_streambuf::xsputn 0 0% 79.09% 32ms 0.69% PMPI_Init_thread 16ms 0.34% 79.43% 32ms 0.69% hack_digit 0 0% 79.43% 32ms 0.69% ompi_mpi_init 1ms 0.021% 79.46% 31ms 0.66% Node::ClearAppliedForce 1ms 0.021% 79.48% 31ms 0.66% Node::ConstructNodeAttributes (inline) 31ms 0.66% 80.14% 31ms 0.66% __GI___fstatat64 0 0% 80.14% 31ms 0.66% _dl_init 0 0% 80.14% 31ms 0.66% call_init (inline) 1ms 0.021% 80.16% 30ms 0.64% 19ms 0.41% 80.57% 30ms 0.64% AbstractElement::GetNodeLocation 12ms 0.26% 80.83% 30ms 0.64% AbstractTetrahedralMesh::GetElement 23ms 0.49% 81.32% 30ms 0.64% CellPropertyCollection::GetProperty 0 0% 81.32% 29ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 81.32% 29ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 29ms 0.62% 81.94% 29ms 0.62% __GI___mkdir 12ms 0.26% 82.20% 29ms 0.62% boost::numeric::ublas::indexing_vector_assign 29ms 0.62% 82.82% 29ms 0.62% std::_Rb_tree_increment 0 0% 82.82% 28ms 0.6% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 11ms 0.24% 83.05% 27ms 0.58% Determinant (inline) 0 0% 83.05% 27ms 0.58% _dl_start_user 0 0% 83.05% 26ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 26ms 0.56% 83.61% 26ms 0.56% __memcpy_avx512_unaligned_erms 26ms 0.56% 84.17% 26ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 84.17% 24ms 0.51% BoundaryNodeWriter::Visit 2ms 0.043% 84.21% 24ms 0.51% boost::serialization::singleton::get_instance