File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 7029ms, 85.73% of 8199ms total Dropped 589 nodes (cum <= 40.99ms) flat flat% sum% cum cum% 0 0% 0% 8156ms 99.48% __libc_start_call_main 0 0% 0% 8156ms 99.48% __libc_start_main_impl 0 0% 0% 8156ms 99.48% _start 0 0% 0% 8138ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8138ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8138ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8138ms 99.26% main 0 0% 0% 8090ms 98.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 8090ms 98.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 8090ms 98.67% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 8088ms 98.65% AbstractCellBasedSimulation::Solve 0 0% 0% 3502ms 42.71% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.037% 0.037% 3043ms 37.11% MeshBasedCellPopulation::Update 1ms 0.012% 0.049% 2987ms 36.43% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.061% 1592ms 19.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.061% 1524ms 18.59% MutableMesh::ReMesh 1ms 0.012% 0.073% 1453ms 17.72% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.085% 1444ms 17.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.12% 0.21% 1385ms 16.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 24ms 0.29% 0.5% 1240ms 15.12% MeshBasedCellPopulation::SpringIterator::operator++ 86ms 1.05% 1.55% 982ms 11.98% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.061% 1.61% 974ms 11.88% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.049% 1.66% 959ms 11.70% AbstractTwoBodyInteractionForce::AddForceContribution 277ms 3.38% 5.04% 952ms 11.61% __dynamic_cast 460ms 5.61% 10.65% 946ms 11.54% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.16% 10.81% 922ms 11.25% CellPopulationElementWriter::Visit 14ms 0.17% 10.98% 904ms 11.03% CellPropertyCollection::GetPropertiesType (inline) 45ms 0.55% 11.53% 862ms 10.51% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.061% 11.59% 835ms 10.18% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.37% 11.95% 768ms 9.37% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.12% 12.07% 731ms 8.92% TetrahedralMesh::ImportFromMesher 2ms 0.024% 12.10% 712ms 8.68% AbstractCellProperty::IsSubType (inline) 3ms 0.037% 12.14% 622ms 7.59% std::ostream::operator<< (inline) 95ms 1.16% 13.29% 619ms 7.55% std::ostream::_M_insert 2ms 0.024% 13.32% 603ms 7.35% triangulate 54ms 0.66% 13.98% 585ms 7.14% std::map::operator[] (partial-inline) 40ms 0.49% 14.47% 556ms 6.78% operator new 552ms 6.73% 21.20% 552ms 6.73% __strcmp_avx2 5ms 0.061% 21.26% 527ms 6.43% Cell::GetCellProliferativeType 4ms 0.049% 21.31% 527ms 6.43% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 21.31% 521ms 6.35% delaunay 3ms 0.037% 21.34% 519ms 6.33% divconqdelaunay 167ms 2.04% 23.38% 514ms 6.27% __GI___libc_malloc 4ms 0.049% 23.43% 513ms 6.26% std::set::insert (inline) 7ms 0.085% 23.52% 509ms 6.21% std::_Rb_tree::_M_insert_unique 28ms 0.34% 23.86% 508ms 6.20% std::_Rb_tree::find (inline) 37ms 0.45% 24.31% 502ms 6.12% std::__new_allocator::allocate (inline) 218ms 2.66% 26.97% 498ms 6.07% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.97% 498ms 6.07% std::allocator_traits::allocate (inline) 0 0% 26.97% 491ms 5.99% std::_Rb_tree::lower_bound (inline) 0 0% 26.97% 491ms 5.99% std::map::lower_bound (inline) 38ms 0.46% 27.43% 477ms 5.82% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.43% 457ms 5.57% std::set::count (inline) 0 0% 27.43% 456ms 5.56% std::set::~set (inline) 3ms 0.037% 27.47% 446ms 5.44% AbstractCellBasedSimulation::DoCellBirth 99ms 1.21% 28.67% 431ms 5.26% std::_Rb_tree::_M_erase 0 0% 28.67% 413ms 5.04% std::_Rb_tree::_M_create_node (inline) 2ms 0.024% 28.70% 397ms 4.84% Cell::GetMutationState 0 0% 28.70% 389ms 4.74% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.70% 386ms 4.71% std::_Rb_tree::_M_get_node (inline) 117ms 1.43% 30.13% 367ms 4.48% __GI___libc_free 2ms 0.024% 30.15% 362ms 4.42% NodeLocationWriter::Visit 25ms 0.3% 30.45% 358ms 4.37% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 30.45% 333ms 4.06% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 30.45% 332ms 4.05% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.024% 30.48% 331ms 4.04% MeshBasedCellPopulation::GetDampingConstant 7ms 0.085% 30.56% 329ms 4.01% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 30.56% 329ms 4.01% OutputFileHandler::OpenOutputFile 11ms 0.13% 30.70% 326ms 3.98% std::less::operator() (inline) 6ms 0.073% 30.77% 320ms 3.90% std::set::set (inline) 315ms 3.84% 34.61% 315ms 3.84% std::operator< (inline) 0 0% 34.61% 314ms 3.83% std::_Rb_tree::_M_drop_node (inline) 23ms 0.28% 34.89% 314ms 3.83% std::num_put::_M_insert_float 11ms 0.13% 35.03% 309ms 3.77% std::__new_allocator::deallocate (inline) 19ms 0.23% 35.26% 305ms 3.72% std::_Rb_tree::_M_insert_ (inline) 0 0% 35.26% 301ms 3.67% std::allocator_traits::deallocate (inline) 8ms 0.098% 35.36% 298ms 3.63% AbstractCellPopulation::IsCellAttachedToLocationIndex 296ms 3.61% 38.97% 296ms 3.61% std::_Rb_tree::_S_right (inline) 8ms 0.098% 39.07% 293ms 3.57% Cell::ReadyToDivide 35ms 0.43% 39.49% 293ms 3.57% std::_Rb_tree::_M_copy (inline) 9ms 0.11% 39.60% 283ms 3.45% divconqrecurse 166ms 2.02% 41.63% 278ms 3.39% _int_malloc 2ms 0.024% 41.65% 277ms 3.38% Element::Element 66ms 0.8% 42.46% 269ms 3.28% mergehulls 1ms 0.012% 42.47% 266ms 3.24% CellProliferativeTypesWriter::VisitCell 5ms 0.061% 42.53% 259ms 3.16% std::__cxx11::collate::do_transform 0 0% 42.53% 256ms 3.12% std::_Rb_tree::_M_put_node (inline) 58ms 0.71% 43.24% 252ms 3.07% std::_Rb_tree::_M_clone_node (inline) 208ms 2.54% 45.77% 249ms 3.04% _int_free 2ms 0.024% 45.80% 246ms 3.00% ___vsnprintf 0 0% 45.80% 244ms 2.98% __vsnprintf_internal (inline) 4ms 0.049% 45.85% 242ms 2.95% AbstractCellProperty::IsType (inline) 7ms 0.085% 45.93% 241ms 2.94% TetrahedralMesh::Clear 43ms 0.52% 46.46% 240ms 2.93% __printf_buffer 6ms 0.073% 46.53% 227ms 2.77% CellPropertyCollection::HasProperty 0 0% 46.53% 224ms 2.73% Cell::HasCellProperty (inline) 14ms 0.17% 46.70% 210ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.061% 46.76% 202ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 65ms 0.79% 47.55% 197ms 2.40% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.049% 47.60% 190ms 2.32% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.098% 47.70% 183ms 2.23% __printf_fp_l_buffer 0 0% 47.70% 183ms 2.23% __printf_fp_spec (inline) 0 0% 47.70% 182ms 2.22% std::basic_ofstream::basic_ofstream (inline) 1ms 0.012% 47.71% 175ms 2.13% Element::RegisterWithNodes (inline) 4ms 0.049% 47.76% 174ms 2.12% std::basic_filebuf::open 0 0% 47.76% 174ms 2.12% std::basic_ofstream::open (inline) 29ms 0.35% 48.12% 173ms 2.11% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.037% 48.15% 172ms 2.10% Node::AddElement 96ms 1.17% 49.32% 170ms 2.07% __printf_fp_buffer_1 15ms 0.18% 49.51% 168ms 2.05% AbstractTetrahedralElement::CalculateJacobian 27ms 0.33% 49.84% 165ms 2.01% AbstractCellProperty::IsSame 1ms 0.012% 49.85% 163ms 1.99% OutputFileHandler::OutputFileHandler 0 0% 49.85% 163ms 1.99% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.037% 49.88% 162ms 1.98% OutputFileHandler::CommonConstructor 1ms 0.012% 49.90% 156ms 1.90% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 49.90% 154ms 1.88% AbstractCellBasedWriter::CloseFile 0 0% 49.90% 154ms 1.88% AbstractCellPopulation::CloseRoundRobinWritersFiles 8ms 0.098% 49.99% 154ms 1.88% Node::~Node 1ms 0.012% 50.01% 154ms 1.88% std::basic_filebuf::close 0 0% 50.01% 154ms 1.88% std::basic_ofstream::close (inline) 45ms 0.55% 50.55% 151ms 1.84% std::__ostream_insert 7ms 0.085% 50.64% 148ms 1.81% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 50.64% 148ms 1.81% alternateaxes 142ms 1.73% 52.37% 148ms 1.81% vertexmedian 26ms 0.32% 52.69% 138ms 1.68% std::type_info::operator== (inline) 88ms 1.07% 53.76% 137ms 1.67% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 44ms 0.54% 54.30% 137ms 1.67% std::num_put::_M_insert_int 131ms 1.60% 55.90% 131ms 1.60% incircle 1ms 0.012% 55.91% 129ms 1.57% std::__basic_file::open 1ms 0.012% 55.92% 128ms 1.56% _IO_new_fopen 1ms 0.012% 55.93% 127ms 1.55% __fopen_internal (inline) 1ms 0.012% 55.95% 126ms 1.54% _IO_new_file_fopen 0 0% 55.95% 124ms 1.51% __GI__IO_file_open 0 0% 55.95% 124ms 1.51% std::operator<< (inline) 19ms 0.23% 56.18% 123ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 56.18% 121ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 56.18% 121ms 1.48% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.037% 56.21% 121ms 1.48% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.012% 56.23% 121ms 1.48% std::filesystem::permissions 12ms 0.15% 56.37% 120ms 1.46% MeshBasedCellPopulation::SpringIterator::SpringIterator 120ms 1.46% 57.84% 120ms 1.46% __GI_fchmodat 8ms 0.098% 57.93% 119ms 1.45% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.024% 57.96% 116ms 1.41% std::vector::push_back (inline) 25ms 0.3% 58.26% 115ms 1.40% AbstractTetrahedralElement::RefreshJacobian 10ms 0.12% 58.39% 115ms 1.40% boost::detail::shared_count::~shared_count (inline) 0 0% 58.39% 115ms 1.40% boost::shared_ptr::~shared_ptr (inline) 115ms 1.40% 59.79% 115ms 1.40% std::_Rb_tree_increment 2ms 0.024% 59.81% 114ms 1.39% std::_Vector_base::_M_allocate (inline) 1ms 0.012% 59.82% 113ms 1.38% boost::numeric::ublas::vector_assign (inline) 13ms 0.16% 59.98% 112ms 1.37% std::vector::_M_realloc_insert 110ms 1.34% 61.32% 110ms 1.34% __libc_open64 0 0% 61.32% 109ms 1.33% std::basic_filebuf::_M_terminate_output 70ms 0.85% 62.18% 109ms 1.33% std::basic_filebuf::xsputn 0 0% 62.18% 108ms 1.32% std::basic_filebuf::overflow 107ms 1.31% 63.48% 107ms 1.31% __GI___libc_write 0 0% 63.48% 107ms 1.31% std::__basic_file::xsputn 0 0% 63.48% 107ms 1.31% std::basic_filebuf::_M_convert_to_external 1ms 0.012% 63.50% 106ms 1.29% AbstractTetrahedralElement::AbstractTetrahedralElement 98ms 1.20% 64.69% 98ms 1.20% boost::detail::sp_counted_base::release 4ms 0.049% 64.74% 97ms 1.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 95ms 1.16% 65.90% 95ms 1.16% std::_Rb_tree_insert_and_rebalance 94ms 1.15% 67.04% 94ms 1.15% [libchaste_cell_based.so] 3ms 0.037% 67.08% 91ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 40ms 0.49% 67.57% 91ms 1.11% boost::shared_ptr::shared_ptr (inline) 0 0% 67.57% 89ms 1.09% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 89ms 1.09% 68.65% 89ms 1.09% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 62ms 0.76% 69.41% 89ms 1.09% malloc_consolidate 0 0% 69.41% 89ms 1.09% std::filesystem::create_directory 1ms 0.012% 69.42% 89ms 1.09% std::filesystem::status 88ms 1.07% 70.50% 88ms 1.07% __GI___fstatat64 71ms 0.87% 71.36% 78ms 0.95% vertexsort 3ms 0.037% 71.40% 77ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.91% 72.31% 75ms 0.91% std::vector::size (inline) 29ms 0.35% 72.67% 74ms 0.9% AbstractElement::GetNodeLocation 7ms 0.085% 72.75% 73ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 72.75% 73ms 0.89% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.75% 73ms 0.89% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.061% 72.81% 72ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 70ms 0.85% 73.67% 70ms 0.85% counterclockwise 2ms 0.024% 73.69% 68ms 0.83% Cell::GetCellId 35ms 0.43% 74.12% 66ms 0.8% AbstractTetrahedralMesh::GetElement 66ms 0.8% 74.92% 66ms 0.8% Node::GetIndex 22ms 0.27% 75.19% 65ms 0.79% boost::numeric::ublas::indexing_vector_assign 53ms 0.65% 75.84% 65ms 0.79% std::num_put::do_put 64ms 0.78% 76.62% 64ms 0.78% __memcpy_avx_unaligned_erms 55ms 0.67% 77.29% 62ms 0.76% AbstractElement::GetNodeGlobalIndex 0 0% 77.29% 61ms 0.74% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 77.29% 60ms 0.73% Node::ClearAppliedForce 0 0% 77.29% 60ms 0.73% Node::ConstructNodeAttributes (inline) 0 0% 77.29% 59ms 0.72% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 77.29% 58ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.29% 58ms 0.71% std::__new_allocator::destroy (inline) 0 0% 77.29% 58ms 0.71% std::allocator_traits::destroy (inline) 37ms 0.45% 77.74% 58ms 0.71% std::basic_streambuf::xsputn 35ms 0.43% 78.17% 57ms 0.7% boost::numeric::ublas::c_matrix::operator() (partial-inline) 57ms 0.7% 78.86% 57ms 0.7% boost::shared_ptr::operator-> (inline) 56ms 0.68% 79.55% 56ms 0.68% [libchaste_mesh.so] 17ms 0.21% 79.75% 55ms 0.67% Determinant (inline) 55ms 0.67% 80.42% 55ms 0.67% std::ostream::sentry::sentry 0 0% 80.42% 55ms 0.67% std::vector::vector (inline) 0 0% 80.42% 54ms 0.66% tcache_get (inline) 54ms 0.66% 81.08% 54ms 0.66% tcache_get_n (inline) 0 0% 81.08% 52ms 0.63% std::_Vector_base::_Vector_base (inline) 8ms 0.098% 81.18% 51ms 0.62% CellPropertyCollection::AddProperty 51ms 0.62% 81.80% 51ms 0.62% boost::detail::shared_count::shared_count (inline) 51ms 0.62% 82.42% 51ms 0.62% boost::numeric::ublas::c_vector::operator() (partial-inline) 1ms 0.012% 82.44% 51ms 0.62% std::_Vector_base::_M_create_storage (inline) 3ms 0.037% 82.47% 50ms 0.61% NodeAttributes::NodeAttributes 49ms 0.6% 83.07% 49ms 0.6% [libstdc++.so.6.0.33] 19ms 0.23% 83.30% 48ms 0.59% AbstractCellCycleModel::GetAge 0 0% 83.30% 48ms 0.59% boost::numeric::ublas::norm_2 (inline) 20ms 0.24% 83.55% 48ms 0.59% boost::numeric::ublas::vector_norm_2::apply (inline) 6ms 0.073% 83.62% 48ms 0.59% std::_Vector_base::_M_deallocate (inline) 0 0% 83.62% 46ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.012% 83.63% 45ms 0.55% BoundaryNodeWriter::Visit 0 0% 83.63% 45ms 0.55% std::map::map (inline) 0 0% 83.63% 44ms 0.54% CxxTest::RealWorldDescription::setUp 0 0% 83.63% 44ms 0.54% PetscInitialize 0 0% 83.63% 44ms 0.54% PetscSetup::setUpWorld 0 0% 83.63% 44ms 0.54% PetscSetupUtils::CommonSetup 0 0% 83.63% 44ms 0.54% PetscSetupUtils::InitialisePetsc 44ms 0.54% 84.17% 44ms 0.54% unlink_chunk 0 0% 84.17% 43ms 0.52% CellPropertyCollection::~CellPropertyCollection (inline) 16ms 0.2% 84.36% 43ms 0.52% Inverse 0 0% 84.36% 43ms 0.52% PMPI_Init_thread 1ms 0.012% 84.38% 43ms 0.52% _IO_new_fclose 0 0% 84.38% 43ms 0.52% _dl_init 0 0% 84.38% 43ms 0.52% call_init (inline) 0 0% 84.38% 43ms 0.52% ompi_mpi_init 0 0% 84.38% 43ms 0.52% std::__basic_file::close 0 0% 84.38% 42ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.51% 84.89% 42ms 0.51% __GI___mkdir 22ms 0.27% 85.16% 42ms 0.51% hack_digit 6ms 0.073% 85.23% 41ms 0.5% Element::~Element 41ms 0.5% 85.73% 41ms 0.5% Node::IsDeleted 0 0% 85.73% 41ms 0.5% _dl_start_user 0 0% 85.73% 41ms 0.5% std::basic_filebuf::_M_allocate_internal_buffer