File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 3737ms, 85.73% of 4359ms total Dropped 452 nodes (cum <= 21.80ms) flat flat% sum% cum cum% 0 0% 0% 4333ms 99.40% __libc_start_call_main 0 0% 0% 4333ms 99.40% __libc_start_main_impl 0 0% 0% 4333ms 99.40% _start 0 0% 0% 4321ms 99.13% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4321ms 99.13% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4321ms 99.13% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4321ms 99.13% main 0 0% 0% 4290ms 98.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4290ms 98.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4290ms 98.42% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4288ms 98.37% AbstractCellBasedSimulation::Solve 0 0% 0% 1928ms 44.23% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 1709ms 39.21% MeshBasedCellPopulation::Update 1ms 0.023% 0.023% 1595ms 36.59% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.023% 848ms 19.45% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.023% 838ms 19.22% MutableMesh::ReMesh 0 0% 0.023% 762ms 17.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.25% 0.28% 749ms 17.18% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.023% 0.3% 672ms 15.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.046% 0.34% 648ms 14.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 69ms 1.58% 1.93% 599ms 13.74% TetrahedralMesh::EdgeIterator::operator++ 11ms 0.25% 2.18% 541ms 12.41% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 241ms 5.53% 7.71% 504ms 11.56% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.21% 7.91% 501ms 11.49% CellPopulationElementWriter::Visit 3ms 0.069% 7.98% 466ms 10.69% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.46% 8.44% 450ms 10.32% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.11% 8.56% 431ms 9.89% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.046% 8.60% 425ms 9.75% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.069% 8.67% 423ms 9.70% TetrahedralMesh::ImportFromMesher 96ms 2.20% 10.87% 422ms 9.68% __dynamic_cast 22ms 0.5% 11.38% 421ms 9.66% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 25ms 0.57% 11.95% 357ms 8.19% operator new 2ms 0.046% 12.00% 354ms 8.12% AbstractCellProperty::IsSubType (inline) 71ms 1.63% 13.63% 348ms 7.98% std::_Rb_tree::~_Rb_tree (inline) 0 0% 13.63% 332ms 7.62% std::set::~set (inline) 136ms 3.12% 16.75% 327ms 7.50% __GI___libc_malloc 5ms 0.11% 16.86% 324ms 7.43% std::set::insert (inline) 0 0% 16.86% 321ms 7.36% triangulate 11ms 0.25% 17.11% 320ms 7.34% std::__new_allocator::allocate (inline) 6ms 0.14% 17.25% 319ms 7.32% std::_Rb_tree::_M_insert_unique 0 0% 17.25% 319ms 7.32% std::allocator_traits::allocate (inline) 11ms 0.25% 17.50% 314ms 7.20% std::_Rb_tree::find (inline) 0 0% 17.50% 299ms 6.86% std::set::count (inline) 2ms 0.046% 17.55% 291ms 6.68% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.023% 17.57% 277ms 6.35% Cell::GetCellProliferativeType 1ms 0.023% 17.60% 276ms 6.33% delaunay 1ms 0.023% 17.62% 275ms 6.31% divconqdelaunay 17ms 0.39% 18.01% 275ms 6.31% std::_Rb_tree::_M_erase 1ms 0.023% 18.03% 271ms 6.22% std::ostream::operator<< (inline) 26ms 0.6% 18.63% 270ms 6.19% std::map::operator[] (partial-inline) 36ms 0.83% 19.45% 269ms 6.17% std::ostream::_M_insert 0 0% 19.45% 257ms 5.90% std::_Rb_tree::_M_drop_node (inline) 0 0% 19.45% 253ms 5.80% std::_Rb_tree::_M_create_node (inline) 250ms 5.74% 25.19% 250ms 5.74% __strcmp_evex 0 0% 25.19% 243ms 5.57% std::_Rb_tree::_M_get_node (inline) 6ms 0.14% 25.33% 240ms 5.51% boost::detail::shared_count::~shared_count (inline) 0 0% 25.33% 240ms 5.51% boost::shared_ptr::~shared_ptr (inline) 0 0% 25.33% 236ms 5.41% std::_Rb_tree::_Alloc_node::operator() (inline) 132ms 3.03% 28.36% 232ms 5.32% __cxxabiv1::__si_class_type_info::__do_dyncast 230ms 5.28% 33.63% 231ms 5.30% boost::detail::sp_counted_base::release 11ms 0.25% 33.88% 230ms 5.28% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 33.88% 221ms 5.07% std::set::set (inline) 2ms 0.046% 33.93% 215ms 4.93% AbstractCellBasedSimulation::DoCellBirth 0 0% 33.93% 213ms 4.89% std::_Rb_tree::lower_bound (inline) 0 0% 33.93% 213ms 4.89% std::map::lower_bound (inline) 26ms 0.6% 34.53% 205ms 4.70% std::_Rb_tree::_M_insert_ (inline) 27ms 0.62% 35.15% 201ms 4.61% std::_Rb_tree::_M_copy (inline) 6ms 0.14% 35.28% 198ms 4.54% std::less::operator() (inline) 0 0% 35.28% 197ms 4.52% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 35ms 0.8% 36.09% 197ms 4.52% __GI___libc_free 1ms 0.023% 36.11% 196ms 4.50% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 36.11% 194ms 4.45% OutputFileHandler::OpenOutputFile 192ms 4.40% 40.51% 192ms 4.40% std::operator< (inline) 0 0% 40.51% 189ms 4.34% Element::Element 6ms 0.14% 40.65% 187ms 4.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.046% 40.70% 183ms 4.20% Cell::GetMutationState 76ms 1.74% 42.44% 173ms 3.97% std::_Rb_tree::_M_clone_node (inline) 2ms 0.046% 42.49% 167ms 3.83% std::__new_allocator::deallocate (inline) 0 0% 42.49% 164ms 3.76% std::allocator_traits::deallocate (inline) 0 0% 42.49% 162ms 3.72% NodeLocationWriter::Visit 155ms 3.56% 46.04% 162ms 3.72% _int_free 101ms 2.32% 48.36% 158ms 3.62% _int_malloc 1ms 0.023% 48.38% 152ms 3.49% MeshBasedCellPopulation::GetDampingConstant 13ms 0.3% 48.68% 152ms 3.49% std::num_put::_M_insert_float 0 0% 48.68% 151ms 3.46% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 48.68% 146ms 3.35% std::_Rb_tree::_M_put_node (inline) 0 0% 48.68% 137ms 3.14% Cell::ReadyToDivide 3ms 0.069% 48.75% 137ms 3.14% divconqrecurse 2ms 0.046% 48.80% 133ms 3.05% CellPropertyCollection::HasProperty 0 0% 48.80% 132ms 3.03% Cell::HasCellProperty (inline) 7ms 0.16% 48.96% 128ms 2.94% AbstractCellProperty::IsType (inline) 30ms 0.69% 49.64% 128ms 2.94% mergehulls 3ms 0.069% 49.71% 127ms 2.91% Element::RegisterWithNodes (inline) 5ms 0.11% 49.83% 126ms 2.89% std::__cxx11::collate::do_transform 124ms 2.84% 52.67% 124ms 2.84% std::_Rb_tree::_S_right (inline) 1ms 0.023% 52.70% 123ms 2.82% CellProliferativeTypesWriter::VisitCell 1ms 0.023% 52.72% 123ms 2.82% Node::AddElement 2ms 0.046% 52.76% 117ms 2.68% ___vsnprintf 6ms 0.14% 52.90% 116ms 2.66% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 52.90% 115ms 2.64% __vsnprintf_internal (inline) 14ms 0.32% 53.22% 112ms 2.57% __printf_buffer 0 0% 53.22% 111ms 2.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 53.22% 111ms 2.55% std::__new_allocator::destroy (inline) 0 0% 53.22% 111ms 2.55% std::allocator_traits::destroy (inline) 41ms 0.94% 54.16% 108ms 2.48% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 54.16% 107ms 2.45% TetrahedralMesh::Clear 0 0% 54.16% 101ms 2.32% FilesystemPermissions::SetFilePermissions (inline) 101ms 2.32% 56.48% 101ms 2.32% __GI_fchmodat 0 0% 56.48% 101ms 2.32% std::filesystem::permissions 0 0% 56.48% 98ms 2.25% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.069% 56.55% 97ms 2.23% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.37% 56.92% 97ms 2.23% TetrahedralMesh::EdgesEnd (partial-inline) 19ms 0.44% 57.35% 94ms 2.16% AbstractCellProperty::IsSame 1ms 0.023% 57.38% 92ms 2.11% AbstractTetrahedralElement::CalculateJacobian 2ms 0.046% 57.42% 92ms 2.11% alternateaxes 2ms 0.046% 57.47% 92ms 2.11% std::basic_filebuf::close 0 0% 57.47% 91ms 2.09% AbstractCellBasedWriter::CloseFile 0 0% 57.47% 91ms 2.09% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 57.47% 91ms 2.09% std::basic_ofstream::close (inline) 86ms 1.97% 59.44% 90ms 2.06% vertexmedian 0 0% 59.44% 85ms 1.95% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.023% 59.46% 85ms 1.95% __printf_fp_spec (inline) 0 0% 59.46% 84ms 1.93% __printf_fp_l_buffer 37ms 0.85% 60.31% 83ms 1.90% __printf_fp_buffer_1 3ms 0.069% 60.38% 78ms 1.79% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.32% 60.70% 78ms 1.79% MeshBasedCellPopulation::SpringIterator::SpringIterator 49ms 1.12% 61.83% 78ms 1.79% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 61.83% 76ms 1.74% std::_Vector_base::_M_allocate (inline) 0 0% 61.83% 76ms 1.74% std::basic_ofstream::basic_ofstream (inline) 0 0% 61.83% 75ms 1.72% std::basic_filebuf::open 0 0% 61.83% 75ms 1.72% std::basic_ofstream::open (inline) 8ms 0.18% 62.01% 75ms 1.72% std::type_info::operator== (inline) 1ms 0.023% 62.03% 70ms 1.61% OutputFileHandler::OutputFileHandler 0 0% 62.03% 69ms 1.58% OutputFileHandler::CommonConstructor 0 0% 62.03% 69ms 1.58% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.069% 62.10% 66ms 1.51% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.23% 62.33% 66ms 1.51% AbstractTetrahedralElement::RefreshJacobian 0 0% 62.33% 66ms 1.51% Node::~Node 1ms 0.023% 62.35% 66ms 1.51% std::basic_filebuf::_M_terminate_output 65ms 1.49% 63.84% 65ms 1.49% __GI___libc_write 0 0% 63.84% 65ms 1.49% std::__basic_file::xsputn 0 0% 63.84% 65ms 1.49% std::basic_filebuf::_M_convert_to_external 0 0% 63.84% 65ms 1.49% std::basic_filebuf::overflow 2ms 0.046% 63.89% 64ms 1.47% std::vector::push_back (inline) 15ms 0.34% 64.23% 63ms 1.45% std::num_put::_M_insert_int 7ms 0.16% 64.40% 62ms 1.42% std::vector::_M_realloc_insert 60ms 1.38% 65.77% 60ms 1.38% [libchaste_cell_based.so] 0 0% 65.77% 58ms 1.33% _IO_new_fopen 0 0% 65.77% 58ms 1.33% __fopen_internal (inline) 58ms 1.33% 67.10% 58ms 1.33% incircle 0 0% 67.10% 58ms 1.33% std::__basic_file::open 0 0% 67.10% 56ms 1.28% _IO_new_file_fopen 2ms 0.046% 67.15% 55ms 1.26% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.15% 55ms 1.26% __GI__IO_file_open 0 0% 67.15% 54ms 1.24% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.069% 67.22% 53ms 1.22% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 1.22% 68.43% 53ms 1.22% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 51ms 1.17% 69.60% 51ms 1.17% std::_Rb_tree_insert_and_rebalance 34ms 0.78% 70.38% 49ms 1.12% malloc_consolidate 47ms 1.08% 71.46% 48ms 1.10% __libc_open64 4ms 0.092% 71.55% 48ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.3% 71.85% 48ms 1.10% std::__ostream_insert 47ms 1.08% 72.93% 47ms 1.08% __GI___fstatat64 1ms 0.023% 72.95% 47ms 1.08% std::filesystem::status 47ms 1.08% 74.03% 47ms 1.08% std::vector::size (inline) 29ms 0.67% 74.70% 46ms 1.06% AbstractElement::GetNodeLocation 3ms 0.069% 74.76% 46ms 1.06% boost::numeric::ublas::vector_assign (inline) 4ms 0.092% 74.86% 44ms 1.01% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.069% 74.93% 44ms 1.01% CellPropertyCollection::AddProperty 1ms 0.023% 74.95% 43ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.069% 75.02% 42ms 0.96% std::operator<< (inline) 39ms 0.89% 75.91% 42ms 0.96% vertexsort 30ms 0.69% 76.60% 41ms 0.94% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 76.60% 40ms 0.92% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 76.60% 40ms 0.92% std::filesystem::create_directory 12ms 0.28% 76.88% 38ms 0.87% Determinant (inline) 37ms 0.85% 77.72% 37ms 0.85% counterclockwise 0 0% 77.72% 36ms 0.83% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 77.72% 35ms 0.8% Cell::GetCellId 35ms 0.8% 78.53% 35ms 0.8% [libchaste_mesh.so] 27ms 0.62% 79.15% 35ms 0.8% std::basic_streambuf::xsputn 23ms 0.53% 79.67% 34ms 0.78% AbstractElement::GetNodeGlobalIndex 2ms 0.046% 79.72% 32ms 0.73% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 79.72% 31ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 31ms 0.71% 80.43% 31ms 0.71% std::_Rb_tree_increment 19ms 0.44% 80.87% 31ms 0.71% std::basic_filebuf::xsputn 0 0% 80.87% 31ms 0.71% std::vector::vector (inline) 0 0% 80.87% 30ms 0.69% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.21% 81.07% 30ms 0.69% AbstractTetrahedralMesh::GetElement 25ms 0.57% 81.65% 30ms 0.69% CellPropertyCollection::GetProperty 0 0% 81.65% 30ms 0.69% CxxTest::RealWorldDescription::setUp 0 0% 81.65% 30ms 0.69% PMPI_Init_thread 0 0% 81.65% 30ms 0.69% PetscInitialize 0 0% 81.65% 30ms 0.69% PetscSetup::setUpWorld 0 0% 81.65% 30ms 0.69% PetscSetupUtils::CommonSetup 0 0% 81.65% 30ms 0.69% PetscSetupUtils::InitialisePetsc 0 0% 81.65% 30ms 0.69% ompi_mpi_init 0 0% 81.65% 29ms 0.67% 29ms 0.67% 82.31% 29ms 0.67% __memcpy_avx512_unaligned_erms 0 0% 82.31% 29ms 0.67% _dl_init 0 0% 82.31% 29ms 0.67% call_init (inline) 3ms 0.069% 82.38% 29ms 0.67% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.38% 29ms 0.67% std::_Vector_base::_Vector_base (inline) 21ms 0.48% 82.86% 28ms 0.64% boost::shared_ptr::shared_ptr (inline) 16ms 0.37% 83.23% 28ms 0.64% hack_digit 0 0% 83.23% 28ms 0.64% tcache_get (inline) 28ms 0.64% 83.87% 28ms 0.64% tcache_get_n (inline) 7ms 0.16% 84.03% 27ms 0.62% Inverse 0 0% 84.03% 27ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.023% 84.06% 27ms 0.62% std::_Vector_base::_M_create_storage (inline) 11ms 0.25% 84.31% 26ms 0.6% AbstractTetrahedralMesh::GetNumAllElements 0 0% 84.31% 26ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 26ms 0.6% 84.90% 26ms 0.6% [libstdc++.so.6.0.33] 9ms 0.21% 85.11% 26ms 0.6% boost::numeric::ublas::indexing_vector_assign 21ms 0.48% 85.59% 26ms 0.6% std::num_put::do_put 0 0% 85.59% 24ms 0.55% _dl_start_user 1ms 0.023% 85.62% 24ms 0.55% std::__basic_file::close 1ms 0.023% 85.64% 23ms 0.53% Node::ConstructNodeAttributes (inline) 2ms 0.046% 85.68% 23ms 0.53% _IO_new_fclose 1ms 0.023% 85.71% 22ms 0.5% BoundaryNodeWriter::Visit 0 0% 85.71% 22ms 0.5% Node::ClearAppliedForce 1ms 0.023% 85.73% 22ms 0.5% boost::serialization::singleton::get_instance