File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5160ms, 83.78% of 6159ms total Dropped 535 nodes (cum <= 30.80ms) flat flat% sum% cum cum% 0 0% 0% 6128ms 99.50% __libc_start_call_main 0 0% 0% 6128ms 99.50% __libc_start_main_impl 0 0% 0% 6128ms 99.50% _start 0 0% 0% 6113ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6113ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6113ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6113ms 99.25% main 0 0% 0% 6073ms 98.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6073ms 98.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6073ms 98.60% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6070ms 98.55% AbstractCellBasedSimulation::Solve 0 0% 0% 2644ms 42.93% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.049% 0.049% 2273ms 36.91% MeshBasedCellPopulation::Update 0 0% 0.049% 2248ms 36.50% AbstractCellPopulation::WriteResultsToFiles 1ms 0.016% 0.065% 1173ms 19.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.016% 0.081% 1156ms 18.77% MutableMesh::ReMesh 0 0% 0.081% 1078ms 17.50% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.016% 0.097% 1054ms 17.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.065% 0.16% 1011ms 16.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 23ms 0.37% 0.54% 942ms 15.29% MeshBasedCellPopulation::SpringIterator::operator++ 373ms 6.06% 6.59% 801ms 13.01% std::_Rb_tree::_M_lower_bound (inline) 88ms 1.43% 8.02% 746ms 12.11% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.016% 8.04% 732ms 11.89% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.016% 8.05% 717ms 11.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.065% 8.12% 706ms 11.46% CellPopulationElementWriter::Visit 177ms 2.87% 10.99% 694ms 11.27% __dynamic_cast 7ms 0.11% 11.11% 664ms 10.78% CellPropertyCollection::GetPropertiesType (inline) 21ms 0.34% 11.45% 663ms 10.76% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 32ms 0.52% 11.97% 637ms 10.34% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.11% 12.08% 593ms 9.63% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.13% 12.21% 588ms 9.55% TetrahedralMesh::ImportFromMesher 2ms 0.032% 12.24% 533ms 8.65% AbstractCellProperty::IsSubType (inline) 48ms 0.78% 13.02% 506ms 8.22% std::map::operator[] (partial-inline) 2ms 0.032% 13.05% 445ms 7.23% triangulate 441ms 7.16% 20.21% 441ms 7.16% __strcmp_evex 3ms 0.049% 20.26% 432ms 7.01% std::ostream::operator<< (inline) 30ms 0.49% 20.75% 431ms 7.00% operator new 60ms 0.97% 21.72% 428ms 6.95% std::ostream::_M_insert 19ms 0.31% 22.03% 427ms 6.93% std::_Rb_tree::find (inline) 0 0% 22.03% 415ms 6.74% std::_Rb_tree::lower_bound (inline) 0 0% 22.03% 415ms 6.74% std::map::lower_bound (inline) 4ms 0.065% 22.10% 398ms 6.46% Cell::GetCellProliferativeType 132ms 2.14% 24.24% 395ms 6.41% __GI___libc_malloc 1ms 0.016% 24.26% 389ms 6.32% delaunay 0 0% 24.26% 386ms 6.27% divconqdelaunay 0 0% 24.26% 384ms 6.23% std::set::count (inline) 4ms 0.065% 24.32% 378ms 6.14% std::set::insert (inline) 11ms 0.18% 24.50% 374ms 6.07% std::_Rb_tree::_M_insert_unique 19ms 0.31% 24.81% 371ms 6.02% std::__new_allocator::allocate (inline) 0 0% 24.81% 366ms 5.94% std::allocator_traits::allocate (inline) 1ms 0.016% 24.83% 362ms 5.88% AbstractCellBasedSimulation::DoCellBirth 3ms 0.049% 24.87% 362ms 5.88% LegacyCellProliferativeTypesWriter::VisitCell 27ms 0.44% 25.31% 353ms 5.73% std::_Rb_tree::~_Rb_tree (inline) 158ms 2.57% 27.88% 339ms 5.50% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.88% 333ms 5.41% std::set::~set (inline) 61ms 0.99% 28.87% 323ms 5.24% std::_Rb_tree::_M_erase 0 0% 28.87% 320ms 5.20% std::_Rb_tree::_M_create_node (inline) 0 0% 28.87% 299ms 4.85% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.87% 293ms 4.76% std::_Rb_tree::_M_get_node (inline) 19ms 0.31% 29.18% 283ms 4.59% std::_Rb_tree::_Rb_tree (partial-inline) 275ms 4.47% 33.64% 275ms 4.47% std::_Rb_tree::_S_right (inline) 6ms 0.097% 33.74% 263ms 4.27% std::set::set (inline) 0 0% 33.74% 261ms 4.24% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.74% 261ms 4.24% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.016% 33.76% 260ms 4.22% NodeLocationWriter::Visit 77ms 1.25% 35.01% 259ms 4.21% __GI___libc_free 4ms 0.065% 35.07% 257ms 4.17% Cell::GetMutationState 0 0% 35.07% 256ms 4.16% OutputFileHandler::OpenOutputFile 6ms 0.097% 35.17% 255ms 4.14% std::less::operator() (inline) 5ms 0.081% 35.25% 254ms 4.12% Cell::ReadyToDivide 8ms 0.13% 35.38% 251ms 4.08% AbstractCellPopulation::IsCellAttachedToLocationIndex 249ms 4.04% 39.42% 249ms 4.04% std::operator< (inline) 13ms 0.21% 39.63% 240ms 3.90% std::_Rb_tree::_M_insert_ (inline) 0 0% 39.63% 238ms 3.86% std::_Rb_tree::_M_drop_node (inline) 21ms 0.34% 39.97% 237ms 3.85% std::num_put::_M_insert_float 34ms 0.55% 40.53% 233ms 3.78% std::_Rb_tree::_M_copy (inline) 1ms 0.016% 40.54% 231ms 3.75% Element::Element 3ms 0.049% 40.59% 218ms 3.54% std::__new_allocator::deallocate (inline) 2ms 0.032% 40.62% 216ms 3.51% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 40.62% 216ms 3.51% MeshBasedCellPopulation::GetDampingConstant 0 0% 40.62% 215ms 3.49% std::allocator_traits::deallocate (inline) 4ms 0.065% 40.69% 208ms 3.38% divconqrecurse 0 0% 40.69% 203ms 3.30% AbstractCellProperty::IsType (inline) 131ms 2.13% 42.82% 203ms 3.30% _int_malloc 55ms 0.89% 43.71% 196ms 3.18% mergehulls 1ms 0.016% 43.72% 195ms 3.17% CellProliferativeTypesWriter::VisitCell 2ms 0.032% 43.76% 194ms 3.15% CellPropertyCollection::HasProperty 0 0% 43.76% 193ms 3.13% Cell::HasCellProperty (inline) 56ms 0.91% 44.67% 190ms 3.08% std::_Rb_tree::_M_clone_node (inline) 3ms 0.049% 44.72% 190ms 3.08% std::__cxx11::collate::do_transform 10ms 0.16% 44.88% 189ms 3.07% TetrahedralMesh::Clear 0 0% 44.88% 189ms 3.07% std::_Rb_tree::_M_put_node (inline) 1ms 0.016% 44.89% 181ms 2.94% ___vsnprintf 16ms 0.26% 45.15% 180ms 2.92% __printf_buffer 0 0% 45.15% 180ms 2.92% __vsnprintf_internal (inline) 155ms 2.52% 47.67% 179ms 2.91% _int_free 5ms 0.081% 47.75% 173ms 2.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.065% 47.82% 164ms 2.66% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 42ms 0.68% 48.50% 163ms 2.65% AbstractCellProperty::IsSame 5ms 0.081% 48.58% 151ms 2.45% Element::RegisterWithNodes (inline) 4ms 0.065% 48.64% 151ms 2.45% __printf_fp_l_buffer 0 0% 48.64% 151ms 2.45% __printf_fp_spec (inline) 6ms 0.097% 48.74% 144ms 2.34% MeshBasedCellPopulation::SpringsEnd (inline) 69ms 1.12% 49.86% 143ms 2.32% __printf_fp_buffer_1 3ms 0.049% 49.91% 140ms 2.27% Node::AddElement 1ms 0.016% 49.93% 140ms 2.27% std::basic_filebuf::open 0 0% 49.93% 140ms 2.27% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.93% 140ms 2.27% std::basic_ofstream::open (inline) 21ms 0.34% 50.27% 127ms 2.06% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.27% 126ms 2.05% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.27% 125ms 2.03% AbstractCellBasedWriter::CloseFile 1ms 0.016% 50.28% 125ms 2.03% std::basic_ofstream::close (inline) 0 0% 50.28% 124ms 2.01% OutputFileHandler::CommonConstructor 0 0% 50.28% 124ms 2.01% OutputFileHandler::OutputFileHandler 2ms 0.032% 50.32% 124ms 2.01% std::basic_filebuf::close 15ms 0.24% 50.56% 123ms 2.00% AbstractTetrahedralElement::CalculateJacobian 43ms 0.7% 51.26% 123ms 2.00% std::_Rb_tree::_M_get_insert_unique_pos (inline) 26ms 0.42% 51.68% 121ms 1.96% std::type_info::operator== (inline) 1ms 0.016% 51.70% 119ms 1.93% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.016% 51.71% 118ms 1.92% Node::~Node 2ms 0.032% 51.75% 114ms 1.85% alternateaxes 103ms 1.67% 53.42% 112ms 1.82% vertexmedian 0 0% 53.42% 106ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 0 0% 53.42% 105ms 1.70% _IO_new_fopen 0 0% 53.42% 105ms 1.70% __fopen_internal (inline) 2ms 0.032% 53.45% 104ms 1.69% _IO_new_file_fopen 0 0% 53.45% 104ms 1.69% std::__basic_file::open 2ms 0.032% 53.48% 102ms 1.66% boost::numeric::ublas::vector_assign (inline) 1ms 0.016% 53.50% 101ms 1.64% __GI__IO_file_open 66ms 1.07% 54.57% 100ms 1.62% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.049% 54.62% 98ms 1.59% boost::numeric::ublas::c_vector::c_vector (inline) 24ms 0.39% 55.01% 98ms 1.59% std::num_put::_M_insert_int 13ms 0.21% 55.22% 97ms 1.57% boost::detail::shared_count::~shared_count (inline) 0 0% 55.22% 97ms 1.57% boost::shared_ptr::~shared_ptr (inline) 6ms 0.097% 55.32% 94ms 1.53% AbstractTetrahedralElement::CalculateInverseJacobian 94ms 1.53% 56.84% 94ms 1.53% incircle 0 0% 56.84% 93ms 1.51% FilesystemPermissions::SetFilePermissions (inline) 93ms 1.51% 58.35% 93ms 1.51% __GI_fchmodat 0 0% 58.35% 93ms 1.51% std::filesystem::permissions 36ms 0.58% 58.94% 91ms 1.48% std::__ostream_insert 6ms 0.097% 59.04% 89ms 1.45% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.032% 59.07% 89ms 1.45% std::basic_filebuf::_M_terminate_output 12ms 0.19% 59.26% 87ms 1.41% AbstractTetrahedralElement::RefreshJacobian 86ms 1.40% 60.66% 87ms 1.41% __libc_open64 1ms 0.016% 60.68% 87ms 1.41% std::basic_filebuf::overflow 5ms 0.081% 60.76% 86ms 1.40% AbstractTetrahedralElement::AbstractTetrahedralElement 85ms 1.38% 62.14% 86ms 1.40% __GI___libc_write 0 0% 62.14% 86ms 1.40% std::__basic_file::xsputn 0 0% 62.14% 86ms 1.40% std::basic_filebuf::_M_convert_to_external 0 0% 62.14% 80ms 1.30% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.15% 62.28% 79ms 1.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 77ms 1.25% 63.53% 79ms 1.28% boost::detail::sp_counted_base::release 36ms 0.58% 64.12% 79ms 1.28% boost::shared_ptr::shared_ptr (inline) 3ms 0.049% 64.17% 76ms 1.23% std::vector::push_back (inline) 76ms 1.23% 65.40% 76ms 1.23% std::vector::size (inline) 1ms 0.016% 65.42% 74ms 1.20% std::operator<< (inline) 5ms 0.081% 65.50% 73ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 65.50% 73ms 1.19% std::_Vector_base::_M_allocate (inline) 72ms 1.17% 66.67% 72ms 1.17% std::_Rb_tree_insert_and_rebalance 25ms 0.41% 67.07% 71ms 1.15% boost::numeric::ublas::indexing_vector_assign 69ms 1.12% 68.19% 69ms 1.12% [libchaste_cell_based.so] 5ms 0.081% 68.27% 69ms 1.12% std::vector::_M_realloc_insert 0 0% 68.27% 65ms 1.06% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 68.27% 65ms 1.06% Cell::GetCellId 64ms 1.04% 69.31% 64ms 1.04% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 43ms 0.7% 70.01% 64ms 1.04% std::basic_filebuf::xsputn 25ms 0.41% 70.42% 62ms 1.01% AbstractElement::GetNodeLocation 5ms 0.081% 70.50% 62ms 1.01% TetrahedralMesh::EdgeIterator::GetNodeB 7ms 0.11% 70.61% 62ms 1.01% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.016% 70.63% 61ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.63% 61ms 0.99% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.63% 61ms 0.99% std::filesystem::create_directory 59ms 0.96% 71.59% 59ms 0.96% std::_Rb_tree_increment 54ms 0.88% 72.46% 58ms 0.94% vertexsort 35ms 0.57% 73.03% 56ms 0.91% malloc_consolidate 0 0% 73.03% 54ms 0.88% tcache_get (inline) 54ms 0.88% 73.91% 54ms 0.88% tcache_get_n (inline) 53ms 0.86% 74.77% 53ms 0.86% __memcpy_avx512_unaligned_erms 52ms 0.84% 75.61% 52ms 0.84% __GI___fstatat64 0 0% 75.61% 51ms 0.83% std::filesystem::status 50ms 0.81% 76.42% 50ms 0.81% boost::shared_ptr::operator-> (inline) 0 0% 76.42% 49ms 0.8% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.42% 49ms 0.8% std::__new_allocator::destroy (inline) 0 0% 76.42% 49ms 0.8% std::allocator_traits::destroy (inline) 48ms 0.78% 77.20% 48ms 0.78% counterclockwise 29ms 0.47% 77.67% 46ms 0.75% AbstractElement::GetNodeGlobalIndex 6ms 0.097% 77.77% 46ms 0.75% CellPropertyCollection::AddProperty 6ms 0.097% 77.87% 46ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 28ms 0.45% 78.32% 44ms 0.71% std::basic_streambuf::xsputn 43ms 0.7% 79.02% 43ms 0.7% boost::detail::shared_count::shared_count (inline) 1ms 0.016% 79.04% 43ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 31ms 0.5% 79.54% 42ms 0.68% boost::numeric::ublas::c_matrix::operator() (partial-inline) 17ms 0.28% 79.82% 41ms 0.67% AbstractTetrahedralMesh::GetNumAllElements 41ms 0.67% 80.48% 41ms 0.67% Node::GetIndex 1ms 0.016% 80.50% 39ms 0.63% Node::ConstructNodeAttributes (inline) 39ms 0.63% 81.13% 39ms 0.63% __GI___mkdir 22ms 0.36% 81.49% 39ms 0.63% hack_digit 35ms 0.57% 82.06% 39ms 0.63% std::num_put::do_put 0 0% 82.06% 38ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.06% 38ms 0.62% Node::ClearAppliedForce 0 0% 82.06% 37ms 0.6% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 82.06% 37ms 0.6% std::map::find (inline) 0 0% 82.06% 36ms 0.58% CxxTest::RealWorldDescription::setUp 0 0% 82.06% 36ms 0.58% PetscInitialize 0 0% 82.06% 36ms 0.58% PetscSetup::setUpWorld 0 0% 82.06% 36ms 0.58% PetscSetupUtils::CommonSetup 0 0% 82.06% 36ms 0.58% PetscSetupUtils::InitialisePetsc 0 0% 82.06% 36ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 16ms 0.26% 82.32% 35ms 0.57% AbstractCellCycleModel::GetAge 0 0% 82.32% 35ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.32% 35ms 0.57% PMPI_Init_thread 0 0% 82.32% 35ms 0.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.32% 35ms 0.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 82.32% 35ms 0.57% ompi_mpi_init 0 0% 82.32% 35ms 0.57% std::basic_filebuf::_M_allocate_internal_buffer 1ms 0.016% 82.33% 34ms 0.55% 1ms 0.016% 82.35% 34ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 8ms 0.13% 82.48% 34ms 0.55% Determinant (inline) 0 0% 82.48% 32ms 0.52% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.016% 82.50% 32ms 0.52% NodeAttributes::NodeAttributes 32ms 0.52% 83.02% 32ms 0.52% boost::numeric::ublas::same_impl_ex 1ms 0.016% 83.03% 32ms 0.52% std::__basic_file::close 13ms 0.21% 83.24% 31ms 0.5% AbstractTetrahedralMesh::GetElement 31ms 0.5% 83.75% 31ms 0.5% [libstdc++.so.6.0.33] 2ms 0.032% 83.78% 31ms 0.5% _IO_new_fclose 0 0% 83.78% 31ms 0.5% _dl_init 0 0% 83.78% 31ms 0.5% call_init (inline) 0 0% 83.78% 31ms 0.5% std::__new_allocator::construct (inline) 0 0% 83.78% 31ms 0.5% std::allocator_traits::construct (inline)