File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5233ms, 84.90% of 6164ms total Dropped 513 nodes (cum <= 30.82ms) flat flat% sum% cum cum% 0 0% 0% 6132ms 99.48% __libc_start_call_main 0 0% 0% 6132ms 99.48% __libc_start_main_impl 0 0% 0% 6132ms 99.48% _start 0 0% 0% 6116ms 99.22% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6116ms 99.22% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6116ms 99.22% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6116ms 99.22% main 0 0% 0% 6075ms 98.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6075ms 98.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6075ms 98.56% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6072ms 98.51% AbstractCellBasedSimulation::Solve 0 0% 0% 2635ms 42.75% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.016% 0.016% 2264ms 36.73% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.016% 2260ms 36.66% MeshBasedCellPopulation::Update 0 0% 0.016% 1169ms 18.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.016% 1117ms 18.12% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.016% 1117ms 18.12% MutableMesh::ReMesh 0 0% 0.016% 1054ms 17.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.13% 0.15% 1002ms 16.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 11ms 0.18% 0.32% 974ms 15.80% MeshBasedCellPopulation::SpringIterator::operator++ 75ms 1.22% 1.54% 789ms 12.80% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.049% 1.59% 738ms 11.97% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 336ms 5.45% 7.04% 723ms 11.73% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.04% 708ms 11.49% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.049% 7.09% 686ms 11.13% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.081% 7.17% 679ms 11.02% CellPopulationElementWriter::Visit 182ms 2.95% 10.12% 667ms 10.82% __dynamic_cast 33ms 0.54% 10.66% 637ms 10.33% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.081% 10.74% 613ms 9.94% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.34% 11.08% 596ms 9.67% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.13% 11.21% 570ms 9.25% TetrahedralMesh::ImportFromMesher 2ms 0.032% 11.24% 538ms 8.73% AbstractCellProperty::IsSubType (inline) 82ms 1.33% 12.57% 493ms 8.00% std::ostream::_M_insert 0 0% 12.57% 493ms 8.00% std::ostream::operator<< (inline) 25ms 0.41% 12.98% 454ms 7.37% operator new 5ms 0.081% 13.06% 445ms 7.22% std::set::insert (inline) 9ms 0.15% 13.21% 440ms 7.14% std::_Rb_tree::_M_insert_unique 45ms 0.73% 13.94% 439ms 7.12% std::map::operator[] (partial-inline) 149ms 2.42% 16.35% 436ms 7.07% __GI___libc_malloc 0 0% 16.35% 427ms 6.93% triangulate 24ms 0.39% 16.74% 414ms 6.72% std::__new_allocator::allocate (inline) 413ms 6.70% 23.44% 413ms 6.70% __strcmp_evex 0 0% 23.44% 411ms 6.67% std::allocator_traits::allocate (inline) 2ms 0.032% 23.48% 410ms 6.65% Cell::GetCellProliferativeType 18ms 0.29% 23.77% 397ms 6.44% std::_Rb_tree::find (inline) 6ms 0.097% 23.86% 390ms 6.33% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.86% 376ms 6.10% delaunay 1ms 0.016% 23.88% 375ms 6.08% divconqdelaunay 6ms 0.097% 23.98% 368ms 5.97% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.98% 362ms 5.87% std::set::count (inline) 0 0% 23.98% 361ms 5.86% std::_Rb_tree::lower_bound (inline) 0 0% 23.98% 361ms 5.86% std::map::lower_bound (inline) 0 0% 23.98% 352ms 5.71% std::_Rb_tree::_M_create_node (inline) 33ms 0.54% 24.51% 350ms 5.68% std::_Rb_tree::~_Rb_tree (inline) 0 0% 24.51% 335ms 5.43% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 24.51% 330ms 5.35% std::set::~set (inline) 0 0% 24.51% 325ms 5.27% std::_Rb_tree::_M_get_node (inline) 59ms 0.96% 25.47% 316ms 5.13% std::_Rb_tree::_M_erase 146ms 2.37% 27.84% 311ms 5.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.84% 303ms 4.92% NodeLocationWriter::Visit 22ms 0.36% 28.20% 300ms 4.87% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.21% 28.41% 279ms 4.53% std::_Rb_tree::_M_insert_ (inline) 3ms 0.049% 28.46% 276ms 4.48% std::less::operator() (inline) 4ms 0.065% 28.52% 274ms 4.45% std::set::set (inline) 273ms 4.43% 32.95% 273ms 4.43% std::operator< (inline) 2ms 0.032% 32.98% 266ms 4.32% Cell::GetMutationState 5ms 0.081% 33.06% 262ms 4.25% Cell::ReadyToDivide 23ms 0.37% 33.44% 256ms 4.15% std::num_put::_M_insert_float 2ms 0.032% 33.47% 251ms 4.07% Element::Element 0 0% 33.47% 247ms 4.01% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.47% 247ms 4.01% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.016% 33.48% 246ms 3.99% OutputFileHandler::OpenOutputFile 6ms 0.097% 33.58% 244ms 3.96% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.28% 33.86% 244ms 3.96% std::_Rb_tree::_M_copy (inline) 0 0% 33.86% 239ms 3.88% std::_Rb_tree::_M_drop_node (inline) 1ms 0.016% 33.87% 233ms 3.78% MeshBasedCellPopulation::GetDampingConstant 6ms 0.097% 33.97% 232ms 3.76% AbstractCentreBasedCellPopulation::GetDampingConstant 77ms 1.25% 35.22% 227ms 3.68% __GI___libc_free 225ms 3.65% 38.87% 225ms 3.65% std::_Rb_tree::_S_right (inline) 71ms 1.15% 40.02% 223ms 3.62% std::_Rb_tree::_M_clone_node (inline) 6ms 0.097% 40.12% 213ms 3.46% divconqrecurse 10ms 0.16% 40.28% 211ms 3.42% std::__new_allocator::deallocate (inline) 144ms 2.34% 42.62% 209ms 3.39% _int_malloc 0 0% 42.62% 209ms 3.39% std::allocator_traits::deallocate (inline) 3ms 0.049% 42.67% 206ms 3.34% std::__cxx11::collate::do_transform 3ms 0.049% 42.72% 202ms 3.28% ___vsnprintf 50ms 0.81% 43.53% 201ms 3.26% mergehulls 0 0% 43.53% 199ms 3.23% __vsnprintf_internal (inline) 28ms 0.45% 43.98% 198ms 3.21% __printf_buffer 4ms 0.065% 44.05% 195ms 3.16% AbstractCellProperty::IsType (inline) 1ms 0.016% 44.06% 194ms 3.15% CellProliferativeTypesWriter::VisitCell 3ms 0.049% 44.11% 194ms 3.15% CellPropertyCollection::HasProperty 0 0% 44.11% 193ms 3.13% Cell::HasCellProperty (inline) 0 0% 44.11% 180ms 2.92% std::_Rb_tree::_M_put_node (inline) 3ms 0.049% 44.16% 178ms 2.89% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.081% 44.24% 171ms 2.77% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.16% 44.40% 161ms 2.61% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.065% 44.47% 156ms 2.53% __printf_fp_l_buffer 0 0% 44.47% 156ms 2.53% __printf_fp_spec (inline) 6ms 0.097% 44.57% 154ms 2.50% Element::RegisterWithNodes (inline) 47ms 0.76% 45.33% 152ms 2.47% std::_Rb_tree::_M_get_insert_unique_pos (inline) 31ms 0.5% 45.83% 151ms 2.45% AbstractCellProperty::IsSame 124ms 2.01% 47.84% 149ms 2.42% _int_free 78ms 1.27% 49.11% 148ms 2.40% __printf_fp_buffer_1 5ms 0.081% 49.19% 144ms 2.34% Node::AddElement 10ms 0.16% 49.35% 142ms 2.30% AbstractTetrahedralElement::CalculateJacobian 11ms 0.18% 49.53% 142ms 2.30% TetrahedralMesh::Clear 0 0% 49.53% 137ms 2.22% std::basic_ofstream::basic_ofstream (inline) 1ms 0.016% 49.55% 134ms 2.17% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.016% 49.56% 134ms 2.17% std::basic_filebuf::open 0 0% 49.56% 134ms 2.17% std::basic_ofstream::open (inline) 1ms 0.016% 49.58% 133ms 2.16% std::basic_filebuf::close 0 0% 49.58% 132ms 2.14% AbstractCellBasedWriter::CloseFile 0 0% 49.58% 132ms 2.14% std::basic_ofstream::close (inline) 23ms 0.37% 49.95% 128ms 2.08% TetrahedralMesh::EdgesEnd (partial-inline) 26ms 0.42% 50.37% 120ms 1.95% std::type_info::operator== (inline) 19ms 0.31% 50.68% 110ms 1.78% AbstractTetrahedralElement::RefreshJacobian 67ms 1.09% 51.77% 106ms 1.72% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.032% 51.80% 106ms 1.72% std::__basic_file::open 26ms 0.42% 52.22% 105ms 1.70% std::num_put::_M_insert_int 8ms 0.13% 52.35% 104ms 1.69% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 52.35% 104ms 1.69% TetrahedralMesh::RefreshJacobianCachedData 0 0% 52.35% 104ms 1.69% _IO_new_fopen 0 0% 52.35% 104ms 1.69% __fopen_internal (inline) 38ms 0.62% 52.97% 104ms 1.69% std::__ostream_insert 8ms 0.13% 53.10% 103ms 1.67% std::vector::push_back (inline) 9ms 0.15% 53.24% 102ms 1.65% boost::detail::shared_count::~shared_count (inline) 0 0% 53.24% 102ms 1.65% boost::shared_ptr::~shared_ptr (inline) 3ms 0.049% 53.29% 101ms 1.64% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.016% 53.31% 100ms 1.62% _IO_new_file_fopen 0 0% 53.31% 99ms 1.61% OutputFileHandler::CommonConstructor 0 0% 53.31% 99ms 1.61% OutputFileHandler::OutputFileHandler 1ms 0.016% 53.33% 99ms 1.61% alternateaxes 93ms 1.51% 54.83% 98ms 1.59% vertexmedian 5ms 0.081% 54.92% 97ms 1.57% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.92% 97ms 1.57% __GI__IO_file_open 96ms 1.56% 56.47% 96ms 1.56% incircle 0 0% 56.47% 95ms 1.54% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.016% 56.49% 92ms 1.49% std::basic_filebuf::_M_convert_to_external 0 0% 56.49% 92ms 1.49% std::basic_filebuf::_M_terminate_output 0 0% 56.49% 92ms 1.49% std::basic_filebuf::overflow 90ms 1.46% 57.95% 91ms 1.48% __GI___libc_write 0 0% 57.95% 91ms 1.48% std::__basic_file::xsputn 36ms 0.58% 58.53% 90ms 1.46% boost::shared_ptr::shared_ptr (inline) 3ms 0.049% 58.58% 90ms 1.46% std::operator<< (inline) 1ms 0.016% 58.60% 89ms 1.44% boost::numeric::ublas::vector_assign (inline) 0 0% 58.60% 88ms 1.43% FilesystemPermissions::SetFilePermissions (inline) 88ms 1.43% 60.03% 88ms 1.43% __GI_fchmodat 88ms 1.43% 61.45% 88ms 1.43% std::_Rb_tree_insert_and_rebalance 0 0% 61.45% 88ms 1.43% std::filesystem::permissions 1ms 0.016% 61.47% 87ms 1.41% std::_Vector_base::_M_allocate (inline) 8ms 0.13% 61.60% 87ms 1.41% std::vector::_M_realloc_insert 86ms 1.40% 62.99% 86ms 1.40% __libc_open64 3ms 0.049% 63.04% 85ms 1.38% Node::~Node 7ms 0.11% 63.16% 84ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.16% 84ms 1.36% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.049% 63.21% 84ms 1.36% boost::numeric::ublas::c_vector::c_vector (inline) 80ms 1.30% 64.50% 80ms 1.30% [libchaste_cell_based.so] 79ms 1.28% 65.79% 80ms 1.30% boost::detail::sp_counted_base::release 8ms 0.13% 65.91% 75ms 1.22% std::_Rb_tree_const_iterator::operator++ (inline) 75ms 1.22% 67.13% 75ms 1.22% std::_Rb_tree_increment 0 0% 67.13% 73ms 1.18% tcache_get (inline) 73ms 1.18% 68.32% 73ms 1.18% tcache_get_n (inline) 72ms 1.17% 69.48% 72ms 1.17% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.032% 69.52% 71ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 31ms 0.5% 70.02% 70ms 1.14% AbstractElement::GetNodeLocation 0 0% 70.02% 68ms 1.10% Cell::GetCellId 7ms 0.11% 70.13% 68ms 1.10% CellPropertyCollection::AddProperty 0 0% 70.13% 65ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 31ms 0.5% 70.64% 64ms 1.04% boost::numeric::ublas::indexing_vector_assign 40ms 0.65% 71.28% 62ms 1.01% std::basic_filebuf::xsputn 61ms 0.99% 72.27% 61ms 0.99% std::vector::size (inline) 9ms 0.15% 72.42% 60ms 0.97% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 72.42% 59ms 0.96% std::_Rb_tree::_M_destroy_node (inline) 0 0% 72.42% 59ms 0.96% std::__new_allocator::destroy (inline) 0 0% 72.42% 59ms 0.96% std::allocator_traits::destroy (inline) 47ms 0.76% 73.18% 59ms 0.96% std::num_put::do_put 47ms 0.76% 73.95% 56ms 0.91% vertexsort 0 0% 73.95% 55ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 55ms 0.89% 74.84% 55ms 0.89% __GI___fstatat64 0 0% 74.84% 55ms 0.89% std::filesystem::create_directory 0 0% 74.84% 55ms 0.89% std::filesystem::status 0 0% 74.84% 54ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 54ms 0.88% 75.71% 54ms 0.88% boost::detail::shared_count::shared_count (inline) 54ms 0.88% 76.59% 54ms 0.88% counterclockwise 32ms 0.52% 77.11% 51ms 0.83% malloc_consolidate 47ms 0.76% 77.87% 47ms 0.76% __memcpy_avx512_unaligned_erms 46ms 0.75% 78.62% 46ms 0.75% Node::GetIndex 28ms 0.45% 79.07% 46ms 0.75% std::basic_streambuf::xsputn 29ms 0.47% 79.54% 45ms 0.73% hack_digit 22ms 0.36% 79.90% 44ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 24ms 0.39% 80.29% 43ms 0.7% AbstractTetrahedralMesh::GetElement 29ms 0.47% 80.76% 42ms 0.68% AbstractElement::GetNodeGlobalIndex 1ms 0.016% 80.78% 41ms 0.67% BoundaryNodeWriter::Visit 0 0% 80.78% 40ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.016% 80.79% 40ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 80.79% 40ms 0.65% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 80.79% 40ms 0.65% std::vector::vector (inline) 0 0% 80.79% 39ms 0.63% AbstractCentreBasedCellPopulation::CreateCellPair 21ms 0.34% 81.13% 38ms 0.62% AbstractCellCycleModel::GetAge 38ms 0.62% 81.75% 38ms 0.62% [libstdc++.so.6.0.33] 0 0% 81.75% 38ms 0.62% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.75% 38ms 0.62% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.75% 37ms 0.6% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 81.75% 37ms 0.6% CxxTest::RealWorldDescription::setUp 0 0% 81.75% 37ms 0.6% PMPI_Init_thread 0 0% 81.75% 37ms 0.6% PetscInitialize 0 0% 81.75% 37ms 0.6% PetscSetup::setUpWorld 0 0% 81.75% 37ms 0.6% PetscSetupUtils::CommonSetup 0 0% 81.75% 37ms 0.6% PetscSetupUtils::InitialisePetsc 37ms 0.6% 82.35% 37ms 0.6% [libchaste_mesh.so] 0 0% 82.35% 37ms 0.6% _dl_init 37ms 0.6% 82.95% 37ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 82.95% 37ms 0.6% call_init (inline) 0 0% 82.95% 37ms 0.6% ompi_mpi_init 0 0% 82.95% 35ms 0.57% Node::ClearAppliedForce 3ms 0.049% 83.00% 35ms 0.57% Node::ConstructNodeAttributes (inline) 0 0% 83.00% 35ms 0.57% _IO_new_fclose 0 0% 83.00% 35ms 0.57% std::__basic_file::close 0 0% 83.00% 34ms 0.55% std::__new_allocator::construct (inline) 0 0% 83.00% 34ms 0.55% std::allocator_traits::construct (inline) 16ms 0.26% 83.26% 33ms 0.54% AbstractMesh::GetNode 0 0% 83.26% 33ms 0.54% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.032% 83.29% 33ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.29% 33ms 0.54% std::_Vector_base::_Vector_base (inline) 2ms 0.032% 83.32% 32ms 0.52% 1ms 0.016% 83.34% 32ms 0.52% _IO_new_file_close_it 0 0% 83.34% 32ms 0.52% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.049% 83.39% 32ms 0.52% std::_Rb_tree_header::_Rb_tree_header (inline) 31ms 0.5% 83.89% 31ms 0.5% Node::rGetLocation 31ms 0.5% 84.39% 31ms 0.5% __GI___close_nocancel 0 0% 84.39% 31ms 0.5% _dl_start_user 0 0% 84.39% 31ms 0.5% std::_Vector_base::_M_create_storage (inline) 31ms 0.5% 84.90% 31ms 0.5% std::ostream::sentry::sentry