File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5271ms, 86.18% of 6116ms total Dropped 535 nodes (cum <= 30.58ms) flat flat% sum% cum cum% 0 0% 0% 6086ms 99.51% __libc_start_call_main 0 0% 0% 6086ms 99.51% __libc_start_main_impl 0 0% 0% 6086ms 99.51% _start 0 0% 0% 6072ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6072ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6072ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6072ms 99.28% main 0 0% 0% 6031ms 98.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6031ms 98.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6031ms 98.61% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6029ms 98.58% AbstractCellBasedSimulation::Solve 0 0% 0% 2664ms 43.56% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.016% 0.016% 2315ms 37.85% MeshBasedCellPopulation::Update 0 0% 0.016% 2260ms 36.95% AbstractCellPopulation::WriteResultsToFiles 3ms 0.049% 0.065% 1150ms 18.80% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.065% 1131ms 18.49% MutableMesh::ReMesh 0 0% 0.065% 1099ms 17.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.065% 996ms 16.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 48ms 0.78% 0.85% 986ms 16.12% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.098% 0.95% 949ms 15.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 92ms 1.50% 2.45% 785ms 12.84% TetrahedralMesh::EdgeIterator::operator++ 361ms 5.90% 8.36% 767ms 12.54% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.033% 8.39% 726ms 11.87% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.18% 8.57% 720ms 11.77% CellPopulationElementWriter::Visit 213ms 3.48% 12.05% 714ms 11.67% __dynamic_cast 8ms 0.13% 12.18% 686ms 11.22% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.016% 12.20% 672ms 10.99% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.082% 12.28% 612ms 10.01% MeshBasedCellPopulation::AcceptCellWriter 41ms 0.67% 12.95% 591ms 9.66% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 30ms 0.49% 13.44% 582ms 9.52% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.049% 13.49% 577ms 9.43% AbstractCellProperty::IsSubType (inline) 5ms 0.082% 13.57% 577ms 9.43% TetrahedralMesh::ImportFromMesher 26ms 0.43% 14.00% 458ms 7.49% operator new 34ms 0.56% 14.55% 446ms 7.29% std::map::operator[] (partial-inline) 24ms 0.39% 14.94% 445ms 7.28% std::_Rb_tree::find (inline) 62ms 1.01% 15.96% 438ms 7.16% std::ostream::_M_insert 0 0% 15.96% 438ms 7.16% std::ostream::operator<< (inline) 151ms 2.47% 18.43% 432ms 7.06% __GI___libc_malloc 3ms 0.049% 18.48% 426ms 6.97% triangulate 1ms 0.016% 18.49% 412ms 6.74% Cell::GetCellProliferativeType 411ms 6.72% 25.21% 411ms 6.72% __strcmp_evex 22ms 0.36% 25.57% 404ms 6.61% std::__new_allocator::allocate (inline) 0 0% 25.57% 399ms 6.52% std::allocator_traits::allocate (inline) 0 0% 25.57% 395ms 6.46% std::set::count (inline) 2ms 0.033% 25.60% 387ms 6.33% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.049% 25.65% 375ms 6.13% std::set::insert (inline) 6ms 0.098% 25.75% 372ms 6.08% std::_Rb_tree::_M_insert_unique 0 0% 25.75% 366ms 5.98% std::_Rb_tree::lower_bound (inline) 0 0% 25.75% 366ms 5.98% std::map::lower_bound (inline) 0 0% 25.75% 365ms 5.97% delaunay 2ms 0.033% 25.78% 362ms 5.92% divconqdelaunay 3ms 0.049% 25.83% 335ms 5.48% AbstractCellBasedSimulation::DoCellBirth 29ms 0.47% 26.31% 326ms 5.33% std::_Rb_tree::~_Rb_tree (inline) 160ms 2.62% 28.92% 324ms 5.30% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.92% 310ms 5.07% std::set::~set (inline) 0 0% 28.92% 308ms 5.04% std::_Rb_tree::_M_create_node (inline) 68ms 1.11% 30.04% 292ms 4.77% std::_Rb_tree::_M_erase 0 0% 30.04% 291ms 4.76% std::_Rb_tree::_M_get_node (inline) 0 0% 30.04% 290ms 4.74% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.082% 30.12% 271ms 4.43% std::less::operator() (inline) 2ms 0.033% 30.15% 267ms 4.37% Cell::GetMutationState 266ms 4.35% 34.50% 266ms 4.35% std::operator< (inline) 13ms 0.21% 34.71% 264ms 4.32% std::_Rb_tree::_Rb_tree (partial-inline) 74ms 1.21% 35.92% 255ms 4.17% __GI___libc_free 0 0% 35.92% 254ms 4.15% NodeLocationWriter::Visit 2ms 0.033% 35.95% 250ms 4.09% std::set::set (inline) 0 0% 35.95% 247ms 4.04% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 35.95% 247ms 4.04% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 35.95% 245ms 4.01% OutputFileHandler::OpenOutputFile 17ms 0.28% 36.23% 233ms 3.81% std::_Rb_tree::_M_insert_ (inline) 12ms 0.2% 36.43% 233ms 3.81% std::__new_allocator::deallocate (inline) 0 0% 36.43% 233ms 3.81% std::allocator_traits::deallocate (inline) 24ms 0.39% 36.82% 233ms 3.81% std::num_put::_M_insert_float 7ms 0.11% 36.94% 231ms 3.78% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.049% 36.98% 230ms 3.76% Element::Element 228ms 3.73% 40.71% 228ms 3.73% std::_Rb_tree::_S_right (inline) 145ms 2.37% 43.08% 225ms 3.68% _int_malloc 3ms 0.049% 43.13% 223ms 3.65% Cell::ReadyToDivide 5ms 0.082% 43.21% 222ms 3.63% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 43.21% 222ms 3.63% MeshBasedCellPopulation::GetDampingConstant 0 0% 43.21% 217ms 3.55% std::_Rb_tree::_M_drop_node (inline) 10ms 0.16% 43.38% 211ms 3.45% divconqrecurse 22ms 0.36% 43.74% 211ms 3.45% std::_Rb_tree::_M_copy (inline) 72ms 1.18% 44.91% 195ms 3.19% mergehulls 1ms 0.016% 44.93% 191ms 3.12% CellProliferativeTypesWriter::VisitCell 1ms 0.016% 44.95% 189ms 3.09% AbstractCellProperty::IsType (inline) 4ms 0.065% 45.01% 188ms 3.07% CellPropertyCollection::HasProperty 0 0% 45.01% 187ms 3.06% Cell::HasCellProperty (inline) 58ms 0.95% 45.96% 186ms 3.04% std::_Rb_tree::_M_clone_node (inline) 1ms 0.016% 45.98% 185ms 3.02% std::__cxx11::collate::do_transform 0 0% 45.98% 184ms 3.01% std::_Rb_tree::_M_put_node (inline) 151ms 2.47% 48.45% 181ms 2.96% _int_free 2ms 0.033% 48.48% 179ms 2.93% ___vsnprintf 0 0% 48.48% 177ms 2.89% __vsnprintf_internal (inline) 22ms 0.36% 48.84% 174ms 2.84% __printf_buffer 4ms 0.065% 48.90% 154ms 2.52% Element::RegisterWithNodes (inline) 11ms 0.18% 49.08% 150ms 2.45% TetrahedralMesh::Clear 6ms 0.098% 49.18% 149ms 2.44% Node::AddElement 3ms 0.049% 49.23% 147ms 2.40% AbstractPhaseBasedCellCycleModel::ReadyToDivide 36ms 0.59% 49.82% 146ms 2.39% AbstractCellProperty::IsSame 0 0% 49.82% 142ms 2.32% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.098% 49.92% 140ms 2.29% __printf_fp_l_buffer 0 0% 49.92% 140ms 2.29% __printf_fp_spec (inline) 51ms 0.83% 50.75% 133ms 2.17% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 50.75% 132ms 2.16% std::basic_ofstream::basic_ofstream (inline) 67ms 1.10% 51.85% 131ms 2.14% __printf_fp_buffer_1 2ms 0.033% 51.88% 130ms 2.13% std::basic_filebuf::open 0 0% 51.88% 130ms 2.13% std::basic_ofstream::open (inline) 0 0% 51.88% 125ms 2.04% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.016% 51.90% 123ms 2.01% std::basic_filebuf::close 0 0% 51.90% 122ms 1.99% AbstractCellBasedWriter::CloseFile 0 0% 51.90% 122ms 1.99% std::basic_ofstream::close (inline) 3ms 0.049% 51.95% 121ms 1.98% MeshBasedCellPopulation::SpringsEnd (inline) 35ms 0.57% 52.52% 121ms 1.98% std::__ostream_insert 6ms 0.098% 52.62% 115ms 1.88% AbstractTetrahedralElement::CalculateJacobian 0 0% 52.62% 111ms 1.81% TetrahedralMesh::RefreshJacobianCachedData 24ms 0.39% 53.01% 110ms 1.80% std::type_info::operator== (inline) 1ms 0.016% 53.02% 109ms 1.78% std::_Vector_base::_M_allocate (inline) 0 0% 53.02% 105ms 1.72% _IO_new_fopen 0 0% 53.02% 105ms 1.72% __fopen_internal (inline) 1ms 0.016% 53.04% 105ms 1.72% std::operator<< (inline) 0 0% 53.04% 104ms 1.70% OutputFileHandler::CommonConstructor 0 0% 53.04% 104ms 1.70% OutputFileHandler::OutputFileHandler 0 0% 53.04% 104ms 1.70% std::__basic_file::open 1ms 0.016% 53.06% 102ms 1.67% _IO_new_file_fopen 6ms 0.098% 53.16% 100ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 53.16% 100ms 1.64% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.016% 53.17% 100ms 1.64% __GI__IO_file_open 6ms 0.098% 53.27% 99ms 1.62% Node::~Node 4ms 0.065% 53.34% 97ms 1.59% std::vector::push_back (inline) 0 0% 53.34% 95ms 1.55% FilesystemPermissions::SetFilePermissions (inline) 95ms 1.55% 54.89% 95ms 1.55% __GI_fchmodat 0 0% 54.89% 95ms 1.55% std::filesystem::permissions 58ms 0.95% 55.84% 94ms 1.54% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 8ms 0.13% 55.97% 91ms 1.49% std::vector::_M_realloc_insert 11ms 0.18% 56.15% 90ms 1.47% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 56.15% 89ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 87ms 1.42% 57.57% 88ms 1.44% __libc_open64 18ms 0.29% 57.86% 88ms 1.44% std::num_put::_M_insert_int 9ms 0.15% 58.01% 87ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 14ms 0.23% 58.24% 87ms 1.42% AbstractTetrahedralElement::RefreshJacobian 9ms 0.15% 58.39% 87ms 1.42% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 58.39% 86ms 1.41% alternateaxes 2ms 0.033% 58.42% 86ms 1.41% std::basic_filebuf::_M_terminate_output 54ms 0.88% 59.30% 86ms 1.41% std::basic_filebuf::xsputn 85ms 1.39% 60.69% 85ms 1.39% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.016% 60.71% 85ms 1.39% std::basic_filebuf::overflow 81ms 1.32% 62.03% 85ms 1.39% vertexmedian 83ms 1.36% 63.39% 84ms 1.37% __GI___libc_write 0 0% 63.39% 84ms 1.37% std::__basic_file::xsputn 0 0% 63.39% 84ms 1.37% std::basic_filebuf::_M_convert_to_external 3ms 0.049% 63.44% 82ms 1.34% boost::numeric::ublas::vector_assign (inline) 5ms 0.082% 63.52% 80ms 1.31% boost::detail::shared_count::~shared_count (inline) 3ms 0.049% 63.57% 80ms 1.31% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 63.57% 80ms 1.31% boost::shared_ptr::~shared_ptr (inline) 4ms 0.065% 63.64% 77ms 1.26% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.033% 63.67% 75ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 75ms 1.23% 64.90% 75ms 1.23% incircle 68ms 1.11% 66.01% 69ms 1.13% boost::detail::sp_counted_base::release 36ms 0.59% 66.60% 69ms 1.13% boost::shared_ptr::shared_ptr (inline) 0 0% 66.60% 68ms 1.11% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.60% 68ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 12ms 0.2% 66.79% 68ms 1.11% TetrahedralMesh::EdgeIterator::GetNodeA 43ms 0.7% 67.50% 66ms 1.08% malloc_consolidate 25ms 0.41% 67.90% 64ms 1.05% AbstractElement::GetNodeLocation 4ms 0.065% 67.97% 64ms 1.05% TetrahedralMesh::EdgeIterator::GetNodeB 64ms 1.05% 69.02% 64ms 1.05% std::_Rb_tree_insert_and_rebalance 59ms 0.96% 69.98% 59ms 0.96% [libchaste_cell_based.so] 59ms 0.96% 70.95% 59ms 0.96% std::_Rb_tree_increment 0 0% 70.95% 58ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 17ms 0.28% 71.22% 58ms 0.95% boost::numeric::ublas::indexing_vector_assign 7ms 0.11% 71.34% 58ms 0.95% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.34% 58ms 0.95% std::filesystem::create_directory 0 0% 71.34% 56ms 0.92% Cell::GetCellId 56ms 0.92% 72.25% 56ms 0.92% Node::GetIndex 55ms 0.9% 73.15% 55ms 0.9% __memcpy_avx512_unaligned_erms 0 0% 73.15% 54ms 0.88% std::vector::vector (inline) 47ms 0.77% 73.92% 54ms 0.88% vertexsort 41ms 0.67% 74.59% 53ms 0.87% AbstractElement::GetNodeGlobalIndex 1ms 0.016% 74.61% 53ms 0.87% std::filesystem::status 52ms 0.85% 75.46% 52ms 0.85% __GI___fstatat64 0 0% 75.46% 52ms 0.85% std::_Vector_base::_Vector_base (inline) 5ms 0.082% 75.54% 51ms 0.83% std::_Vector_base::_M_deallocate (inline) 27ms 0.44% 75.98% 50ms 0.82% std::basic_streambuf::xsputn 1ms 0.016% 76.00% 49ms 0.8% std::_Vector_base::_M_create_storage (inline) 0 0% 76.00% 48ms 0.78% tcache_get (inline) 48ms 0.78% 76.78% 48ms 0.78% tcache_get_n (inline) 47ms 0.77% 77.55% 47ms 0.77% counterclockwise 0 0% 77.55% 46ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.082% 77.63% 46ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 39ms 0.64% 78.27% 46ms 0.75% std::num_put::do_put 22ms 0.36% 78.63% 45ms 0.74% AbstractTetrahedralMesh::GetElement 0 0% 78.63% 44ms 0.72% BoundaryNodeWriter::Visit 44ms 0.72% 79.35% 44ms 0.72% [libstdc++.so.6.0.33] 44ms 0.72% 80.07% 44ms 0.72% boost::shared_ptr::operator-> (inline) 0 0% 80.07% 43ms 0.7% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.07% 42ms 0.69% std::map::find (inline) 41ms 0.67% 80.74% 41ms 0.67% std::vector::size (inline) 40ms 0.65% 81.39% 40ms 0.65% [libchaste_mesh.so] 0 0% 81.39% 38ms 0.62% CxxTest::RealWorldDescription::setUp 0 0% 81.39% 38ms 0.62% PetscInitialize 0 0% 81.39% 38ms 0.62% PetscSetup::setUpWorld 0 0% 81.39% 38ms 0.62% PetscSetupUtils::CommonSetup 0 0% 81.39% 38ms 0.62% PetscSetupUtils::InitialisePetsc 26ms 0.43% 81.82% 38ms 0.62% boost::numeric::ublas::c_matrix::operator() 0 0% 81.82% 37ms 0.6% PMPI_Init_thread 0 0% 81.82% 37ms 0.6% ompi_mpi_init 0 0% 81.82% 36ms 0.59% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.033% 81.85% 36ms 0.59% std::_Rb_tree_header::_Rb_tree_header (inline) 31ms 0.51% 82.36% 36ms 0.59% writeedges 0 0% 82.36% 34ms 0.56% 6ms 0.098% 82.46% 34ms 0.56% CellPropertyCollection::AddProperty 9ms 0.15% 82.60% 34ms 0.56% Determinant (inline) 0 0% 82.60% 34ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.60% 34ms 0.56% _dl_init 0 0% 82.60% 34ms 0.56% call_init (inline) 34ms 0.56% 83.16% 34ms 0.56% std::_Rb_tree_header::_M_reset (inline) 34ms 0.56% 83.71% 34ms 0.56% std::ostream::sentry::sentry 1ms 0.016% 83.73% 33ms 0.54% _IO_new_fclose 33ms 0.54% 84.27% 33ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 84.27% 33ms 0.54% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.27% 33ms 0.54% std::__basic_file::close 0 0% 84.27% 33ms 0.54% std::__new_allocator::destroy (inline) 0 0% 84.27% 33ms 0.54% std::allocator_traits::destroy (inline) 0 0% 84.27% 32ms 0.52% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 84.27% 32ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 2ms 0.033% 84.30% 32ms 0.52% Node::ConstructNodeAttributes (inline) 32ms 0.52% 84.83% 32ms 0.52% unlink_chunk 0 0% 84.83% 31ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 31ms 0.51% 85.33% 31ms 0.51% Node::rGetLocation 31ms 0.51% 85.84% 31ms 0.51% __GI___mkdir 21ms 0.34% 86.18% 31ms 0.51% hack_digit