File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6569ms, 83.36% of 7880ms total Dropped 590 nodes (cum <= 39.40ms) flat flat% sum% cum cum% 0 0% 0% 7842ms 99.52% __libc_start_call_main 0 0% 0% 7842ms 99.52% __libc_start_main_impl 0 0% 0% 7842ms 99.52% _start 0 0% 0% 7823ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7823ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7823ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7823ms 99.28% main 0 0% 0% 7780ms 98.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7780ms 98.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7780ms 98.73% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7777ms 98.69% AbstractCellBasedSimulation::Solve 0 0% 0% 3392ms 43.05% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2920ms 37.06% MeshBasedCellPopulation::Update 1ms 0.013% 0.025% 2817ms 35.75% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.038% 1555ms 19.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1444ms 18.32% MutableMesh::ReMesh 0 0% 0.038% 1424ms 18.07% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.038% 1409ms 17.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.11% 0.15% 1347ms 17.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 32ms 0.41% 0.56% 1239ms 15.72% MeshBasedCellPopulation::SpringIterator::operator++ 117ms 1.48% 2.04% 993ms 12.60% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.051% 2.09% 944ms 11.98% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 267ms 3.39% 5.48% 917ms 11.64% __dynamic_cast 3ms 0.038% 5.52% 915ms 11.61% AbstractTwoBodyInteractionForce::AddForceContribution 402ms 5.10% 10.62% 913ms 11.59% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.14% 10.76% 897ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.063% 10.82% 814ms 10.33% CellPopulationElementWriter::Visit 49ms 0.62% 11.45% 807ms 10.24% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 6ms 0.076% 11.52% 781ms 9.91% MeshBasedCellPopulation::AcceptCellWriter 43ms 0.55% 12.07% 769ms 9.76% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 12.08% 723ms 9.18% AbstractCellProperty::IsSubType (inline) 10ms 0.13% 12.21% 692ms 8.78% TetrahedralMesh::ImportFromMesher 0 0% 12.21% 580ms 7.36% triangulate 46ms 0.58% 12.79% 569ms 7.22% operator new 0 0% 12.79% 546ms 6.93% std::ostream::operator<< (inline) 98ms 1.24% 14.04% 543ms 6.89% std::ostream::_M_insert 45ms 0.57% 14.61% 537ms 6.81% std::map::operator[] (partial-inline) 7ms 0.089% 14.70% 527ms 6.69% std::set::insert (inline) 525ms 6.66% 21.36% 525ms 6.66% __strcmp_avx2 12ms 0.15% 21.51% 520ms 6.60% std::_Rb_tree::_M_insert_unique 4ms 0.051% 21.56% 517ms 6.56% Cell::GetCellProliferativeType 0 0% 21.56% 515ms 6.54% delaunay 2ms 0.025% 21.59% 513ms 6.51% divconqdelaunay 182ms 2.31% 23.90% 510ms 6.47% __GI___libc_malloc 24ms 0.3% 24.20% 510ms 6.47% std::__new_allocator::allocate (inline) 18ms 0.23% 24.43% 509ms 6.46% std::_Rb_tree::find (inline) 0 0% 24.43% 504ms 6.40% std::allocator_traits::allocate (inline) 5ms 0.063% 24.49% 494ms 6.27% LegacyCellProliferativeTypesWriter::VisitCell 236ms 2.99% 27.49% 479ms 6.08% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.013% 27.50% 460ms 5.84% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.50% 460ms 5.84% std::set::count (inline) 0 0% 27.50% 446ms 5.66% std::_Rb_tree::lower_bound (inline) 0 0% 27.50% 446ms 5.66% std::map::lower_bound (inline) 0 0% 27.50% 426ms 5.41% std::_Rb_tree::_M_create_node (inline) 34ms 0.43% 27.93% 407ms 5.16% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.93% 402ms 5.10% std::_Rb_tree::_M_get_node (inline) 0 0% 27.93% 400ms 5.08% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.93% 385ms 4.89% std::set::~set (inline) 3ms 0.038% 27.97% 375ms 4.76% Cell::GetMutationState 34ms 0.43% 28.40% 371ms 4.71% std::_Rb_tree::_Rb_tree (partial-inline) 79ms 1.00% 29.40% 368ms 4.67% std::_Rb_tree::_M_erase 11ms 0.14% 29.54% 363ms 4.61% std::less::operator() (inline) 352ms 4.47% 34.01% 352ms 4.47% std::operator< (inline) 3ms 0.038% 34.05% 348ms 4.42% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 34.10% 345ms 4.38% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.025% 34.12% 341ms 4.33% NodeLocationWriter::Visit 1ms 0.013% 34.14% 338ms 4.29% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.063% 34.20% 338ms 4.29% std::set::set (inline) 0 0% 34.20% 336ms 4.26% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.20% 335ms 4.25% OutputFileHandler::OpenOutputFile 15ms 0.19% 34.39% 317ms 4.02% std::_Rb_tree::_M_insert_ (inline) 5ms 0.063% 34.45% 311ms 3.95% Cell::ReadyToDivide 32ms 0.41% 34.86% 301ms 3.82% std::_Rb_tree::_M_copy (inline) 3ms 0.038% 34.90% 300ms 3.81% Element::Element 78ms 0.99% 35.89% 296ms 3.76% __GI___libc_free 16ms 0.2% 36.09% 294ms 3.73% divconqrecurse 29ms 0.37% 36.46% 293ms 3.72% std::num_put::_M_insert_float 286ms 3.63% 40.09% 286ms 3.63% std::_Rb_tree::_S_right (inline) 0 0% 40.09% 275ms 3.49% std::_Rb_tree::_M_drop_node (inline) 83ms 1.05% 41.14% 267ms 3.39% mergehulls 71ms 0.9% 42.04% 263ms 3.34% std::_Rb_tree::_M_clone_node (inline) 14ms 0.18% 42.22% 257ms 3.26% std::__new_allocator::deallocate (inline) 2ms 0.025% 42.25% 255ms 3.24% AbstractCellProperty::IsType (inline) 0 0% 42.25% 255ms 3.24% std::allocator_traits::deallocate (inline) 8ms 0.1% 42.35% 249ms 3.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 150ms 1.90% 44.25% 246ms 3.12% _int_malloc 4ms 0.051% 44.30% 245ms 3.11% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 44.34% 234ms 2.97% CellPropertyCollection::HasProperty 0 0% 44.34% 232ms 2.94% Cell::HasCellProperty (inline) 8ms 0.1% 44.44% 232ms 2.94% std::__cxx11::collate::do_transform 0 0% 44.44% 223ms 2.83% std::_Rb_tree::_M_put_node (inline) 186ms 2.36% 46.80% 218ms 2.77% _int_free 0 0% 46.80% 214ms 2.72% ___vsnprintf 0 0% 46.80% 214ms 2.72% __vsnprintf_internal (inline) 26ms 0.33% 47.13% 213ms 2.70% __printf_buffer 7ms 0.089% 47.22% 209ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 7ms 0.089% 47.31% 205ms 2.60% TetrahedralMesh::Clear 4ms 0.051% 47.36% 199ms 2.53% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 47.40% 199ms 2.53% Element::RegisterWithNodes (inline) 5ms 0.063% 47.46% 195ms 2.47% Node::AddElement 61ms 0.77% 48.24% 191ms 2.42% std::_Rb_tree::_M_get_insert_unique_pos (inline) 40ms 0.51% 48.74% 190ms 2.41% AbstractCellProperty::IsSame 2ms 0.025% 48.77% 188ms 2.39% MeshBasedCellPopulation::SpringsEnd (inline) 50ms 0.63% 49.40% 174ms 2.21% TetrahedralMesh::EdgesEnd (partial-inline) 5ms 0.063% 49.47% 171ms 2.17% __printf_fp_l_buffer 0 0% 49.47% 171ms 2.17% __printf_fp_spec (inline) 7ms 0.089% 49.56% 161ms 2.04% AbstractTetrahedralElement::CalculateJacobian 82ms 1.04% 50.60% 158ms 2.01% __printf_fp_buffer_1 0 0% 50.60% 156ms 1.98% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.60% 155ms 1.97% AbstractCellBasedWriter::CloseFile 0 0% 50.60% 155ms 1.97% AbstractCellPopulation::CloseRoundRobinWritersFiles 50ms 0.63% 51.23% 155ms 1.97% std::__ostream_insert 3ms 0.038% 51.27% 155ms 1.97% std::basic_filebuf::close 0 0% 51.27% 155ms 1.97% std::basic_ofstream::close (inline) 0 0% 51.27% 150ms 1.90% std::basic_ofstream::basic_ofstream (inline) 34ms 0.43% 51.70% 150ms 1.90% std::type_info::operator== (inline) 0 0% 51.70% 149ms 1.89% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 51.71% 149ms 1.89% std::filesystem::permissions 148ms 1.88% 53.59% 148ms 1.88% __GI_fchmodat 4ms 0.051% 53.64% 146ms 1.85% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 53.65% 145ms 1.84% std::basic_filebuf::open 0 0% 53.65% 145ms 1.84% std::basic_ofstream::open (inline) 1ms 0.013% 53.67% 142ms 1.80% OutputFileHandler::OutputFileHandler 0 0% 53.67% 141ms 1.79% OutputFileHandler::CommonConstructor 0 0% 53.67% 132ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.063% 53.73% 131ms 1.66% Node::~Node 126ms 1.60% 55.33% 126ms 1.60% incircle 0 0% 55.33% 124ms 1.57% std::operator<< (inline) 3ms 0.038% 55.37% 120ms 1.52% alternateaxes 6ms 0.076% 55.44% 118ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 15ms 0.19% 55.63% 118ms 1.50% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 55.63% 117ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 82ms 1.04% 56.68% 116ms 1.47% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 108ms 1.37% 58.05% 116ms 1.47% vertexmedian 2ms 0.025% 58.07% 115ms 1.46% boost::numeric::ublas::vector_assign (inline) 0 0% 58.07% 113ms 1.43% _IO_new_fopen 0 0% 58.07% 113ms 1.43% __fopen_internal (inline) 2ms 0.025% 58.10% 113ms 1.43% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 58.10% 112ms 1.42% _IO_new_file_fopen 0 0% 58.10% 112ms 1.42% std::__basic_file::open 0 0% 58.10% 111ms 1.41% std::basic_filebuf::_M_terminate_output 1ms 0.013% 58.11% 111ms 1.41% std::basic_filebuf::overflow 0 0% 58.11% 110ms 1.40% __GI__IO_file_open 12ms 0.15% 58.26% 110ms 1.40% boost::detail::shared_count::~shared_count (inline) 0 0% 58.26% 110ms 1.40% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 58.27% 110ms 1.40% std::basic_filebuf::_M_convert_to_external 25ms 0.32% 58.59% 110ms 1.40% std::num_put::_M_insert_int 106ms 1.35% 59.94% 108ms 1.37% __GI___libc_write 0 0% 59.94% 108ms 1.37% std::__basic_file::xsputn 18ms 0.23% 60.16% 105ms 1.33% AbstractTetrahedralElement::RefreshJacobian 105ms 1.33% 61.50% 105ms 1.33% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 61.54% 103ms 1.31% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 61.55% 103ms 1.31% std::_Vector_base::_M_allocate (inline) 46ms 0.58% 62.13% 101ms 1.28% boost::shared_ptr::shared_ptr (inline) 99ms 1.26% 63.39% 99ms 1.26% __libc_open64 4ms 0.051% 63.44% 98ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.1% 63.54% 93ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 91ms 1.15% 64.70% 93ms 1.18% boost::detail::sp_counted_base::release 55ms 0.7% 65.39% 93ms 1.18% std::basic_filebuf::xsputn 92ms 1.17% 66.56% 92ms 1.17% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 4ms 0.051% 66.61% 92ms 1.17% std::_Rb_tree_const_iterator::operator++ (inline) 8ms 0.1% 66.71% 92ms 1.17% std::vector::push_back (inline) 89ms 1.13% 67.84% 89ms 1.13% std::_Rb_tree_increment 84ms 1.07% 68.91% 88ms 1.12% vertexsort 85ms 1.08% 69.99% 85ms 1.08% [libchaste_cell_based.so] 8ms 0.1% 70.09% 80ms 1.02% std::vector::_M_realloc_insert 28ms 0.36% 70.44% 79ms 1.00% boost::numeric::ublas::indexing_vector_assign 0 0% 70.44% 76ms 0.96% Cell::GetCellId 0 0% 70.44% 76ms 0.96% tcache_get (inline) 76ms 0.96% 71.41% 76ms 0.96% tcache_get_n (inline) 51ms 0.65% 72.06% 75ms 0.95% malloc_consolidate 1ms 0.013% 72.07% 74ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.038% 72.11% 73ms 0.93% TetrahedralMesh::EdgeIterator::GetNodeB 25ms 0.32% 72.42% 71ms 0.9% AbstractElement::GetNodeLocation 51ms 0.65% 73.07% 68ms 0.86% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 73.08% 68ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 67ms 0.85% 73.93% 67ms 0.85% __GI___fstatat64 67ms 0.85% 74.78% 67ms 0.85% __memcpy_avx_unaligned_erms 39ms 0.49% 75.28% 67ms 0.85% std::basic_streambuf::xsputn 0 0% 75.28% 67ms 0.85% std::filesystem::create_directory 43ms 0.55% 75.82% 66ms 0.84% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.013% 75.84% 66ms 0.84% std::filesystem::status 7ms 0.089% 75.93% 65ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeA 23ms 0.29% 76.22% 64ms 0.81% Determinant (inline) 62ms 0.79% 77.01% 62ms 0.79% [libstdc++.so.6.0.33] 62ms 0.79% 77.79% 62ms 0.79% std::vector::size (inline) 8ms 0.1% 77.89% 61ms 0.77% CellPropertyCollection::AddProperty 59ms 0.75% 78.64% 59ms 0.75% counterclockwise 0 0% 78.64% 59ms 0.75% std::vector::vector (inline) 55ms 0.7% 79.34% 55ms 0.7% Node::GetIndex 0 0% 79.34% 55ms 0.7% std::_Vector_base::_Vector_base (inline) 53ms 0.67% 80.01% 54ms 0.69% boost::detail::shared_count::shared_count (inline) 0 0% 80.01% 53ms 0.67% std::_Vector_base::_M_create_storage (inline) 25ms 0.32% 80.33% 52ms 0.66% AbstractCellCycleModel::GetAge 52ms 0.66% 80.99% 52ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 80.99% 52ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.99% 52ms 0.66% std::__new_allocator::destroy (inline) 0 0% 80.99% 52ms 0.66% std::allocator_traits::destroy (inline) 51ms 0.65% 81.64% 51ms 0.65% [libchaste_mesh.so] 0 0% 81.64% 50ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.051% 81.69% 49ms 0.62% Node::ConstructNodeAttributes (inline) 0 0% 81.69% 48ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 81.70% 46ms 0.58% Node::ClearAppliedForce 0 0% 81.70% 46ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 27ms 0.34% 82.04% 45ms 0.57% hack_digit 20ms 0.25% 82.30% 44ms 0.56% AbstractTetrahedralMesh::GetElement 43ms 0.55% 82.84% 43ms 0.55% Node::IsDeleted 1ms 0.013% 82.86% 42ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 82.86% 42ms 0.53% BoundaryNodeWriter::Visit 33ms 0.42% 83.27% 42ms 0.53% std::num_put::do_put 0 0% 83.27% 41ms 0.52% _dl_init 0 0% 83.27% 41ms 0.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.27% 41ms 0.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.27% 41ms 0.52% call_init (inline) 0 0% 83.27% 41ms 0.52% std::map::find (inline) 0 0% 83.27% 40ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 6ms 0.076% 83.35% 40ms 0.51% Inverse 1ms 0.013% 83.36% 40ms 0.51% _IO_new_fclose 0 0% 83.36% 40ms 0.51% std::__basic_file::close