File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6709ms, 85.27% of 7868ms total Dropped 583 nodes (cum <= 39.34ms) flat flat% sum% cum cum% 0 0% 0% 7830ms 99.52% __libc_start_call_main 0 0% 0% 7830ms 99.52% __libc_start_main_impl 0 0% 0% 7830ms 99.52% _start 0 0% 0% 7816ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7816ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7816ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7816ms 99.34% main 0 0% 0% 7779ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7779ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7779ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7775ms 98.82% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3380ms 42.96% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.051% 0.064% 2940ms 37.37% MeshBasedCellPopulation::Update 1ms 0.013% 0.076% 2844ms 36.15% AbstractCellPopulation::WriteResultsToFiles 5ms 0.064% 0.14% 1543ms 19.61% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.14% 1448ms 18.40% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.14% 1426ms 18.12% MutableMesh::ReMesh 1ms 0.013% 0.15% 1393ms 17.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.25% 1333ms 16.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.17% 0.42% 1260ms 16.01% MeshBasedCellPopulation::SpringIterator::operator++ 121ms 1.54% 1.96% 1032ms 13.12% TetrahedralMesh::EdgeIterator::operator++ 402ms 5.11% 7.07% 954ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.064% 7.13% 929ms 11.81% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.089% 7.22% 891ms 11.32% CellPopulationElementWriter::Visit 0 0% 7.22% 886ms 11.26% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 14ms 0.18% 7.40% 844ms 10.73% CellPropertyCollection::GetPropertiesType (inline) 270ms 3.43% 10.83% 828ms 10.52% __dynamic_cast 23ms 0.29% 11.12% 798ms 10.14% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 31ms 0.39% 11.51% 742ms 9.43% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 11.65% 733ms 9.32% TetrahedralMesh::ImportFromMesher 2ms 0.025% 11.68% 714ms 9.07% MeshBasedCellPopulation::AcceptCellWriter 96ms 1.22% 12.90% 643ms 8.17% std::ostream::_M_insert 0 0% 12.90% 643ms 8.17% std::ostream::operator<< (inline) 5ms 0.064% 12.96% 639ms 8.12% AbstractCellProperty::IsSubType (inline) 56ms 0.71% 13.68% 634ms 8.06% operator new 47ms 0.6% 14.27% 602ms 7.65% std::map::operator[] (partial-inline) 208ms 2.64% 16.92% 575ms 7.31% __GI___libc_malloc 8ms 0.1% 17.02% 573ms 7.28% std::set::insert (inline) 17ms 0.22% 17.23% 565ms 7.18% std::_Rb_tree::_M_insert_unique 1ms 0.013% 17.25% 552ms 7.02% triangulate 29ms 0.37% 17.62% 549ms 6.98% std::__new_allocator::allocate (inline) 0 0% 17.62% 543ms 6.90% std::allocator_traits::allocate (inline) 0 0% 17.62% 509ms 6.47% std::_Rb_tree::lower_bound (inline) 0 0% 17.62% 509ms 6.47% std::map::lower_bound (inline) 20ms 0.25% 17.87% 500ms 6.35% std::_Rb_tree::find (inline) 0 0% 17.87% 482ms 6.13% delaunay 7ms 0.089% 17.96% 479ms 6.09% Cell::GetCellProliferativeType 3ms 0.038% 18.00% 478ms 6.08% divconqdelaunay 0 0% 18.00% 463ms 5.88% std::_Rb_tree::_M_create_node (inline) 462ms 5.87% 23.87% 462ms 5.87% __strcmp_avx2 0 0% 23.87% 461ms 5.86% std::set::count (inline) 4ms 0.051% 23.92% 439ms 5.58% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.92% 438ms 5.57% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.051% 23.97% 429ms 5.45% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.97% 422ms 5.36% std::_Rb_tree::_M_get_node (inline) 33ms 0.42% 24.39% 401ms 5.10% std::_Rb_tree::~_Rb_tree (inline) 182ms 2.31% 26.70% 399ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.051% 26.75% 396ms 5.03% NodeLocationWriter::Visit 0 0% 26.75% 374ms 4.75% std::set::~set (inline) 72ms 0.92% 27.67% 366ms 4.65% std::_Rb_tree::_M_erase 12ms 0.15% 27.82% 364ms 4.63% std::less::operator() (inline) 3ms 0.038% 27.86% 360ms 4.58% Cell::GetMutationState 358ms 4.55% 32.41% 358ms 4.55% std::_Rb_tree::_S_right (inline) 21ms 0.27% 32.68% 354ms 4.50% std::_Rb_tree::_M_insert_ (inline) 14ms 0.18% 32.85% 353ms 4.49% std::_Rb_tree::_Rb_tree (partial-inline) 352ms 4.47% 37.33% 352ms 4.47% std::operator< (inline) 26ms 0.33% 37.66% 348ms 4.42% std::num_put::_M_insert_float 1ms 0.013% 37.67% 335ms 4.26% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.67% 335ms 4.26% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 37.68% 327ms 4.16% OutputFileHandler::OpenOutputFile 3ms 0.038% 37.72% 321ms 4.08% std::set::set (inline) 2ms 0.025% 37.75% 319ms 4.05% Element::Element 0 0% 37.75% 308ms 3.91% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 37.76% 307ms 3.90% AbstractCentreBasedCellPopulation::GetDampingConstant 29ms 0.37% 38.13% 306ms 3.89% std::_Rb_tree::_M_copy (inline) 4ms 0.051% 38.18% 299ms 3.80% AbstractCellPopulation::IsCellAttachedToLocationIndex 194ms 2.47% 40.65% 298ms 3.79% _int_malloc 1ms 0.013% 40.66% 297ms 3.77% Cell::ReadyToDivide 108ms 1.37% 42.03% 289ms 3.67% __GI___libc_free 6ms 0.076% 42.11% 273ms 3.47% std::__cxx11::collate::do_transform 11ms 0.14% 42.25% 272ms 3.46% divconqrecurse 78ms 0.99% 43.24% 271ms 3.44% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.24% 268ms 3.41% std::_Rb_tree::_M_drop_node (inline) 13ms 0.17% 43.40% 261ms 3.32% std::__new_allocator::deallocate (inline) 0 0% 43.40% 259ms 3.29% ___vsnprintf 0 0% 43.40% 259ms 3.29% __vsnprintf_internal (inline) 0 0% 43.40% 257ms 3.27% std::allocator_traits::deallocate (inline) 37ms 0.47% 43.87% 253ms 3.22% __printf_buffer 76ms 0.97% 44.84% 253ms 3.22% mergehulls 1ms 0.013% 44.85% 242ms 3.08% CellProliferativeTypesWriter::VisitCell 2ms 0.025% 44.88% 228ms 2.90% AbstractCellProperty::IsType (inline) 8ms 0.1% 44.98% 219ms 2.78% CellPropertyCollection::HasProperty 0 0% 44.98% 218ms 2.77% Cell::HasCellProperty (inline) 0 0% 44.98% 216ms 2.75% std::_Rb_tree::_M_put_node (inline) 6ms 0.076% 45.06% 210ms 2.67% Element::RegisterWithNodes (inline) 6ms 0.076% 45.13% 202ms 2.57% Node::AddElement 5ms 0.064% 45.20% 201ms 2.55% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.038% 45.23% 196ms 2.49% __printf_fp_spec (inline) 7ms 0.089% 45.32% 194ms 2.47% AbstractPhaseBasedCellCycleModel::ReadyToDivide 64ms 0.81% 46.14% 194ms 2.47% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.089% 46.23% 193ms 2.45% __printf_fp_l_buffer 15ms 0.19% 46.42% 188ms 2.39% TetrahedralMesh::Clear 7ms 0.089% 46.50% 183ms 2.33% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 153ms 1.94% 48.45% 180ms 2.29% _int_free 92ms 1.17% 49.62% 178ms 2.26% __printf_fp_buffer_1 0 0% 49.62% 175ms 2.22% std::basic_ofstream::basic_ofstream (inline) 53ms 0.67% 50.29% 174ms 2.21% AbstractCellProperty::IsSame 45ms 0.57% 50.86% 170ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 50.88% 167ms 2.12% std::basic_ofstream::open (inline) 0 0% 50.88% 165ms 2.10% std::basic_filebuf::open 3ms 0.038% 50.92% 160ms 2.03% boost::numeric::ublas::vector_assign (inline) 4ms 0.051% 50.97% 152ms 1.93% boost::numeric::ublas::c_vector::c_vector (inline) 11ms 0.14% 51.11% 151ms 1.92% AbstractTetrahedralElement::CalculateJacobian 66ms 0.84% 51.94% 144ms 1.83% std::__ostream_insert 40ms 0.51% 52.45% 138ms 1.75% std::num_put::_M_insert_int 0 0% 52.45% 135ms 1.72% OutputFileHandler::CommonConstructor 0 0% 52.45% 135ms 1.72% OutputFileHandler::OutputFileHandler 0 0% 52.45% 131ms 1.66% TetrahedralMesh::RefreshJacobianCachedData 0 0% 52.45% 129ms 1.64% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.038% 52.49% 129ms 1.64% alternateaxes 17ms 0.22% 52.71% 128ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 115ms 1.46% 54.17% 126ms 1.60% vertexmedian 1ms 0.013% 54.18% 125ms 1.59% std::__basic_file::open 0 0% 54.18% 124ms 1.58% _IO_new_fopen 0 0% 54.18% 124ms 1.58% __fopen_internal (inline) 30ms 0.38% 54.56% 123ms 1.56% boost::numeric::ublas::indexing_vector_assign 0 0% 54.56% 122ms 1.55% FilesystemPermissions::SetFilePermissions (inline) 122ms 1.55% 56.11% 122ms 1.55% __GI_fchmodat 0 0% 56.11% 122ms 1.55% std::filesystem::permissions 0 0% 56.11% 121ms 1.54% std::_Vector_base::_M_allocate (inline) 23ms 0.29% 56.41% 121ms 1.54% std::type_info::operator== (inline) 3ms 0.038% 56.44% 119ms 1.51% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 56.46% 119ms 1.51% _IO_new_file_fopen 2ms 0.025% 56.48% 118ms 1.50% std::operator<< (inline) 0 0% 56.48% 116ms 1.47% __GI__IO_file_open 5ms 0.064% 56.55% 115ms 1.46% Node::~Node 8ms 0.1% 56.65% 115ms 1.46% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 56.65% 114ms 1.45% AbstractCellBasedWriter::CloseFile 0 0% 56.65% 114ms 1.45% AbstractCellPopulation::CloseRoundRobinWritersFiles 114ms 1.45% 58.10% 114ms 1.45% incircle 1ms 0.013% 58.11% 114ms 1.45% std::basic_ofstream::close (inline) 3ms 0.038% 58.15% 113ms 1.44% std::basic_filebuf::close 74ms 0.94% 59.09% 111ms 1.41% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 59.10% 109ms 1.39% AbstractTetrahedralElement::AbstractTetrahedralElement 13ms 0.17% 59.27% 109ms 1.39% AbstractTetrahedralElement::RefreshJacobian 108ms 1.37% 60.64% 108ms 1.37% std::_Rb_tree_increment 4ms 0.051% 60.69% 106ms 1.35% std::vector::push_back (inline) 15ms 0.19% 60.88% 105ms 1.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 104ms 1.32% 62.20% 104ms 1.32% [libchaste_cell_based.so] 104ms 1.32% 63.52% 104ms 1.32% __libc_open64 0 0% 63.52% 102ms 1.30% AbstractCellPopulation::Iterator::operator++ (inline) 47ms 0.6% 64.12% 102ms 1.30% boost::shared_ptr::shared_ptr (inline) 7ms 0.089% 64.21% 99ms 1.26% boost::detail::shared_count::~shared_count (inline) 0 0% 64.21% 99ms 1.26% boost::shared_ptr::~shared_ptr (inline) 9ms 0.11% 64.32% 95ms 1.21% std::vector::_M_realloc_insert 94ms 1.19% 65.52% 94ms 1.19% std::_Rb_tree_insert_and_rebalance 88ms 1.12% 66.64% 89ms 1.13% boost::detail::sp_counted_base::release 38ms 0.48% 67.12% 88ms 1.12% AbstractElement::GetNodeLocation 88ms 1.12% 68.24% 88ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.038% 68.28% 86ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 86ms 1.09% 69.37% 86ms 1.09% Node::GetIndex 3ms 0.038% 69.41% 86ms 1.09% std::basic_filebuf::_M_convert_to_external 0 0% 69.41% 86ms 1.09% std::basic_filebuf::_M_terminate_output 0 0% 69.41% 86ms 1.09% std::basic_filebuf::overflow 0 0% 69.41% 83ms 1.05% std::__basic_file::xsputn 0 0% 69.41% 81ms 1.03% Cell::GetCellId 81ms 1.03% 70.44% 81ms 1.03% __GI___libc_write 64ms 0.81% 71.25% 81ms 1.03% std::basic_streambuf::xsputn 52ms 0.66% 71.91% 79ms 1.00% malloc_consolidate 49ms 0.62% 72.53% 79ms 1.00% std::basic_filebuf::xsputn 2ms 0.025% 72.56% 77ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 72.59% 74ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 7ms 0.089% 72.67% 71ms 0.9% CellPropertyCollection::AddProperty 62ms 0.79% 73.46% 71ms 0.9% vertexsort 1ms 0.013% 73.47% 70ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 50ms 0.64% 74.11% 70ms 0.89% std::num_put::do_put 0 0% 74.11% 69ms 0.88% std::filesystem::create_directory 4ms 0.051% 74.16% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 74.16% 65ms 0.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.16% 65ms 0.83% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 64ms 0.81% 74.97% 64ms 0.81% std::vector::size (inline) 1ms 0.013% 74.99% 63ms 0.8% tcache_get (inline) 62ms 0.79% 75.78% 62ms 0.79% tcache_get_n (inline) 59ms 0.75% 76.53% 59ms 0.75% __GI___fstatat64 0 0% 76.53% 59ms 0.75% std::filesystem::status 57ms 0.72% 77.25% 57ms 0.72% __memcpy_avx_unaligned_erms 57ms 0.72% 77.97% 57ms 0.72% boost::numeric::ublas::c_vector::operator() (partial-inline) 56ms 0.71% 78.69% 56ms 0.71% counterclockwise 53ms 0.67% 79.36% 55ms 0.7% boost::detail::shared_count::shared_count (inline) 0 0% 79.36% 55ms 0.7% std::vector::vector (inline) 44ms 0.56% 79.92% 54ms 0.69% AbstractElement::GetNodeGlobalIndex 5ms 0.064% 79.98% 54ms 0.69% Node::ConstructNodeAttributes (inline) 53ms 0.67% 80.66% 53ms 0.67% [libchaste_mesh.so] 0 0% 80.66% 52ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.66% 52ms 0.66% std::__new_allocator::destroy (inline) 0 0% 80.66% 52ms 0.66% std::allocator_traits::destroy (inline) 0 0% 80.66% 51ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 2ms 0.025% 80.68% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.013% 80.69% 50ms 0.64% BoundaryNodeWriter::Visit 1ms 0.013% 80.71% 50ms 0.64% Node::ClearAppliedForce 0 0% 80.71% 50ms 0.64% std::_Vector_base::_M_create_storage (inline) 0 0% 80.71% 50ms 0.64% std::_Vector_base::_Vector_base (inline) 23ms 0.29% 81.00% 49ms 0.62% AbstractTetrahedralMesh::GetElement 0 0% 81.00% 47ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 81.00% 47ms 0.6% boost::numeric::ublas::norm_2 (inline) 13ms 0.17% 81.16% 47ms 0.6% boost::numeric::ublas::vector_norm_2::apply (inline) 47ms 0.6% 81.76% 47ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 81.76% 46ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.76% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 81.77% 45ms 0.57% std::__new_allocator::construct (inline) 0 0% 81.77% 45ms 0.57% std::allocator_traits::construct (inline) 4ms 0.051% 81.83% 44ms 0.56% std::_Vector_base::_M_deallocate (inline) 24ms 0.31% 82.13% 43ms 0.55% hack_digit 42ms 0.53% 82.66% 42ms 0.53% Node::IsDeleted 42ms 0.53% 83.20% 42ms 0.53% __GI___mkdir 27ms 0.34% 83.54% 42ms 0.53% boost::numeric::ublas::c_matrix::operator() 41ms 0.52% 84.06% 41ms 0.52% boost::numeric::ublas::same_impl_ex 0 0% 84.06% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 41ms 0.52% 84.58% 41ms 0.52% std::ostream::sentry::sentry 14ms 0.18% 84.76% 40ms 0.51% AbstractTetrahedralMesh::GetNumAllElements 40ms 0.51% 85.27% 40ms 0.51% unlink_chunk