File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6633ms, 84.38% of 7861ms total Dropped 568 nodes (cum <= 39.30ms) flat flat% sum% cum cum% 0 0% 0% 7819ms 99.47% __libc_start_call_main 0 0% 0% 7819ms 99.47% __libc_start_main_impl 0 0% 0% 7819ms 99.47% _start 0 0% 0% 7804ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7804ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7804ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7804ms 99.27% main 0 0% 0% 7764ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7764ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7764ms 98.77% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7760ms 98.72% AbstractCellBasedSimulation::Solve 0 0% 0% 3356ms 42.69% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2886ms 36.71% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2865ms 36.45% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.064% 1528ms 19.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.064% 1423ms 18.10% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.064% 1400ms 17.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.064% 1396ms 17.76% MutableMesh::ReMesh 8ms 0.1% 0.17% 1361ms 17.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.34% 1208ms 15.37% MeshBasedCellPopulation::SpringIterator::operator++ 134ms 1.70% 2.05% 1007ms 12.81% TetrahedralMesh::EdgeIterator::operator++ 437ms 5.56% 7.61% 978ms 12.44% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.63% 919ms 11.69% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.038% 7.67% 910ms 11.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.80% 893ms 11.36% CellPopulationElementWriter::Visit 9ms 0.11% 7.91% 892ms 11.35% CellPropertyCollection::GetPropertiesType (inline) 265ms 3.37% 11.28% 884ms 11.25% __dynamic_cast 42ms 0.53% 11.82% 828ms 10.53% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 24ms 0.31% 12.12% 765ms 9.73% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.16% 742ms 9.44% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.076% 12.24% 706ms 8.98% TetrahedralMesh::ImportFromMesher 6ms 0.076% 12.31% 698ms 8.88% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.33% 617ms 7.85% std::ostream::operator<< (inline) 95ms 1.21% 13.54% 616ms 7.84% std::ostream::_M_insert 45ms 0.57% 14.11% 582ms 7.40% operator new 45ms 0.57% 14.68% 571ms 7.26% std::map::operator[] (partial-inline) 23ms 0.29% 14.97% 547ms 6.96% std::_Rb_tree::find (inline) 166ms 2.11% 17.08% 537ms 6.83% __GI___libc_malloc 0 0% 17.08% 527ms 6.70% triangulate 30ms 0.38% 17.47% 519ms 6.60% std::__new_allocator::allocate (inline) 0 0% 17.47% 514ms 6.54% std::allocator_traits::allocate (inline) 6ms 0.076% 17.54% 498ms 6.34% std::set::insert (inline) 7ms 0.089% 17.63% 497ms 6.32% Cell::GetCellProliferativeType 0 0% 17.63% 494ms 6.28% std::set::count (inline) 13ms 0.17% 17.80% 493ms 6.27% std::_Rb_tree::_M_insert_unique 0 0% 17.80% 486ms 6.18% std::_Rb_tree::lower_bound (inline) 0 0% 17.80% 486ms 6.18% std::map::lower_bound (inline) 474ms 6.03% 23.83% 474ms 6.03% __strcmp_avx2 0 0% 23.83% 467ms 5.94% delaunay 1ms 0.013% 23.84% 467ms 5.94% divconqdelaunay 2ms 0.025% 23.86% 459ms 5.84% AbstractCellBasedSimulation::DoCellBirth 4ms 0.051% 23.92% 455ms 5.79% LegacyCellProliferativeTypesWriter::VisitCell 220ms 2.80% 26.71% 453ms 5.76% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.71% 437ms 5.56% std::_Rb_tree::_M_create_node (inline) 0 0% 26.71% 416ms 5.29% std::_Rb_tree::_Alloc_node::operator() (inline) 34ms 0.43% 27.15% 399ms 5.08% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.15% 397ms 5.05% std::_Rb_tree::_M_get_node (inline) 6ms 0.076% 27.22% 392ms 4.99% Cell::GetMutationState 5ms 0.064% 27.29% 390ms 4.96% NodeLocationWriter::Visit 21ms 0.27% 27.55% 384ms 4.88% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.55% 368ms 4.68% std::set::~set (inline) 71ms 0.9% 28.46% 362ms 4.61% std::_Rb_tree::_M_erase 5ms 0.064% 28.52% 362ms 4.61% std::set::set (inline) 10ms 0.13% 28.65% 354ms 4.50% std::less::operator() (inline) 344ms 4.38% 33.02% 344ms 4.38% std::operator< (inline) 1ms 0.013% 33.04% 337ms 4.29% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.04% 336ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 16ms 0.2% 33.24% 333ms 4.24% std::num_put::_M_insert_float 110ms 1.40% 34.64% 331ms 4.21% __GI___libc_free 27ms 0.34% 34.98% 322ms 4.10% std::_Rb_tree::_M_copy (inline) 317ms 4.03% 39.02% 317ms 4.03% std::_Rb_tree::_S_right (inline) 17ms 0.22% 39.23% 313ms 3.98% std::_Rb_tree::_M_insert_ (inline) 0 0% 39.23% 312ms 3.97% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.23% 311ms 3.96% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 39.23% 308ms 3.92% OutputFileHandler::OpenOutputFile 3ms 0.038% 39.27% 302ms 3.84% Cell::ReadyToDivide 4ms 0.051% 39.32% 290ms 3.69% Element::Element 5ms 0.064% 39.38% 289ms 3.68% AbstractCellPopulation::IsCellAttachedToLocationIndex 72ms 0.92% 40.30% 289ms 3.68% std::_Rb_tree::_M_clone_node (inline) 8ms 0.1% 40.40% 283ms 3.60% std::__new_allocator::deallocate (inline) 0 0% 40.40% 277ms 3.52% std::allocator_traits::deallocate (inline) 181ms 2.30% 42.70% 274ms 3.49% _int_malloc 13ms 0.17% 42.87% 274ms 3.49% divconqrecurse 0 0% 42.87% 271ms 3.45% std::_Rb_tree::_M_drop_node (inline) 6ms 0.076% 42.95% 265ms 3.37% std::__cxx11::collate::do_transform 2ms 0.025% 42.97% 253ms 3.22% ___vsnprintf 72ms 0.92% 43.89% 253ms 3.22% mergehulls 0 0% 43.89% 252ms 3.21% __vsnprintf_internal (inline) 30ms 0.38% 44.27% 246ms 3.13% __printf_buffer 0 0% 44.27% 245ms 3.12% CellProliferativeTypesWriter::VisitCell 0 0% 44.27% 227ms 2.89% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 44.33% 225ms 2.86% AbstractCellProperty::IsType (inline) 184ms 2.34% 46.67% 221ms 2.81% _int_free 8ms 0.1% 46.78% 217ms 2.76% CellPropertyCollection::HasProperty 0 0% 46.78% 215ms 2.74% Cell::HasCellProperty (inline) 9ms 0.11% 46.89% 208ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 19ms 0.24% 47.13% 201ms 2.56% TetrahedralMesh::Clear 7ms 0.089% 47.22% 201ms 2.56% __printf_fp_l_buffer 0 0% 47.22% 201ms 2.56% __printf_fp_spec (inline) 21ms 0.27% 47.49% 198ms 2.52% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.051% 47.54% 191ms 2.43% Element::RegisterWithNodes (inline) 5ms 0.064% 47.60% 187ms 2.38% Node::AddElement 106ms 1.35% 48.95% 186ms 2.37% __printf_fp_buffer_1 5ms 0.064% 49.01% 181ms 2.30% MeshBasedCellPopulation::SpringsEnd (inline) 70ms 0.89% 49.90% 167ms 2.12% std::_Rb_tree::_M_get_insert_unique_pos (inline) 48ms 0.61% 50.52% 158ms 2.01% AbstractCellProperty::IsSame 0 0% 50.52% 154ms 1.96% std::basic_ofstream::basic_ofstream (inline) 25ms 0.32% 50.83% 151ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.83% 148ms 1.88% std::basic_ofstream::open (inline) 64ms 0.81% 51.65% 147ms 1.87% std::__ostream_insert 0 0% 51.65% 147ms 1.87% std::basic_filebuf::open 1ms 0.013% 51.66% 145ms 1.84% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.66% 144ms 1.83% AbstractCellBasedWriter::CloseFile 1ms 0.013% 51.67% 144ms 1.83% std::basic_filebuf::close 0 0% 51.67% 144ms 1.83% std::basic_ofstream::close (inline) 11ms 0.14% 51.81% 142ms 1.81% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.81% 134ms 1.70% OutputFileHandler::CommonConstructor 0 0% 51.81% 134ms 1.70% OutputFileHandler::OutputFileHandler 15ms 0.19% 52.00% 133ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 52.00% 132ms 1.68% TetrahedralMesh::RefreshJacobianCachedData 37ms 0.47% 52.47% 130ms 1.65% std::num_put::_M_insert_int 0 0% 52.47% 129ms 1.64% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 52.47% 129ms 1.64% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.038% 52.51% 128ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 52.53% 128ms 1.63% std::filesystem::permissions 1ms 0.013% 52.54% 127ms 1.62% OutputFileHandler::MakeFoldersAndReturnFullPath 127ms 1.62% 54.15% 127ms 1.62% __GI_fchmodat 2ms 0.025% 54.18% 127ms 1.62% boost::numeric::ublas::vector_assign (inline) 3ms 0.038% 54.22% 119ms 1.51% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.22% 117ms 1.49% std::_Vector_base::_M_allocate (inline) 0 0% 54.22% 117ms 1.49% std::operator<< (inline) 3ms 0.038% 54.26% 115ms 1.46% alternateaxes 51ms 0.65% 54.90% 114ms 1.45% boost::shared_ptr::shared_ptr (inline) 5ms 0.064% 54.97% 114ms 1.45% std::vector::push_back (inline) 27ms 0.34% 55.31% 113ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 9ms 0.11% 55.43% 112ms 1.42% Node::~Node 112ms 1.42% 56.85% 112ms 1.42% incircle 99ms 1.26% 58.11% 112ms 1.42% vertexmedian 26ms 0.33% 58.44% 110ms 1.40% std::type_info::operator== (inline) 13ms 0.17% 58.61% 109ms 1.39% AbstractTetrahedralElement::RefreshJacobian 108ms 1.37% 59.98% 108ms 1.37% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 60.01% 108ms 1.37% std::__basic_file::open 0 0% 60.01% 106ms 1.35% _IO_new_fopen 0 0% 60.01% 106ms 1.35% __fopen_internal (inline) 106ms 1.35% 61.35% 106ms 1.35% std::_Rb_tree_increment 5ms 0.064% 61.42% 105ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 61.43% 105ms 1.34% _IO_new_file_fopen 0 0% 61.43% 104ms 1.32% __GI__IO_file_open 13ms 0.17% 61.60% 104ms 1.32% boost::detail::shared_count::~shared_count (inline) 0 0% 61.60% 104ms 1.32% boost::shared_ptr::~shared_ptr (inline) 8ms 0.1% 61.70% 103ms 1.31% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.15% 61.85% 102ms 1.30% std::vector::_M_realloc_insert 6ms 0.076% 61.93% 101ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 61.94% 101ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.73% 62.66% 101ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 62.66% 101ms 1.28% std::basic_filebuf::_M_terminate_output 3ms 0.038% 62.70% 100ms 1.27% std::basic_filebuf::overflow 0 0% 62.70% 97ms 1.23% std::__basic_file::xsputn 0 0% 62.70% 97ms 1.23% std::basic_filebuf::_M_convert_to_external 95ms 1.21% 63.91% 95ms 1.21% __GI___libc_write 73ms 0.93% 64.84% 95ms 1.21% std::basic_streambuf::xsputn 92ms 1.17% 66.01% 92ms 1.17% __libc_open64 91ms 1.16% 67.17% 91ms 1.16% [libchaste_cell_based.so] 83ms 1.06% 68.22% 86ms 1.09% boost::detail::sp_counted_base::release 3ms 0.038% 68.26% 85ms 1.08% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 68.26% 85ms 1.08% tcache_get (inline) 85ms 1.08% 69.34% 85ms 1.08% tcache_get_n (inline) 83ms 1.06% 70.40% 83ms 1.06% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 35ms 0.45% 70.84% 82ms 1.04% AbstractElement::GetNodeLocation 34ms 0.43% 71.28% 81ms 1.03% boost::numeric::ublas::indexing_vector_assign 54ms 0.69% 71.96% 81ms 1.03% malloc_consolidate 0 0% 71.96% 75ms 0.95% Cell::GetCellId 7ms 0.089% 72.05% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 9ms 0.11% 72.17% 66ms 0.84% CellPropertyCollection::AddProperty 2ms 0.025% 72.19% 66ms 0.84% Node::ClearAppliedForce 2ms 0.025% 72.22% 66ms 0.84% Node::ConstructNodeAttributes (inline) 66ms 0.84% 73.06% 66ms 0.84% counterclockwise 65ms 0.83% 73.88% 65ms 0.83% Node::GetIndex 59ms 0.75% 74.63% 65ms 0.83% vertexsort 1ms 0.013% 74.65% 63ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 63ms 0.8% 75.45% 63ms 0.8% __memcpy_avx_unaligned_erms 62ms 0.79% 76.24% 63ms 0.8% boost::detail::shared_count::shared_count (inline) 1ms 0.013% 76.25% 63ms 0.8% std::filesystem::status 62ms 0.79% 77.04% 62ms 0.79% [libchaste_mesh.so] 31ms 0.39% 77.43% 61ms 0.78% std::basic_filebuf::xsputn 61ms 0.78% 78.21% 61ms 0.78% std::vector::size (inline) 45ms 0.57% 78.78% 60ms 0.76% AbstractElement::GetNodeGlobalIndex 0 0% 78.78% 59ms 0.75% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 59ms 0.75% 79.53% 59ms 0.75% __GI___fstatat64 1ms 0.013% 79.54% 59ms 0.75% std::filesystem::create_directory 0 0% 79.54% 57ms 0.73% std::vector::vector (inline) 54ms 0.69% 80.23% 54ms 0.69% Node::IsDeleted 44ms 0.56% 80.79% 54ms 0.69% std::num_put::do_put 53ms 0.67% 81.47% 53ms 0.67% boost::shared_ptr::operator-> (inline) 29ms 0.37% 81.83% 52ms 0.66% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.025% 81.86% 52ms 0.66% std::_Vector_base::_M_deallocate (inline) 0 0% 81.86% 52ms 0.66% std::_Vector_base::_Vector_base (inline) 4ms 0.051% 81.91% 51ms 0.65% NodeAttributes::NodeAttributes 0 0% 81.91% 51ms 0.65% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 81.91% 50ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.91% 50ms 0.64% std::_Vector_base::_M_create_storage (inline) 49ms 0.62% 82.53% 49ms 0.62% std::ostream::sentry::sentry 22ms 0.28% 82.81% 47ms 0.6% AbstractCellCycleModel::GetAge 0 0% 82.81% 45ms 0.57% std::map::find (inline) 21ms 0.27% 83.08% 44ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 83.09% 44ms 0.56% BoundaryNodeWriter::Visit 0 0% 83.09% 44ms 0.56% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.09% 44ms 0.56% std::__new_allocator::destroy (inline) 0 0% 83.09% 44ms 0.56% std::allocator_traits::destroy (inline) 27ms 0.34% 83.44% 43ms 0.55% hack_digit 0 0% 83.44% 43ms 0.55% std::__new_allocator::construct (inline) 0 0% 83.44% 43ms 0.55% std::allocator_traits::construct (inline) 0 0% 83.44% 42ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.013% 83.45% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 83.45% 42ms 0.53% _dl_init 0 0% 83.45% 42ms 0.53% _dl_start_user 0 0% 83.45% 42ms 0.53% call_init (inline) 0 0% 83.45% 41ms 0.52% AbstractCentreBasedCellPopulation::CreateCellPair 20ms 0.25% 83.70% 41ms 0.52% AbstractTetrahedralMesh::GetElement 2ms 0.025% 83.73% 41ms 0.52% Element::~Element 41ms 0.52% 84.25% 41ms 0.52% boost::numeric::ublas::c_vector::operator() (inline) 2ms 0.025% 84.28% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 8ms 0.1% 84.38% 40ms 0.51% Inverse 0 0% 84.38% 40ms 0.51% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.38% 40ms 0.51% std::_Rb_tree::_M_emplace_hint_unique