File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6704ms, 83.84% of 7996ms total Dropped 569 nodes (cum <= 39.98ms) flat flat% sum% cum cum% 0 0% 0% 7959ms 99.54% __libc_start_call_main 0 0% 0% 7959ms 99.54% __libc_start_main_impl 0 0% 0% 7959ms 99.54% _start 0 0% 0% 7941ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7941ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7941ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7941ms 99.31% main 0 0% 0% 7898ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7898ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7898ms 98.77% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7895ms 98.74% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3435ms 42.96% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2970ms 37.14% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 2970ms 37.14% MeshBasedCellPopulation::Update 2ms 0.025% 0.063% 1482ms 18.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.075% 1477ms 18.47% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.075% 1428ms 17.86% MutableMesh::ReMesh 0 0% 0.075% 1340ms 16.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.16% 0.24% 1289ms 16.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.49% 1289ms 16.12% MeshBasedCellPopulation::SpringIterator::operator++ 133ms 1.66% 2.15% 1032ms 12.91% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.038% 2.19% 979ms 12.24% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.1% 2.29% 937ms 11.72% CellPopulationElementWriter::Visit 417ms 5.22% 7.50% 932ms 11.66% std::_Rb_tree::_M_lower_bound (inline) 265ms 3.31% 10.82% 911ms 11.39% __dynamic_cast 6ms 0.075% 10.89% 904ms 11.31% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.013% 10.91% 896ms 11.21% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.025% 10.93% 822ms 10.28% MeshBasedCellPopulation::AcceptCellWriter 43ms 0.54% 11.47% 795ms 9.94% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 35ms 0.44% 11.91% 754ms 9.43% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 11.92% 713ms 8.92% AbstractCellProperty::IsSubType (inline) 9ms 0.11% 12.03% 690ms 8.63% TetrahedralMesh::ImportFromMesher 31ms 0.39% 12.42% 590ms 7.38% operator new 0 0% 12.42% 583ms 7.29% triangulate 51ms 0.64% 13.06% 582ms 7.28% std::map::operator[] (partial-inline) 2ms 0.025% 13.08% 554ms 6.93% std::ostream::operator<< (inline) 3ms 0.038% 13.12% 550ms 6.88% Cell::GetCellProliferativeType 199ms 2.49% 15.61% 550ms 6.88% __GI___libc_malloc 86ms 1.08% 16.68% 550ms 6.88% std::ostream::_M_insert 547ms 6.84% 23.52% 547ms 6.84% __strcmp_avx2 7ms 0.088% 23.61% 537ms 6.72% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.61% 520ms 6.50% delaunay 28ms 0.35% 23.96% 520ms 6.50% std::__new_allocator::allocate (inline) 0 0% 23.96% 517ms 6.47% std::allocator_traits::allocate (inline) 0 0% 23.96% 515ms 6.44% divconqdelaunay 10ms 0.13% 24.09% 509ms 6.37% std::set::insert (inline) 11ms 0.14% 24.22% 499ms 6.24% std::_Rb_tree::_M_insert_unique 26ms 0.33% 24.55% 491ms 6.14% std::_Rb_tree::find (inline) 0 0% 24.55% 488ms 6.10% std::_Rb_tree::lower_bound (inline) 0 0% 24.55% 488ms 6.10% std::map::lower_bound (inline) 4ms 0.05% 24.60% 456ms 5.70% AbstractCellBasedSimulation::DoCellBirth 201ms 2.51% 27.11% 449ms 5.62% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.11% 441ms 5.52% std::set::count (inline) 0 0% 27.11% 430ms 5.38% std::_Rb_tree::_M_create_node (inline) 0 0% 27.11% 418ms 5.23% std::_Rb_tree::_Alloc_node::operator() (inline) 39ms 0.49% 27.60% 409ms 5.12% std::_Rb_tree::~_Rb_tree (inline) 23ms 0.29% 27.89% 398ms 4.98% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.89% 386ms 4.83% std::_Rb_tree::_M_get_node (inline) 0 0% 27.89% 385ms 4.81% std::set::~set (inline) 6ms 0.075% 27.96% 371ms 4.64% std::set::set (inline) 83ms 1.04% 29.00% 363ms 4.54% std::_Rb_tree::_M_erase 1ms 0.013% 29.01% 362ms 4.53% Cell::GetMutationState 8ms 0.1% 29.11% 352ms 4.40% std::less::operator() (inline) 344ms 4.30% 33.42% 344ms 4.30% std::operator< (inline) 12ms 0.15% 33.57% 341ms 4.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 28ms 0.35% 33.92% 336ms 4.20% std::_Rb_tree::_M_copy (inline) 0 0% 33.92% 333ms 4.16% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.92% 332ms 4.15% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.92% 328ms 4.10% OutputFileHandler::OpenOutputFile 1ms 0.013% 33.93% 315ms 3.94% NodeLocationWriter::Visit 89ms 1.11% 35.04% 312ms 3.90% __GI___libc_free 310ms 3.88% 38.92% 310ms 3.88% std::_Rb_tree::_S_right (inline) 3ms 0.038% 38.96% 306ms 3.83% MeshBasedCellPopulation::GetDampingConstant 6ms 0.075% 39.03% 303ms 3.79% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.1% 39.13% 302ms 3.78% divconqrecurse 7ms 0.088% 39.22% 299ms 3.74% Cell::ReadyToDivide 26ms 0.33% 39.54% 298ms 3.73% std::_Rb_tree::_M_insert_ (inline) 75ms 0.94% 40.48% 292ms 3.65% std::_Rb_tree::_M_clone_node (inline) 73ms 0.91% 41.40% 289ms 3.61% mergehulls 11ms 0.14% 41.53% 272ms 3.40% std::__new_allocator::deallocate (inline) 25ms 0.31% 41.85% 271ms 3.39% std::num_put::_M_insert_float 4ms 0.05% 41.90% 268ms 3.35% CellPropertyCollection::HasProperty 0 0% 41.90% 266ms 3.33% Cell::HasCellProperty (inline) 5ms 0.063% 41.96% 265ms 3.31% Element::Element 0 0% 41.96% 265ms 3.31% std::allocator_traits::deallocate (inline) 0 0% 41.96% 262ms 3.28% std::_Rb_tree::_M_drop_node (inline) 2ms 0.025% 41.98% 260ms 3.25% AbstractCellProperty::IsType (inline) 166ms 2.08% 44.06% 254ms 3.18% _int_malloc 1ms 0.013% 44.07% 251ms 3.14% CellProliferativeTypesWriter::VisitCell 188ms 2.35% 46.42% 222ms 2.78% _int_free 0 0% 46.42% 219ms 2.74% std::_Rb_tree::_M_put_node (inline) 6ms 0.075% 46.50% 218ms 2.73% std::__cxx11::collate::do_transform 9ms 0.11% 46.61% 212ms 2.65% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 46.62% 203ms 2.54% ___vsnprintf 50ms 0.63% 47.25% 202ms 2.53% AbstractCellProperty::IsSame 0 0% 47.25% 202ms 2.53% __vsnprintf_internal (inline) 4ms 0.05% 47.30% 198ms 2.48% AbstractPhaseBasedCellCycleModel::ReadyToDivide 20ms 0.25% 47.55% 197ms 2.46% __printf_buffer 9ms 0.11% 47.66% 193ms 2.41% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.063% 47.72% 191ms 2.39% TetrahedralMesh::Clear 51ms 0.64% 48.36% 190ms 2.38% std::_Rb_tree::_M_get_insert_unique_pos (inline) 39ms 0.49% 48.85% 186ms 2.33% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 48.86% 173ms 2.16% OutputFileHandler::CommonConstructor 0 0% 48.86% 173ms 2.16% OutputFileHandler::OutputFileHandler 4ms 0.05% 48.91% 168ms 2.10% __printf_fp_l_buffer 0 0% 48.91% 168ms 2.10% __printf_fp_spec (inline) 13ms 0.16% 49.07% 164ms 2.05% AbstractTetrahedralElement::CalculateJacobian 0 0% 49.07% 163ms 2.04% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 49.07% 163ms 2.04% std::basic_ofstream::basic_ofstream (inline) 72ms 0.9% 49.97% 157ms 1.96% __printf_fp_buffer_1 1ms 0.013% 49.99% 156ms 1.95% std::basic_ofstream::open (inline) 5ms 0.063% 50.05% 154ms 1.93% Element::RegisterWithNodes (inline) 1ms 0.013% 50.06% 154ms 1.93% std::basic_filebuf::open 39ms 0.49% 50.55% 152ms 1.90% std::type_info::operator== (inline) 4ms 0.05% 50.60% 148ms 1.85% Node::AddElement 12ms 0.15% 50.75% 142ms 1.78% MeshBasedCellPopulation::SpringIterator::SpringIterator 106ms 1.33% 52.08% 141ms 1.76% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 52.08% 136ms 1.70% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 52.09% 135ms 1.69% TetrahedralMesh::RefreshJacobianCachedData 52ms 0.65% 52.74% 135ms 1.69% std::__ostream_insert 1ms 0.013% 52.75% 135ms 1.69% std::filesystem::permissions 3ms 0.038% 52.79% 133ms 1.66% alternateaxes 132ms 1.65% 54.44% 132ms 1.65% __GI_fchmodat 56ms 0.7% 55.14% 132ms 1.65% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 55.15% 132ms 1.65% std::_Vector_base::_M_allocate (inline) 0 0% 55.15% 131ms 1.64% AbstractCellBasedWriter::CloseFile 0 0% 55.15% 131ms 1.64% AbstractCellPopulation::CloseRoundRobinWritersFiles 131ms 1.64% 56.79% 131ms 1.64% incircle 1ms 0.013% 56.80% 131ms 1.64% std::basic_filebuf::close 0 0% 56.80% 131ms 1.64% std::basic_ofstream::close (inline) 121ms 1.51% 58.32% 130ms 1.63% vertexmedian 3ms 0.038% 58.35% 129ms 1.61% boost::numeric::ublas::vector_assign (inline) 17ms 0.21% 58.57% 128ms 1.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 32ms 0.4% 58.97% 126ms 1.58% std::num_put::_M_insert_int 0 0% 58.97% 125ms 1.56% AbstractCellPopulation::Iterator::operator++ (inline) 6ms 0.075% 59.04% 124ms 1.55% AbstractTetrahedralElement::CalculateInverseJacobian 25ms 0.31% 59.35% 120ms 1.50% AbstractTetrahedralElement::RefreshJacobian 3ms 0.038% 59.39% 117ms 1.46% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.038% 59.43% 117ms 1.46% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 59.47% 115ms 1.44% Node::~Node 2ms 0.025% 59.49% 115ms 1.44% std::vector::push_back (inline) 0 0% 59.49% 114ms 1.43% _IO_new_fopen 0 0% 59.49% 114ms 1.43% __fopen_internal (inline) 0 0% 59.49% 113ms 1.41% std::__basic_file::open 0 0% 59.49% 112ms 1.40% _IO_new_file_fopen 1ms 0.013% 59.50% 111ms 1.39% __GI__IO_file_open 12ms 0.15% 59.65% 110ms 1.38% std::vector::_M_realloc_insert 0 0% 59.65% 107ms 1.34% std::operator<< (inline) 11ms 0.14% 59.79% 106ms 1.33% boost::detail::shared_count::~shared_count (inline) 0 0% 59.79% 106ms 1.33% boost::shared_ptr::~shared_ptr (inline) 12ms 0.15% 59.94% 100ms 1.25% std::_Rb_tree_const_iterator::operator++ (inline) 98ms 1.23% 61.17% 98ms 1.23% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 97ms 1.21% 62.38% 97ms 1.21% [libchaste_cell_based.so] 94ms 1.18% 63.56% 94ms 1.18% __GI___libc_write 0 0% 63.56% 94ms 1.18% std::__basic_file::xsputn 0 0% 63.56% 94ms 1.18% std::basic_filebuf::_M_convert_to_external 0 0% 63.56% 94ms 1.18% std::basic_filebuf::_M_terminate_output 0 0% 63.56% 94ms 1.18% std::basic_filebuf::overflow 6ms 0.075% 63.63% 93ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 63.66% 93ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 91ms 1.14% 64.79% 92ms 1.15% __libc_open64 1ms 0.013% 64.81% 91ms 1.14% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 91ms 1.14% 65.95% 91ms 1.14% std::_Rb_tree_increment 87ms 1.09% 67.03% 90ms 1.13% boost::detail::sp_counted_base::release 1ms 0.013% 67.05% 90ms 1.13% std::filesystem::create_directory 26ms 0.33% 67.37% 89ms 1.11% boost::numeric::ublas::indexing_vector_assign 0 0% 67.37% 87ms 1.09% tcache_get (inline) 87ms 1.09% 68.46% 87ms 1.09% tcache_get_n (inline) 3ms 0.038% 68.50% 85ms 1.06% std::filesystem::status 71ms 0.89% 69.38% 84ms 1.05% AbstractElement::GetNodeGlobalIndex 84ms 1.05% 70.44% 84ms 1.05% std::_Rb_tree_insert_and_rebalance 81ms 1.01% 71.45% 81ms 1.01% __GI___fstatat64 31ms 0.39% 71.84% 80ms 1.00% AbstractElement::GetNodeLocation 7ms 0.088% 71.92% 80ms 1.00% TetrahedralMesh::EdgeIterator::GetNodeB 80ms 1.00% 72.92% 80ms 1.00% counterclockwise 44ms 0.55% 73.47% 78ms 0.98% std::basic_filebuf::xsputn 1ms 0.013% 73.49% 77ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 56ms 0.7% 74.19% 77ms 0.96% malloc_consolidate 73ms 0.91% 75.10% 76ms 0.95% boost::detail::shared_count::shared_count (inline) 0 0% 75.10% 75ms 0.94% Cell::GetCellId 5ms 0.063% 75.16% 73ms 0.91% CellPropertyCollection::AddProperty 4ms 0.05% 75.21% 70ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 63ms 0.79% 76.00% 69ms 0.86% vertexsort 67ms 0.84% 76.84% 67ms 0.84% std::vector::size (inline) 48ms 0.6% 77.44% 64ms 0.8% std::num_put::do_put 62ms 0.78% 78.21% 62ms 0.78% Node::GetIndex 35ms 0.44% 78.65% 60ms 0.75% std::basic_streambuf::xsputn 1ms 0.013% 78.66% 57ms 0.71% BoundaryNodeWriter::Visit 20ms 0.25% 78.91% 53ms 0.66% AbstractTetrahedralMesh::GetElement 28ms 0.35% 79.26% 53ms 0.66% boost::numeric::ublas::c_matrix::operator() (partial-inline) 28ms 0.35% 79.61% 53ms 0.66% hack_digit 51ms 0.64% 80.25% 51ms 0.64% [libstdc++.so.6.0.33] 24ms 0.3% 80.55% 50ms 0.63% AbstractCellCycleModel::GetAge 0 0% 80.55% 50ms 0.63% std::vector::vector (inline) 1ms 0.013% 80.57% 49ms 0.61% Node::ConstructNodeAttributes (inline) 49ms 0.61% 81.18% 49ms 0.61% [libchaste_mesh.so] 0 0% 81.18% 48ms 0.6% Node::ClearAppliedForce 0 0% 81.18% 48ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 81.18% 47ms 0.59% CellPropertyCollection::~CellPropertyCollection (inline) 47ms 0.59% 81.77% 47ms 0.59% __memcpy_avx_unaligned_erms 2ms 0.025% 81.79% 47ms 0.59% std::__new_allocator::construct (inline) 0 0% 81.79% 47ms 0.59% std::allocator_traits::construct (inline) 46ms 0.58% 82.37% 46ms 0.58% std::ostream::sentry::sentry 15ms 0.19% 82.55% 45ms 0.56% Determinant (inline) 0 0% 82.55% 45ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.038% 82.59% 45ms 0.56% std::_Vector_base::_M_deallocate (inline) 0 0% 82.59% 44ms 0.55% std::_Rb_tree::_M_construct_node (inline) 43ms 0.54% 83.13% 43ms 0.54% Node::rGetLocation 0 0% 83.13% 43ms 0.54% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.025% 83.15% 43ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.013% 83.17% 43ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 83.17% 43ms 0.54% std::__new_allocator::destroy (inline) 0 0% 83.17% 43ms 0.54% std::allocator_traits::destroy (inline) 2ms 0.025% 83.19% 42ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 42ms 0.53% 83.72% 42ms 0.53% __GI___mkdir 0 0% 83.72% 42ms 0.53% std::map::find (inline) 1ms 0.013% 83.73% 40ms 0.5% AbstractCentreBasedCellPopulation::IsMarkedSpring 8ms 0.1% 83.83% 40ms 0.5% Inverse 0 0% 83.83% 40ms 0.5% _dl_init 0 0% 83.83% 40ms 0.5% call_init (inline) 1ms 0.013% 83.84% 40ms 0.5% std::basic_filebuf::_M_allocate_internal_buffer