File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5923ms, 81.76% of 7244ms total Dropped 604 nodes (cum <= 36.22ms) flat flat% sum% cum cum% 0 0% 0% 7206ms 99.48% __libc_start_call_main 0 0% 0% 7206ms 99.48% __libc_start_main_impl 0 0% 0% 7206ms 99.48% _start 0 0% 0% 7190ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7190ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7190ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7190ms 99.25% main 0 0% 0% 7147ms 98.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7147ms 98.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7147ms 98.66% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.014% 0.014% 7144ms 98.62% AbstractCellBasedSimulation::Solve 0 0% 0.014% 2897ms 39.99% AbstractCellPopulation::WriteResultsToFiles 1ms 0.014% 0.028% 2749ms 37.95% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.041% 0.069% 2284ms 31.53% MeshBasedCellPopulation::Update 1ms 0.014% 0.083% 1494ms 20.62% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.014% 0.097% 1371ms 18.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.097% 1357ms 18.73% MutableMesh::ReMesh 4ms 0.055% 0.15% 1320ms 18.22% AbstractNumericalMethod::ComputeForcesIncludingDamping 4ms 0.055% 0.21% 936ms 12.92% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.014% 0.22% 913ms 12.60% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.15% 0.37% 902ms 12.45% CellPopulationElementWriter::Visit 10ms 0.14% 0.51% 901ms 12.44% CellPropertyCollection::GetPropertiesType (inline) 235ms 3.24% 3.75% 867ms 11.97% __dynamic_cast 4ms 0.055% 3.81% 863ms 11.91% MeshBasedCellPopulation::UpdateNodePairs 44ms 0.61% 4.42% 817ms 11.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 28ms 0.39% 4.80% 779ms 10.75% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.069% 4.87% 764ms 10.55% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.11% 4.98% 700ms 9.66% TetrahedralMesh::ImportFromMesher 8ms 0.11% 5.09% 667ms 9.21% AbstractCellProperty::IsSubType (inline) 61ms 0.84% 5.94% 620ms 8.56% std::map::operator[] (partial-inline) 1ms 0.014% 5.95% 612ms 8.45% std::ostream::operator<< (inline) 82ms 1.13% 7.08% 610ms 8.42% std::ostream::_M_insert 17ms 0.23% 7.32% 607ms 8.38% MeshBasedCellPopulation::SpringIterator::operator++ 251ms 3.46% 10.78% 536ms 7.40% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.055% 10.84% 525ms 7.25% Cell::GetCellProliferativeType 36ms 0.5% 11.33% 504ms 6.96% operator new 499ms 6.89% 18.22% 499ms 6.89% __strcmp_avx2 0 0% 18.22% 498ms 6.87% std::_Rb_tree::lower_bound (inline) 0 0% 18.22% 498ms 6.87% std::map::lower_bound (inline) 2ms 0.028% 18.25% 470ms 6.49% triangulate 162ms 2.24% 20.49% 468ms 6.46% __GI___libc_malloc 1ms 0.014% 20.50% 455ms 6.28% AbstractCellBasedSimulation::DoCellBirth 4ms 0.055% 20.55% 449ms 6.20% LegacyCellProliferativeTypesWriter::VisitCell 211ms 2.91% 23.47% 449ms 6.20% __cxxabiv1::__si_class_type_info::__do_dyncast 37ms 0.51% 23.98% 447ms 6.17% std::__new_allocator::allocate (inline) 0 0% 23.98% 444ms 6.13% std::allocator_traits::allocate (inline) 0 0% 23.98% 405ms 5.59% delaunay 0 0% 23.98% 404ms 5.58% divconqdelaunay 5ms 0.069% 24.05% 388ms 5.36% Cell::GetMutationState 4ms 0.055% 24.10% 385ms 5.31% NodeLocationWriter::Visit 59ms 0.81% 24.92% 360ms 4.97% TetrahedralMesh::EdgeIterator::operator++ 36ms 0.5% 25.41% 358ms 4.94% std::_Rb_tree::~_Rb_tree (inline) 21ms 0.29% 25.70% 341ms 4.71% std::num_put::_M_insert_float 0 0% 25.70% 336ms 4.64% std::set::~set (inline) 1ms 0.014% 25.72% 326ms 4.50% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 25.72% 326ms 4.50% MeshBasedCellPopulation::GetDampingConstant 81ms 1.12% 26.84% 322ms 4.45% std::_Rb_tree::_M_erase 0 0% 26.84% 314ms 4.33% std::_Rb_tree::_M_create_node (inline) 104ms 1.44% 28.27% 310ms 4.28% __GI___libc_free 6ms 0.083% 28.35% 300ms 4.14% Cell::ReadyToDivide 300ms 4.14% 32.50% 300ms 4.14% std::_Rb_tree::_S_right (inline) 0 0% 32.50% 290ms 4.00% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 32.50% 288ms 3.98% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.055% 32.55% 288ms 3.98% Element::Element 0 0% 32.55% 286ms 3.95% OutputFileHandler::OpenOutputFile 5ms 0.069% 32.62% 282ms 3.89% std::set::set (inline) 9ms 0.12% 32.74% 281ms 3.88% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.055% 32.80% 277ms 3.82% CellProliferativeTypesWriter::VisitCell 0 0% 32.80% 277ms 3.82% std::_Rb_tree::_M_get_node (inline) 0 0% 32.80% 276ms 3.81% std::_Rb_tree::_Alloc_node::operator() (inline) 24ms 0.33% 33.13% 276ms 3.81% std::_Rb_tree::_Rb_tree 6ms 0.083% 33.21% 263ms 3.63% std::__new_allocator::deallocate (inline) 0 0% 33.21% 261ms 3.60% std::allocator_traits::deallocate (inline) 3ms 0.041% 33.26% 257ms 3.55% std::__cxx11::collate::do_transform 1ms 0.014% 33.27% 244ms 3.37% ___vsnprintf 0 0% 33.27% 243ms 3.35% __vsnprintf_internal (inline) 9ms 0.12% 33.39% 240ms 3.31% divconqrecurse 36ms 0.5% 33.89% 239ms 3.30% __printf_buffer 168ms 2.32% 36.21% 234ms 3.23% _int_malloc 24ms 0.33% 36.54% 234ms 3.23% std::_Rb_tree::_M_copy (inline) 2ms 0.028% 36.57% 225ms 3.11% std::_Rb_tree::_M_insert_unique (inline) 0 0% 36.57% 225ms 3.11% std::set::insert (inline) 0 0% 36.57% 224ms 3.09% std::_Rb_tree::_M_drop_node (inline) 75ms 1.04% 37.60% 221ms 3.05% mergehulls 15ms 0.21% 37.81% 213ms 2.94% MeshBasedCellPopulation::SpringsEnd 2ms 0.028% 37.84% 209ms 2.89% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.041% 37.88% 205ms 2.83% AbstractCellProperty::IsType (inline) 163ms 2.25% 40.13% 205ms 2.83% _int_free 13ms 0.18% 40.31% 204ms 2.82% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.12% 40.43% 204ms 2.82% CellPropertyCollection::HasProperty 67ms 0.92% 41.36% 203ms 2.80% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.36% 200ms 2.76% Cell::HasCellProperty (inline) 14ms 0.19% 41.55% 184ms 2.54% AbstractTetrahedralElement::CalculateJacobian 5ms 0.069% 41.62% 180ms 2.48% __printf_fp_l_buffer 0 0% 41.62% 180ms 2.48% __printf_fp_spec (inline) 13ms 0.18% 41.80% 179ms 2.47% std::_Rb_tree::_M_insert_ (inline) 16ms 0.22% 42.02% 178ms 2.46% TetrahedralMesh::Clear 0 0% 42.02% 176ms 2.43% std::_Rb_tree::_M_put_node (inline) 2ms 0.028% 42.05% 173ms 2.39% Element::RegisterWithNodes (inline) 87ms 1.20% 43.25% 171ms 2.36% __printf_fp_buffer_1 0 0% 43.25% 168ms 2.32% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.028% 43.28% 165ms 2.28% Node::AddElement 2ms 0.028% 43.30% 161ms 2.22% AbstractCellBasedWriter::CloseFile 0 0% 43.30% 161ms 2.22% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.014% 43.32% 159ms 2.19% std::basic_filebuf::close 0 0% 43.32% 159ms 2.19% std::basic_ofstream::close (inline) 35ms 0.48% 43.80% 156ms 2.15% AbstractCellProperty::IsSame 6ms 0.083% 43.88% 153ms 2.11% AbstractTetrahedralElement::CalculateInverseJacobian 32ms 0.44% 44.33% 153ms 2.11% TetrahedralMesh::EdgesEnd (partial-inline) 44ms 0.61% 44.93% 143ms 1.97% MeshBasedCellPopulation::SpringIterator::SpringIterator 20ms 0.28% 45.21% 137ms 1.89% AbstractTetrahedralElement::RefreshJacobian 4ms 0.055% 45.27% 136ms 1.88% boost::numeric::ublas::vector_assign (inline) 17ms 0.23% 45.50% 136ms 1.88% std::_Rb_tree_const_iterator::operator++ (inline) 57ms 0.79% 46.29% 135ms 1.86% std::__ostream_insert 0 0% 46.29% 134ms 1.85% OutputFileHandler::CommonConstructor 0 0% 46.29% 134ms 1.85% OutputFileHandler::OutputFileHandler 132ms 1.82% 48.11% 132ms 1.82% std::_Rb_tree_increment 0 0% 48.11% 130ms 1.79% std::basic_ofstream::basic_ofstream (inline) 18ms 0.25% 48.36% 127ms 1.75% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.014% 48.37% 127ms 1.75% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.014% 48.38% 126ms 1.74% std::basic_filebuf::_M_terminate_output 2ms 0.028% 48.41% 126ms 1.74% std::basic_filebuf::overflow 3ms 0.041% 48.45% 125ms 1.73% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 48.45% 124ms 1.71% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 48.45% 124ms 1.71% std::__basic_file::xsputn 0 0% 48.45% 124ms 1.71% std::basic_filebuf::_M_convert_to_external 0 0% 48.45% 124ms 1.71% std::basic_ofstream::open (inline) 123ms 1.70% 50.15% 123ms 1.70% __GI___libc_write 0 0% 50.15% 123ms 1.70% std::basic_filebuf::open 31ms 0.43% 50.58% 122ms 1.68% std::num_put::_M_insert_int 25ms 0.35% 50.92% 121ms 1.67% std::type_info::operator== (inline) 2ms 0.028% 50.95% 120ms 1.66% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 50.95% 120ms 1.66% FilesystemPermissions::SetFilePermissions (inline) 0 0% 50.95% 120ms 1.66% std::filesystem::permissions 51ms 0.7% 51.66% 119ms 1.64% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 118ms 1.63% 53.29% 118ms 1.63% __GI_fchmodat 54ms 0.75% 54.03% 118ms 1.63% boost::shared_ptr::shared_ptr (inline) 5ms 0.069% 54.10% 114ms 1.57% std::vector::push_back (inline) 2ms 0.028% 54.13% 111ms 1.53% alternateaxes 0 0% 54.13% 111ms 1.53% std::_Hashtable::count (inline) 1ms 0.014% 54.14% 111ms 1.53% std::_Hashtable::find (inline) 0 0% 54.14% 111ms 1.53% std::unordered_set::count (inline) 0 0% 54.14% 108ms 1.49% std::_Hashtable::_M_insert (inline) 5ms 0.069% 54.21% 108ms 1.49% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 54.21% 108ms 1.49% std::__detail::_Insert_base::insert (inline) 0 0% 54.21% 108ms 1.49% std::unordered_set::insert (inline) 96ms 1.33% 55.54% 108ms 1.49% vertexmedian 1ms 0.014% 55.55% 107ms 1.48% std::operator<< (inline) 7ms 0.097% 55.65% 106ms 1.46% std::vector::_M_realloc_insert 14ms 0.19% 55.84% 105ms 1.45% boost::detail::shared_count::~shared_count (inline) 0 0% 55.84% 105ms 1.45% boost::shared_ptr::~shared_ptr (inline) 27ms 0.37% 56.21% 103ms 1.42% boost::numeric::ublas::indexing_vector_assign 7ms 0.097% 56.31% 103ms 1.42% std::_Hashtable::_M_insert_unique 43ms 0.59% 56.90% 102ms 1.41% AbstractElement::GetNodeLocation 6ms 0.083% 56.99% 97ms 1.34% Node::~Node 0 0% 56.99% 97ms 1.34% std::__basic_file::open 1ms 0.014% 57.00% 96ms 1.33% _IO_new_file_fopen 0 0% 57.00% 96ms 1.33% _IO_new_fopen 0 0% 57.00% 96ms 1.33% __fopen_internal (inline) 0 0% 57.00% 95ms 1.31% __GI__IO_file_open 0 0% 57.00% 95ms 1.31% std::_Vector_base::_M_allocate (inline) 3ms 0.041% 57.04% 93ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 93ms 1.28% 58.32% 93ms 1.28% incircle 0 0% 58.32% 90ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 58.32% 89ms 1.23% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 58.32% 89ms 1.23% std::_Hashtable::~_Hashtable (inline) 0 0% 58.32% 89ms 1.23% std::unordered_set::~unordered_set (inline) 88ms 1.21% 59.54% 88ms 1.21% [libchaste_cell_based.so] 87ms 1.20% 60.74% 87ms 1.20% __libc_open64 86ms 1.19% 61.93% 86ms 1.19% boost::detail::sp_counted_base::release 14ms 0.19% 62.12% 83ms 1.15% TetrahedralMesh::EdgeIterator::GetNodeB 43ms 0.59% 62.71% 83ms 1.15% std::_Hashtable::_M_find_before_node (inline) 0 0% 62.71% 83ms 1.15% std::_Hashtable::_M_find_node (inline) 46ms 0.64% 63.35% 83ms 1.15% std::basic_filebuf::xsputn 58ms 0.8% 64.15% 80ms 1.10% std::basic_streambuf::xsputn 79ms 1.09% 65.24% 79ms 1.09% std::vector::size (inline) 77ms 1.06% 66.30% 77ms 1.06% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.041% 66.34% 75ms 1.04% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 1.04% 67.38% 75ms 1.04% __memcpy_avx_unaligned_erms 3ms 0.041% 67.42% 72ms 0.99% Cell::GetCellId 72ms 0.99% 68.42% 72ms 0.99% __GI___fstatat64 0 0% 68.42% 71ms 0.98% std::filesystem::status 70ms 0.97% 69.38% 70ms 0.97% [libchaste_mesh.so] 2ms 0.028% 69.41% 68ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeA 66ms 0.91% 70.32% 66ms 0.91% boost::shared_ptr::operator-> (inline) 4ms 0.055% 70.38% 65ms 0.9% CellPropertyCollection::AddProperty 0 0% 70.38% 65ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.38% 65ms 0.9% std::filesystem::create_directory 0 0% 70.38% 64ms 0.88% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 63ms 0.87% 71.25% 64ms 0.88% boost::detail::shared_count::shared_count (inline) 7ms 0.097% 71.34% 64ms 0.88% std::_Hashtable::clear (inline) 0 0% 71.34% 64ms 0.88% std::__detail::_AllocNode::operator() (inline) 0 0% 71.34% 64ms 0.88% std::__detail::_Hashtable_alloc::_M_allocate_node (inline) 0 0% 71.34% 63ms 0.87% std::__detail::_NodeBuilder::_S_build (inline) 0 0% 71.34% 63ms 0.87% tcache_get (inline) 63ms 0.87% 72.21% 63ms 0.87% tcache_get_n (inline) 44ms 0.61% 72.82% 62ms 0.86% AbstractElement::GetNodeGlobalIndex 0 0% 72.82% 62ms 0.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.82% 62ms 0.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.055% 72.87% 61ms 0.84% Node::ConstructNodeAttributes (inline) 4ms 0.055% 72.93% 61ms 0.84% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.93% 57ms 0.79% Node::ClearAppliedForce 36ms 0.5% 73.43% 57ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 37ms 0.51% 73.94% 57ms 0.79% malloc_consolidate 56ms 0.77% 74.71% 56ms 0.77% Node::GetIndex 42ms 0.58% 75.29% 55ms 0.76% std::num_put::do_put 17ms 0.23% 75.52% 54ms 0.75% Determinant (inline) 54ms 0.75% 76.27% 54ms 0.75% counterclockwise 0 0% 76.27% 53ms 0.73% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 51ms 0.7% 76.97% 51ms 0.7% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 76.97% 48ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 6ms 0.083% 77.06% 48ms 0.66% std::_Rb_tree::find (inline) 0 0% 77.06% 48ms 0.66% std::__new_allocator::destroy (inline) 0 0% 77.06% 48ms 0.66% std::allocator_traits::destroy (inline) 39ms 0.54% 77.60% 48ms 0.66% vertexsort 1ms 0.014% 77.61% 47ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 77.61% 47ms 0.65% BoundaryNodeWriter::Visit 46ms 0.64% 78.24% 46ms 0.64% Node::IsDeleted 3ms 0.041% 78.29% 46ms 0.64% std::_Vector_base::_M_deallocate (inline) 0 0% 78.29% 45ms 0.62% boost::numeric::ublas::norm_2 (inline) 13ms 0.18% 78.46% 45ms 0.62% boost::numeric::ublas::vector_norm_2::apply (inline) 45ms 0.62% 79.09% 45ms 0.62% std::ostream::sentry::sentry 27ms 0.37% 79.46% 44ms 0.61% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 79.46% 43ms 0.59% CellPropertyCollection::~CellPropertyCollection (inline) 3ms 0.041% 79.50% 43ms 0.59% Element::~Element 1ms 0.014% 79.51% 42ms 0.58% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 18ms 0.25% 79.76% 42ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 24ms 0.33% 80.09% 42ms 0.58% hack_digit 5ms 0.069% 80.16% 42ms 0.58% std::__copy_move::__copy_m (inline) 0 0% 80.16% 42ms 0.58% std::__copy_move_a (inline) 0 0% 80.16% 42ms 0.58% std::__copy_move_a1 (inline) 0 0% 80.16% 42ms 0.58% std::__copy_move_a2 (inline) 0 0% 80.16% 42ms 0.58% std::copy (inline) 41ms 0.57% 80.73% 41ms 0.57% Node::rGetLocation 24ms 0.33% 81.06% 40ms 0.55% AbstractCellCycleModel::GetAge 0 0% 81.06% 39ms 0.54% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 39ms 0.54% 81.60% 39ms 0.54% [libstdc++.so.6.0.33] 0 0% 81.60% 38ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 81.60% 38ms 0.52% _dl_init 0 0% 81.60% 38ms 0.52% _dl_start_user 0 0% 81.60% 38ms 0.52% call_init (inline) 0 0% 81.60% 38ms 0.52% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 81.60% 38ms 0.52% std::__new_allocator::construct (inline) 0 0% 81.60% 38ms 0.52% std::allocator_traits::construct (inline) 0 0% 81.60% 38ms 0.52% std::map::find (inline) 0 0% 81.60% 37ms 0.51% CxxTest::RealWorldDescription::setUp 6ms 0.083% 81.68% 37ms 0.51% Inverse 6ms 0.083% 81.76% 37ms 0.51% NodeAttributes::NodeAttributes 0 0% 81.76% 37ms 0.51% PetscInitialize 0 0% 81.76% 37ms 0.51% PetscSetup::setUpWorld 0 0% 81.76% 37ms 0.51% PetscSetupUtils::CommonSetup 0 0% 81.76% 37ms 0.51% PetscSetupUtils::InitialisePetsc 0 0% 81.76% 37ms 0.51% std::_Rb_tree::_M_construct_node (inline)