File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6485ms, 84.44% of 7680ms total Dropped 578 nodes (cum <= 38.40ms) flat flat% sum% cum cum% 0 0% 0% 7644ms 99.53% __libc_start_call_main 0 0% 0% 7644ms 99.53% __libc_start_main_impl 0 0% 0% 7644ms 99.53% _start 0 0% 0% 7629ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7629ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7629ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7629ms 99.34% main 0 0% 0% 7593ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7593ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7593ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7591ms 98.84% AbstractCellBasedSimulation::Solve 0 0% 0% 3282ms 42.73% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2915ms 37.96% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 2792ms 36.35% MeshBasedCellPopulation::Update 0 0% 0% 1431ms 18.63% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.013% 1387ms 18.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.026% 1314ms 17.11% MutableMesh::ReMesh 0 0% 0.026% 1231ms 16.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.18% 0.21% 1214ms 15.81% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.065% 0.27% 1177ms 15.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 128ms 1.67% 1.94% 1006ms 13.10% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.039% 1.98% 974ms 12.68% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.14% 2.12% 916ms 11.93% CellPropertyCollection::GetPropertiesType (inline) 445ms 5.79% 7.92% 898ms 11.69% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.091% 8.01% 894ms 11.64% CellPopulationElementWriter::Visit 261ms 3.40% 11.41% 884ms 11.51% __dynamic_cast 3ms 0.039% 11.45% 829ms 10.79% MeshBasedCellPopulation::AcceptCellWriter 0 0% 11.45% 818ms 10.65% AbstractTwoBodyInteractionForce::AddForceContribution 49ms 0.64% 12.08% 734ms 9.56% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 29ms 0.38% 12.46% 704ms 9.17% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.078% 12.54% 704ms 9.17% AbstractCellProperty::IsSubType (inline) 11ms 0.14% 12.68% 687ms 8.95% TetrahedralMesh::ImportFromMesher 0 0% 12.68% 632ms 8.23% std::ostream::operator<< (inline) 85ms 1.11% 13.79% 630ms 8.20% std::ostream::_M_insert 4ms 0.052% 13.84% 561ms 7.30% Cell::GetCellProliferativeType 45ms 0.59% 14.43% 543ms 7.07% operator new 542ms 7.06% 21.48% 542ms 7.06% __strcmp_avx2 72ms 0.94% 22.42% 540ms 7.03% std::map::operator[] (partial-inline) 28ms 0.36% 22.79% 538ms 7.01% std::_Rb_tree::find (inline) 5ms 0.065% 22.85% 527ms 6.86% std::set::insert (inline) 18ms 0.23% 23.09% 522ms 6.80% std::_Rb_tree::_M_insert_unique 33ms 0.43% 23.52% 519ms 6.76% std::__new_allocator::allocate (inline) 0 0% 23.52% 516ms 6.72% std::allocator_traits::allocate (inline) 6ms 0.078% 23.59% 506ms 6.59% LegacyCellProliferativeTypesWriter::VisitCell 179ms 2.33% 25.92% 496ms 6.46% __GI___libc_malloc 0 0% 25.92% 480ms 6.25% std::set::count (inline) 3ms 0.039% 25.96% 477ms 6.21% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 25.98% 473ms 6.16% triangulate 191ms 2.49% 28.46% 453ms 5.90% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.46% 445ms 5.79% std::_Rb_tree::_M_create_node (inline) 31ms 0.4% 28.87% 438ms 5.70% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.87% 422ms 5.49% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.87% 415ms 5.40% std::_Rb_tree::lower_bound (inline) 0 0% 28.87% 415ms 5.40% std::map::lower_bound (inline) 0 0% 28.87% 411ms 5.35% delaunay 0 0% 28.87% 411ms 5.35% std::set::~set (inline) 2ms 0.026% 28.89% 409ms 5.33% divconqdelaunay 87ms 1.13% 30.03% 405ms 5.27% std::_Rb_tree::_M_erase 0 0% 30.03% 404ms 5.26% std::_Rb_tree::_M_get_node (inline) 0 0% 30.03% 379ms 4.93% NodeLocationWriter::Visit 12ms 0.16% 30.18% 361ms 4.70% std::less::operator() (inline) 22ms 0.29% 30.47% 357ms 4.65% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.039% 30.51% 353ms 4.60% Cell::GetMutationState 349ms 4.54% 35.05% 349ms 4.54% std::operator< (inline) 24ms 0.31% 35.36% 341ms 4.44% std::num_put::_M_insert_float 12ms 0.16% 35.52% 333ms 4.34% std::_Rb_tree::_M_insert_ (inline) 5ms 0.065% 35.59% 325ms 4.23% std::set::set (inline) 6ms 0.078% 35.66% 323ms 4.21% Cell::ReadyToDivide 106ms 1.38% 37.04% 311ms 4.05% __GI___libc_free 33ms 0.43% 37.47% 299ms 3.89% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 37.49% 295ms 3.84% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 6ms 0.078% 37.57% 295ms 3.84% Element::Element 0 0% 37.57% 295ms 3.84% std::_Rb_tree::_M_drop_node (inline) 8ms 0.1% 37.67% 293ms 3.82% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 37.67% 292ms 3.80% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.67% 289ms 3.76% OutputFileHandler::OpenOutputFile 8ms 0.1% 37.77% 285ms 3.71% std::__new_allocator::deallocate (inline) 0 0% 37.77% 282ms 3.67% std::allocator_traits::deallocate (inline) 3ms 0.039% 37.81% 277ms 3.61% CellProliferativeTypesWriter::VisitCell 1ms 0.013% 37.83% 273ms 3.55% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.83% 273ms 3.55% MeshBasedCellPopulation::GetDampingConstant 66ms 0.86% 38.68% 261ms 3.40% std::_Rb_tree::_M_clone_node (inline) 3ms 0.039% 38.72% 259ms 3.37% std::__cxx11::collate::do_transform 6ms 0.078% 38.80% 257ms 3.35% divconqrecurse 2ms 0.026% 38.83% 248ms 3.23% AbstractCellProperty::IsType (inline) 2ms 0.026% 38.85% 247ms 3.22% ___vsnprintf 0 0% 38.85% 245ms 3.19% __vsnprintf_internal (inline) 0 0% 38.85% 244ms 3.18% std::_Rb_tree::_M_put_node (inline) 21ms 0.27% 39.13% 241ms 3.14% __printf_buffer 174ms 2.27% 41.39% 241ms 3.14% _int_malloc 75ms 0.98% 42.37% 241ms 3.14% mergehulls 7ms 0.091% 42.46% 235ms 3.06% CellPropertyCollection::HasProperty 233ms 3.03% 45.49% 233ms 3.03% std::_Rb_tree::_S_right (inline) 0 0% 45.49% 232ms 3.02% Cell::HasCellProperty (inline) 7ms 0.091% 45.59% 217ms 2.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 45.73% 207ms 2.70% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 45.83% 207ms 2.70% __printf_fp_l_buffer 0 0% 45.83% 207ms 2.70% __printf_fp_spec (inline) 4ms 0.052% 45.89% 204ms 2.66% Element::RegisterWithNodes (inline) 178ms 2.32% 48.20% 204ms 2.66% _int_free 53ms 0.69% 48.89% 201ms 2.62% AbstractCellProperty::IsSame 6ms 0.078% 48.97% 198ms 2.58% Node::AddElement 13ms 0.17% 49.14% 197ms 2.57% TetrahedralMesh::Clear 106ms 1.38% 50.52% 192ms 2.50% __printf_fp_buffer_1 7ms 0.091% 50.61% 175ms 2.28% MeshBasedCellPopulation::SpringsEnd (inline) 61ms 0.79% 51.41% 172ms 2.24% std::_Rb_tree::_M_get_insert_unique_pos (inline) 67ms 0.87% 52.28% 159ms 2.07% std::__ostream_insert 42ms 0.55% 52.83% 157ms 2.04% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.026% 52.85% 152ms 1.98% OutputFileHandler::CommonConstructor 0 0% 52.85% 152ms 1.98% OutputFileHandler::OutputFileHandler 31ms 0.4% 53.26% 150ms 1.95% std::num_put::_M_insert_int 23ms 0.3% 53.55% 148ms 1.93% std::type_info::operator== (inline) 0 0% 53.55% 146ms 1.90% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 53.55% 143ms 1.86% std::basic_ofstream::basic_ofstream (inline) 15ms 0.2% 53.75% 142ms 1.85% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 53.76% 138ms 1.80% std::basic_filebuf::open 0 0% 53.76% 138ms 1.80% std::basic_ofstream::open (inline) 0 0% 53.76% 134ms 1.74% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.16% 53.92% 130ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 53.92% 128ms 1.67% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.065% 53.98% 128ms 1.67% Node::~Node 1ms 0.013% 54.00% 128ms 1.67% std::basic_filebuf::close 1ms 0.013% 54.01% 128ms 1.67% std::basic_ofstream::close (inline) 0 0% 54.01% 127ms 1.65% AbstractCellBasedWriter::CloseFile 0 0% 54.01% 127ms 1.65% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.052% 54.06% 127ms 1.65% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.21% 54.27% 123ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.039% 54.31% 123ms 1.60% std::operator<< (inline) 10ms 0.13% 54.44% 121ms 1.58% std::_Rb_tree_const_iterator::operator++ (inline) 120ms 1.56% 56.00% 120ms 1.56% std::_Rb_tree_increment 1ms 0.013% 56.02% 118ms 1.54% boost::numeric::ublas::vector_assign (inline) 9ms 0.12% 56.13% 114ms 1.48% boost::detail::shared_count::~shared_count (inline) 10ms 0.13% 56.26% 114ms 1.48% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 56.26% 114ms 1.48% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 56.28% 113ms 1.47% std::_Vector_base::_M_allocate (inline) 2ms 0.026% 56.30% 113ms 1.47% std::__basic_file::open 0 0% 56.30% 110ms 1.43% _IO_new_fopen 0 0% 56.30% 110ms 1.43% __fopen_internal (inline) 0 0% 56.30% 109ms 1.42% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 56.32% 109ms 1.42% std::filesystem::permissions 72ms 0.94% 57.25% 108ms 1.41% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.026% 57.28% 107ms 1.39% _IO_new_file_fopen 107ms 1.39% 58.67% 107ms 1.39% __GI_fchmodat 106ms 1.38% 60.05% 106ms 1.38% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 60.07% 104ms 1.35% __GI__IO_file_open 2ms 0.026% 60.09% 104ms 1.35% std::vector::push_back (inline) 1ms 0.013% 60.10% 103ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 100ms 1.30% 61.41% 102ms 1.33% boost::detail::sp_counted_base::release 48ms 0.62% 62.03% 102ms 1.33% boost::shared_ptr::shared_ptr (inline) 2ms 0.026% 62.06% 99ms 1.29% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 11ms 0.14% 62.20% 98ms 1.28% std::vector::_M_realloc_insert 13ms 0.17% 62.37% 95ms 1.24% AbstractTetrahedralElement::RefreshJacobian 1ms 0.013% 62.38% 94ms 1.22% AbstractTetrahedralElement::AbstractTetrahedralElement 94ms 1.22% 63.61% 94ms 1.22% __libc_open64 0 0% 63.61% 93ms 1.21% AbstractCellPopulation::GetLocationIndexUsingCell 60ms 0.78% 64.39% 93ms 1.21% std::basic_streambuf::xsputn 35ms 0.46% 64.84% 91ms 1.18% boost::numeric::ublas::indexing_vector_assign 91ms 1.18% 66.03% 91ms 1.18% incircle 87ms 1.13% 67.16% 87ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.026% 67.19% 86ms 1.12% alternateaxes 52ms 0.68% 67.86% 85ms 1.11% std::basic_filebuf::xsputn 77ms 1.00% 68.87% 84ms 1.09% vertexmedian 5ms 0.065% 68.93% 82ms 1.07% TetrahedralMesh::EdgeIterator::GetNodeA 81ms 1.05% 69.99% 81ms 1.05% [libchaste_cell_based.so] 0 0% 69.99% 80ms 1.04% std::basic_filebuf::_M_terminate_output 1ms 0.013% 70.00% 79ms 1.03% std::basic_filebuf::overflow 12ms 0.16% 70.16% 78ms 1.02% CellPropertyCollection::AddProperty 0 0% 70.16% 78ms 1.02% std::basic_filebuf::_M_convert_to_external 76ms 0.99% 71.15% 76ms 0.99% __memcpy_avx_unaligned_erms 0 0% 71.15% 76ms 0.99% std::__basic_file::xsputn 61ms 0.79% 71.94% 75ms 0.98% std::num_put::do_put 0 0% 71.94% 74ms 0.96% Cell::GetCellId 74ms 0.96% 72.90% 74ms 0.96% __GI___libc_write 74ms 0.96% 73.87% 74ms 0.96% counterclockwise 0 0% 73.87% 73ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 5ms 0.065% 73.93% 73ms 0.95% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 73.95% 73ms 0.95% std::filesystem::create_directory 34ms 0.44% 74.39% 69ms 0.9% AbstractElement::GetNodeLocation 1ms 0.013% 74.40% 69ms 0.9% std::filesystem::status 68ms 0.89% 75.29% 68ms 0.89% __GI___fstatat64 67ms 0.87% 76.16% 67ms 0.87% std::vector::size (inline) 0 0% 76.16% 64ms 0.83% tcache_get (inline) 64ms 0.83% 76.99% 64ms 0.83% tcache_get_n (inline) 31ms 0.4% 77.40% 63ms 0.82% AbstractTetrahedralMesh::GetElement 60ms 0.78% 78.18% 60ms 0.78% Node::GetIndex 32ms 0.42% 78.59% 58ms 0.76% boost::numeric::ublas::c_matrix::operator() (partial-inline) 49ms 0.64% 79.23% 55ms 0.72% vertexsort 0 0% 79.23% 54ms 0.7% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 54ms 0.7% 79.93% 54ms 0.7% boost::detail::shared_count::shared_count (inline) 38ms 0.49% 80.43% 53ms 0.69% malloc_consolidate 1ms 0.013% 80.44% 53ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 37ms 0.48% 80.92% 52ms 0.68% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 80.94% 52ms 0.68% BoundaryNodeWriter::Visit 0 0% 80.94% 52ms 0.68% std::vector::vector (inline) 0 0% 80.94% 51ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.94% 51ms 0.66% std::__new_allocator::destroy (inline) 0 0% 80.94% 51ms 0.66% std::allocator_traits::destroy (inline) 0 0% 80.94% 50ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.94% 49ms 0.64% std::map::find (inline) 0 0% 80.94% 48ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 1ms 0.013% 80.95% 48ms 0.62% Node::ClearAppliedForce 3ms 0.039% 80.99% 48ms 0.62% Node::ConstructNodeAttributes (inline) 0 0% 80.99% 48ms 0.62% std::_Vector_base::_Vector_base (inline) 47ms 0.61% 81.60% 47ms 0.61% [libchaste_mesh.so] 0 0% 81.60% 47ms 0.61% _IO_new_fclose 0 0% 81.60% 47ms 0.61% std::__basic_file::close 0 0% 81.60% 46ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.60% 46ms 0.6% std::_Vector_base::_M_create_storage (inline) 3ms 0.039% 81.64% 45ms 0.59% std::__new_allocator::construct (inline) 0 0% 81.64% 45ms 0.59% std::allocator_traits::construct (inline) 20ms 0.26% 81.90% 44ms 0.57% AbstractCellCycleModel::GetAge 1ms 0.013% 81.91% 44ms 0.57% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.013% 81.93% 44ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 13ms 0.17% 82.10% 43ms 0.56% Determinant (inline) 1ms 0.013% 82.11% 43ms 0.56% _IO_new_file_close_it 7ms 0.091% 82.20% 43ms 0.56% std::_Vector_base::_M_deallocate (inline) 42ms 0.55% 82.75% 42ms 0.55% __GI___mkdir 0 0% 82.75% 41ms 0.53% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 41ms 0.53% 83.28% 41ms 0.53% __GI___close_nocancel 0 0% 83.28% 41ms 0.53% std::_Rb_tree::_M_construct_node (inline) 40ms 0.52% 83.80% 40ms 0.52% boost::numeric::ublas::c_vector::operator() (partial-inline) 23ms 0.3% 84.10% 40ms 0.52% hack_digit 1ms 0.013% 84.11% 39ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 18ms 0.23% 84.35% 39ms 0.51% AbstractTetrahedralMesh::GetNumAllElements 7ms 0.091% 84.44% 39ms 0.51% Inverse 0 0% 84.44% 39ms 0.51% std::map::map (inline)