File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5611ms, 85.39% of 6571ms total Dropped 502 nodes (cum <= 32.85ms) flat flat% sum% cum cum% 0 0% 0% 6542ms 99.56% __libc_start_call_main 0 0% 0% 6542ms 99.56% __libc_start_main_impl 0 0% 0% 6542ms 99.56% _start 0 0% 0% 6528ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6528ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6528ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6528ms 99.35% main 0 0% 0% 6491ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6491ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6491ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6490ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0% 3095ms 47.10% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.015% 0.015% 2686ms 40.88% MeshBasedCellPopulation::Update 1ms 0.015% 0.03% 2108ms 32.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.03% 1344ms 20.45% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.03% 1296ms 19.72% MutableMesh::ReMesh 1ms 0.015% 0.046% 1278ms 19.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.27% 0.32% 1173ms 17.85% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.015% 0.33% 1120ms 17.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.33% 1084ms 16.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 106ms 1.61% 1.95% 976ms 14.85% TetrahedralMesh::EdgeIterator::operator++ 379ms 5.77% 7.72% 799ms 12.16% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.12% 7.84% 792ms 12.05% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.061% 7.90% 788ms 11.99% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.21% 8.11% 725ms 11.03% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 189ms 2.88% 10.99% 724ms 11.02% __dynamic_cast 1ms 0.015% 11.00% 701ms 10.67% CellPropertyCollection::GetPropertiesType (inline) 12ms 0.18% 11.19% 695ms 10.58% CellPopulationElementWriter::Visit 9ms 0.14% 11.32% 659ms 10.03% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.091% 11.41% 649ms 9.88% TetrahedralMesh::ImportFromMesher 10ms 0.15% 11.57% 647ms 9.85% AbstractCellPopulation::GetCellUsingLocationIndex 40ms 0.61% 12.17% 615ms 9.36% operator new 216ms 3.29% 15.46% 577ms 8.78% __GI___libc_malloc 6ms 0.091% 15.55% 566ms 8.61% AbstractCellProperty::IsSubType (inline) 9ms 0.14% 15.69% 554ms 8.43% std::set::insert (inline) 8ms 0.12% 15.81% 545ms 8.29% std::_Rb_tree::_M_insert_unique 13ms 0.2% 16.01% 537ms 8.17% std::__new_allocator::allocate (inline) 0 0% 16.01% 534ms 8.13% std::allocator_traits::allocate (inline) 14ms 0.21% 16.22% 518ms 7.88% std::_Rb_tree::find (inline) 3ms 0.046% 16.27% 489ms 7.44% triangulate 0 0% 16.27% 484ms 7.37% std::set::count (inline) 3ms 0.046% 16.31% 469ms 7.14% std::ostream::operator<< (inline) 58ms 0.88% 17.20% 463ms 7.05% std::ostream::_M_insert 57ms 0.87% 18.06% 446ms 6.79% std::_Rb_tree::~_Rb_tree (inline) 0 0% 18.06% 445ms 6.77% LegacyCellProliferativeTypesWriter::VisitCell 58ms 0.88% 18.95% 440ms 6.70% std::map::operator[] (partial-inline) 0 0% 18.95% 438ms 6.67% std::_Rb_tree::_M_create_node (inline) 2ms 0.03% 18.98% 435ms 6.62% Cell::GetCellProliferativeType 0 0% 18.98% 429ms 6.53% delaunay 1ms 0.015% 18.99% 429ms 6.53% divconqdelaunay 425ms 6.47% 25.46% 425ms 6.47% __strcmp_evex 0 0% 25.46% 423ms 6.44% std::set::~set (inline) 0 0% 25.46% 418ms 6.36% std::_Rb_tree::_M_get_node (inline) 0 0% 25.46% 408ms 6.21% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.046% 25.51% 397ms 6.04% AbstractCellBasedSimulation::DoCellBirth 51ms 0.78% 26.28% 388ms 5.90% std::_Rb_tree::_M_erase 41ms 0.62% 26.91% 381ms 5.80% std::_Rb_tree::_M_insert_ (inline) 146ms 2.22% 29.13% 367ms 5.59% __cxxabiv1::__si_class_type_info::__do_dyncast 16ms 0.24% 29.37% 343ms 5.22% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.37% 334ms 5.08% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.37% 329ms 5.01% std::_Rb_tree::lower_bound (inline) 0 0% 29.37% 329ms 5.01% std::map::lower_bound (inline) 1ms 0.015% 29.39% 312ms 4.75% std::set::set (inline) 25ms 0.38% 29.77% 308ms 4.69% std::_Rb_tree::_M_copy (inline) 4ms 0.061% 29.83% 307ms 4.67% Element::Element 2ms 0.03% 29.86% 306ms 4.66% Cell::GetMutationState 9ms 0.14% 30.00% 295ms 4.49% boost::detail::shared_count::~shared_count (inline) 0 0% 30.00% 295ms 4.49% boost::shared_ptr::~shared_ptr (inline) 1ms 0.015% 30.01% 294ms 4.47% NodeLocationWriter::Visit 69ms 1.05% 31.06% 290ms 4.41% __GI___libc_free 211ms 3.21% 34.27% 287ms 4.37% _int_malloc 278ms 4.23% 38.50% 278ms 4.23% boost::detail::sp_counted_base::release 115ms 1.75% 40.25% 277ms 4.22% std::_Rb_tree::_M_clone_node (inline) 21ms 0.32% 40.57% 266ms 4.05% std::num_put::_M_insert_float 7ms 0.11% 40.68% 258ms 3.93% std::__new_allocator::deallocate (inline) 0 0% 40.68% 258ms 3.93% std::allocator_traits::deallocate (inline) 12ms 0.18% 40.86% 254ms 3.87% std::less::operator() (inline) 3ms 0.046% 40.91% 250ms 3.80% AbstractCellPopulation::IsCellAttachedToLocationIndex 245ms 3.73% 44.64% 245ms 3.73% std::_Rb_tree::_S_right (inline) 7ms 0.11% 44.74% 242ms 3.68% divconqrecurse 242ms 3.68% 48.42% 242ms 3.68% std::operator< (inline) 2ms 0.03% 48.46% 240ms 3.65% Cell::ReadyToDivide 1ms 0.015% 48.47% 230ms 3.50% MeshBasedCellPopulation::GetDampingConstant 3ms 0.046% 48.52% 229ms 3.49% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.076% 48.59% 226ms 3.44% Element::RegisterWithNodes (inline) 61ms 0.93% 49.52% 222ms 3.38% mergehulls 0 0% 49.52% 218ms 3.32% std::_Rb_tree::_M_put_node (inline) 9ms 0.14% 49.66% 217ms 3.30% Node::AddElement 176ms 2.68% 52.34% 217ms 3.30% _int_free 9ms 0.14% 52.47% 211ms 3.21% std::__cxx11::collate::do_transform 200ms 3.04% 55.52% 200ms 3.04% [libchaste_cell_based.so] 1ms 0.015% 55.53% 197ms 3.00% ___vsnprintf 0 0% 55.53% 196ms 2.98% __vsnprintf_internal (inline) 19ms 0.29% 55.82% 192ms 2.92% __printf_buffer 6ms 0.091% 55.91% 185ms 2.82% CellPropertyCollection::HasProperty 0 0% 55.91% 182ms 2.77% Cell::HasCellProperty (inline) 8ms 0.12% 56.03% 181ms 2.75% AbstractCellProperty::IsType (inline) 0 0% 56.03% 180ms 2.74% CellProliferativeTypesWriter::VisitCell 1ms 0.015% 56.05% 176ms 2.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.061% 56.11% 172ms 2.62% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.061% 56.17% 168ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.061% 56.23% 157ms 2.39% __printf_fp_l_buffer 0 0% 56.23% 157ms 2.39% __printf_fp_spec (inline) 52ms 0.79% 57.02% 156ms 2.37% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 57.02% 148ms 2.25% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 73ms 1.11% 58.13% 148ms 2.25% __printf_fp_buffer_1 0 0% 58.13% 147ms 2.24% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 58.13% 146ms 2.22% OutputFileHandler::OpenOutputFile 1ms 0.015% 58.15% 142ms 2.16% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.11% 58.26% 140ms 2.13% AbstractTetrahedralElement::CalculateJacobian 2ms 0.03% 58.29% 134ms 2.04% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 58.29% 134ms 2.04% TetrahedralMesh::Clear 15ms 0.23% 58.51% 126ms 1.92% AbstractCellProperty::IsSame 31ms 0.47% 58.99% 126ms 1.92% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.061% 59.05% 120ms 1.83% alternateaxes 15ms 0.23% 59.28% 119ms 1.81% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.015% 59.29% 116ms 1.77% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 59.29% 116ms 1.77% std::_Rb_tree::_M_destroy_node (inline) 0 0% 59.29% 116ms 1.77% std::_Vector_base::_M_allocate (inline) 0 0% 59.29% 116ms 1.77% std::__new_allocator::destroy (inline) 0 0% 59.29% 116ms 1.77% std::allocator_traits::destroy (inline) 104ms 1.58% 60.87% 116ms 1.77% vertexmedian 8ms 0.12% 61.00% 115ms 1.75% AbstractCellPopulation::Iterator::IsRealCell (inline) 14ms 0.21% 61.21% 111ms 1.69% std::type_info::operator== (inline) 0 0% 61.21% 108ms 1.64% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.015% 61.22% 108ms 1.64% boost::numeric::ublas::vector_assign (inline) 4ms 0.061% 61.28% 108ms 1.64% std::vector::push_back (inline) 107ms 1.63% 62.91% 107ms 1.63% [libchaste_mesh.so] 38ms 0.58% 63.49% 107ms 1.63% std::num_put::_M_insert_int 106ms 1.61% 65.10% 106ms 1.61% std::_Rb_tree_insert_and_rebalance 4ms 0.061% 65.17% 99ms 1.51% std::vector::_M_realloc_insert 85ms 1.29% 66.46% 98ms 1.49% TetrahedralMesh::EdgeIterator::EdgeIterator 10ms 0.15% 66.61% 96ms 1.46% AbstractTetrahedralElement::RefreshJacobian 46ms 0.7% 67.31% 95ms 1.45% std::__ostream_insert 11ms 0.17% 67.48% 93ms 1.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 8ms 0.12% 67.60% 90ms 1.37% CellPropertyCollection::AddProperty 2ms 0.03% 67.63% 88ms 1.34% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 88ms 1.34% 68.97% 88ms 1.34% [libstdc++.so.6.0.33] 2ms 0.03% 69.00% 86ms 1.31% Node::~Node 86ms 1.31% 70.31% 86ms 1.31% incircle 3ms 0.046% 70.35% 83ms 1.26% std::operator<< (inline) 2ms 0.03% 70.39% 79ms 1.20% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 70.39% 79ms 1.20% std::basic_ofstream::basic_ofstream (inline) 21ms 0.32% 70.70% 78ms 1.19% boost::numeric::ublas::indexing_vector_assign 0 0% 70.70% 78ms 1.19% std::basic_filebuf::open 0 0% 70.70% 78ms 1.19% std::basic_ofstream::open (inline) 25ms 0.38% 71.09% 77ms 1.17% AbstractElement::GetNodeLocation 58ms 0.88% 71.97% 72ms 1.10% malloc_consolidate 3ms 0.046% 72.01% 67ms 1.02% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.015% 72.03% 67ms 1.02% Cell::GetCellId 65ms 0.99% 73.02% 65ms 0.99% counterclockwise 63ms 0.96% 73.98% 63ms 0.96% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 23ms 0.35% 74.33% 59ms 0.9% Determinant (inline) 2ms 0.03% 74.36% 59ms 0.9% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 74.36% 59ms 0.9% tcache_get (inline) 59ms 0.9% 75.25% 59ms 0.9% tcache_get_n (inline) 0 0% 75.25% 57ms 0.87% OutputFileHandler::CommonConstructor 0 0% 75.25% 57ms 0.87% OutputFileHandler::OutputFileHandler 51ms 0.78% 76.03% 56ms 0.85% vertexsort 0 0% 76.03% 55ms 0.84% OutputFileHandler::MakeFoldersAndReturnFullPath 42ms 0.64% 76.67% 54ms 0.82% CellPropertyCollection::GetProperty 10ms 0.15% 76.82% 53ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 0.81% 77.63% 53ms 0.81% __memcpy_avx512_unaligned_erms 2ms 0.03% 77.66% 53ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 53ms 0.81% 78.47% 53ms 0.81% std::vector::size (inline) 52ms 0.79% 79.26% 52ms 0.79% std::_Rb_tree::_S_left (inline) 0 0% 79.26% 52ms 0.79% std::basic_filebuf::close 0 0% 79.26% 51ms 0.78% AbstractCellBasedWriter::CloseFile 0 0% 79.26% 51ms 0.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 79.26% 51ms 0.78% std::basic_ofstream::close (inline) 33ms 0.5% 79.76% 51ms 0.78% std::basic_streambuf::xsputn 10ms 0.15% 79.91% 49ms 0.75% Inverse 22ms 0.33% 80.25% 49ms 0.75% boost::shared_ptr::shared_ptr (inline) 1ms 0.015% 80.26% 48ms 0.73% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 80.26% 48ms 0.73% Node::ClearAppliedForce 0 0% 80.26% 48ms 0.73% Node::ConstructNodeAttributes (inline) 0 0% 80.26% 48ms 0.73% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 47ms 0.72% 80.98% 47ms 0.72% std::_Rb_tree_increment 35ms 0.53% 81.51% 47ms 0.72% std::num_put::do_put 21ms 0.32% 81.83% 46ms 0.7% AbstractElement::GetNodeGlobalIndex 6ms 0.091% 81.92% 46ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeA 27ms 0.41% 82.33% 46ms 0.7% hack_digit 1ms 0.015% 82.35% 45ms 0.68% FilesystemPermissions::SetFilePermissions (inline) 30ms 0.46% 82.80% 45ms 0.68% std::basic_filebuf::xsputn 0 0% 82.80% 44ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 44ms 0.67% 83.47% 44ms 0.67% __GI_fchmodat 0 0% 83.47% 44ms 0.67% std::filesystem::permissions 1ms 0.015% 83.49% 43ms 0.65% BoundaryNodeWriter::Visit 0 0% 83.49% 42ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.015% 83.50% 41ms 0.62% std::__basic_file::open 0 0% 83.50% 41ms 0.62% std::map::map (inline) 0 0% 83.50% 40ms 0.61% _IO_new_fopen 0 0% 83.50% 40ms 0.61% __fopen_internal (inline) 29ms 0.44% 83.94% 40ms 0.61% boost::numeric::ublas::c_matrix::operator() 0 0% 83.94% 39ms 0.59% std::_Vector_base::_M_deallocate (inline) 0 0% 83.94% 38ms 0.58% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.94% 38ms 0.58% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.94% 38ms 0.58% std::basic_filebuf::_M_convert_to_external 0 0% 83.94% 38ms 0.58% std::basic_filebuf::_M_terminate_output 0 0% 83.94% 38ms 0.58% std::basic_filebuf::overflow 0 0% 83.94% 37ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 83.94% 37ms 0.56% _IO_new_file_fopen 37ms 0.56% 84.51% 37ms 0.56% __GI___libc_write 0 0% 84.51% 37ms 0.56% std::__basic_file::xsputn 0 0% 84.51% 37ms 0.56% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 84.51% 35ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 84.51% 35ms 0.53% __GI__IO_file_open 0 0% 84.51% 35ms 0.53% _dl_init 0 0% 84.51% 35ms 0.53% call_init (inline) 0 0% 84.51% 35ms 0.53% std::vector::vector (inline) 24ms 0.37% 84.87% 34ms 0.52% AbstractTetrahedralMesh::GetElement 34ms 0.52% 85.39% 34ms 0.52% Node::GetIndex 0 0% 85.39% 33ms 0.5% CxxTest::RealWorldDescription::setUp 0 0% 85.39% 33ms 0.5% PetscSetup::setUpWorld 0 0% 85.39% 33ms 0.5% PetscSetupUtils::CommonSetup 0 0% 85.39% 33ms 0.5% std::_Vector_base::_Vector_base (inline)