File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6470ms, 84.75% of 7634ms total Dropped 559 nodes (cum <= 38.17ms) flat flat% sum% cum cum% 0 0% 0% 7600ms 99.55% __libc_start_call_main 0 0% 0% 7600ms 99.55% __libc_start_main_impl 0 0% 0% 7600ms 99.55% _start 0 0% 0% 7585ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7585ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7585ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7585ms 99.36% main 0 0% 0% 7545ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7545ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7545ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7541ms 98.78% AbstractCellBasedSimulation::Solve 0 0% 0% 3299ms 43.21% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2871ms 37.61% MeshBasedCellPopulation::Update 0 0% 0% 2712ms 35.53% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 1518ms 19.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.013% 1411ms 18.48% MutableMesh::ReMesh 0 0% 0.013% 1409ms 18.46% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.052% 0.065% 1358ms 17.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.12% 0.18% 1293ms 16.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 29ms 0.38% 0.56% 1234ms 16.16% MeshBasedCellPopulation::SpringIterator::operator++ 122ms 1.60% 2.16% 993ms 13.01% TetrahedralMesh::EdgeIterator::operator++ 446ms 5.84% 8.00% 983ms 12.88% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 8.02% 929ms 12.17% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.1% 8.12% 907ms 11.88% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.16% 8.28% 904ms 11.84% CellPopulationElementWriter::Visit 8ms 0.1% 8.38% 846ms 11.08% CellPropertyCollection::GetPropertiesType (inline) 237ms 3.10% 11.49% 841ms 11.02% __dynamic_cast 27ms 0.35% 11.84% 798ms 10.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.25% 12.09% 773ms 10.13% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 12.09% 767ms 10.05% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.13% 12.22% 717ms 9.39% TetrahedralMesh::ImportFromMesher 4ms 0.052% 12.27% 667ms 8.74% AbstractCellProperty::IsSubType (inline) 50ms 0.65% 12.93% 603ms 7.90% std::map::operator[] (partial-inline) 38ms 0.5% 13.43% 543ms 7.11% operator new 1ms 0.013% 13.44% 531ms 6.96% triangulate 19ms 0.25% 13.69% 530ms 6.94% std::_Rb_tree::find (inline) 4ms 0.052% 13.74% 523ms 6.85% Cell::GetCellProliferativeType 6ms 0.079% 13.82% 515ms 6.75% std::set::insert (inline) 11ms 0.14% 13.96% 509ms 6.67% std::_Rb_tree::_M_insert_unique 0 0% 13.96% 504ms 6.60% std::_Rb_tree::lower_bound (inline) 0 0% 13.96% 504ms 6.60% std::map::lower_bound (inline) 167ms 2.19% 16.15% 494ms 6.47% __GI___libc_malloc 34ms 0.45% 16.60% 493ms 6.46% std::__new_allocator::allocate (inline) 0 0% 16.60% 489ms 6.41% std::allocator_traits::allocate (inline) 0 0% 16.60% 487ms 6.38% std::set::count (inline) 479ms 6.27% 22.87% 479ms 6.27% __strcmp_avx2 0 0% 22.87% 474ms 6.21% delaunay 1ms 0.013% 22.88% 474ms 6.21% divconqdelaunay 4ms 0.052% 22.94% 460ms 6.03% LegacyCellProliferativeTypesWriter::VisitCell 206ms 2.70% 25.64% 441ms 5.78% __cxxabiv1::__si_class_type_info::__do_dyncast 38ms 0.5% 26.13% 422ms 5.53% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.039% 26.17% 413ms 5.41% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.17% 406ms 5.32% std::_Rb_tree::_M_create_node (inline) 0 0% 26.17% 390ms 5.11% std::set::~set (inline) 0 0% 26.17% 384ms 5.03% std::_Rb_tree::_Alloc_node::operator() (inline) 84ms 1.10% 27.27% 381ms 4.99% std::_Rb_tree::_M_erase 0 0% 27.27% 372ms 4.87% std::_Rb_tree::_M_get_node (inline) 17ms 0.22% 27.50% 361ms 4.73% std::_Rb_tree::_Rb_tree (partial-inline) 15ms 0.2% 27.69% 353ms 4.62% std::less::operator() (inline) 338ms 4.43% 32.12% 338ms 4.43% std::operator< (inline) 1ms 0.013% 32.13% 332ms 4.35% Cell::GetMutationState 324ms 4.24% 36.38% 324ms 4.24% std::_Rb_tree::_S_right (inline) 3ms 0.039% 36.42% 322ms 4.22% std::set::set (inline) 6ms 0.079% 36.49% 320ms 4.19% Element::Element 13ms 0.17% 36.66% 319ms 4.18% std::_Rb_tree::_M_insert_ (inline) 9ms 0.12% 36.78% 311ms 4.07% AbstractCellPopulation::IsCellAttachedToLocationIndex 40ms 0.52% 37.31% 306ms 4.01% std::_Rb_tree::_M_copy (inline) 0 0% 37.31% 305ms 4.00% MeshBasedCellPopulation::GetDampingConstant 4ms 0.052% 37.36% 304ms 3.98% AbstractCentreBasedCellPopulation::GetDampingConstant 107ms 1.40% 38.76% 296ms 3.88% __GI___libc_free 3ms 0.039% 38.80% 294ms 3.85% Cell::ReadyToDivide 0 0% 38.80% 293ms 3.84% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.80% 292ms 3.82% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 38.81% 289ms 3.79% OutputFileHandler::OpenOutputFile 17ms 0.22% 39.04% 284ms 3.72% divconqrecurse 0 0% 39.04% 277ms 3.63% std::_Rb_tree::_M_drop_node (inline) 4ms 0.052% 39.09% 274ms 3.59% CellProliferativeTypesWriter::VisitCell 89ms 1.17% 40.25% 264ms 3.46% std::_Rb_tree::_M_clone_node (inline) 9ms 0.12% 40.37% 261ms 3.42% std::__new_allocator::deallocate (inline) 85ms 1.11% 41.49% 257ms 3.37% mergehulls 176ms 2.31% 43.79% 256ms 3.35% _int_malloc 0 0% 43.79% 256ms 3.35% std::allocator_traits::deallocate (inline) 1ms 0.013% 43.80% 249ms 3.26% std::ostream::operator<< (inline) 52ms 0.68% 44.49% 247ms 3.24% std::ostream::_M_insert 3ms 0.039% 44.52% 238ms 3.12% AbstractCellProperty::IsType (inline) 9ms 0.12% 44.64% 233ms 3.05% CellPropertyCollection::HasProperty 0 0% 44.64% 232ms 3.04% Cell::HasCellProperty (inline) 8ms 0.1% 44.75% 214ms 2.80% Element::RegisterWithNodes (inline) 0 0% 44.75% 203ms 2.66% NodeLocationWriter::Visit 1ms 0.013% 44.76% 202ms 2.65% Node::AddElement 0 0% 44.76% 200ms 2.62% std::_Rb_tree::_M_put_node (inline) 13ms 0.17% 44.93% 191ms 2.50% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.039% 44.97% 190ms 2.49% AbstractPhaseBasedCellCycleModel::ReadyToDivide 162ms 2.12% 47.09% 189ms 2.48% _int_free 0 0% 47.09% 188ms 2.46% AbstractCellBasedWriter::WriteDoubleAndSpace (inline) 49ms 0.64% 47.73% 187ms 2.45% AbstractCellProperty::IsSame 8ms 0.1% 47.84% 179ms 2.34% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 68ms 0.89% 48.73% 179ms 2.34% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.026% 48.76% 170ms 2.23% AbstractCellBasedWriter::WriteDouble (inline) 14ms 0.18% 48.94% 167ms 2.19% TetrahedralMesh::Clear 1ms 0.013% 48.95% 166ms 2.17% OutputFileHandler::OutputFileHandler 1ms 0.013% 48.97% 165ms 2.16% OutputFileHandler::CommonConstructor 41ms 0.54% 49.50% 158ms 2.07% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 49.50% 156ms 2.04% OutputFileHandler::MakeFoldersAndReturnFullPath 12ms 0.16% 49.66% 145ms 1.90% AbstractTetrahedralElement::CalculateJacobian 0 0% 49.66% 144ms 1.89% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.079% 49.74% 142ms 1.86% boost::numeric::ublas::vector_assign (inline) 0 0% 49.74% 141ms 1.85% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 49.74% 141ms 1.85% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.74% 139ms 1.82% AbstractCellBasedWriter::CloseFile 1ms 0.013% 49.75% 139ms 1.82% std::basic_filebuf::close 0 0% 49.75% 139ms 1.82% std::basic_ofstream::close (inline) 16ms 0.21% 49.96% 138ms 1.81% boost::detail::shared_count::~shared_count (inline) 0 0% 49.96% 138ms 1.81% boost::shared_ptr::~shared_ptr (inline) 0 0% 49.96% 138ms 1.81% std::basic_ofstream::open (inline) 34ms 0.45% 50.41% 138ms 1.81% std::type_info::operator== (inline) 0 0% 50.41% 137ms 1.79% std::basic_filebuf::open 131ms 1.72% 52.12% 134ms 1.76% std::from_chars 2ms 0.026% 52.15% 133ms 1.74% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.12% 52.27% 131ms 1.72% AbstractTetrahedralElement::CalculateInverseJacobian 35ms 0.46% 52.72% 121ms 1.59% std::num_put::_M_insert_int 3ms 0.039% 52.76% 120ms 1.57% alternateaxes 2ms 0.026% 52.79% 119ms 1.56% std::_Vector_base::_M_allocate (inline) 46ms 0.6% 53.39% 119ms 1.56% std::__ostream_insert 4ms 0.052% 53.45% 119ms 1.56% std::vector::push_back (inline) 116ms 1.52% 54.96% 117ms 1.53% boost::detail::sp_counted_base::release 110ms 1.44% 56.41% 117ms 1.53% vertexmedian 0 0% 56.41% 116ms 1.52% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 56.42% 116ms 1.52% std::filesystem::permissions 115ms 1.51% 57.93% 115ms 1.51% __GI_fchmodat 2ms 0.026% 57.95% 113ms 1.48% _IO_new_fopen 13ms 0.17% 58.12% 112ms 1.47% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 58.12% 112ms 1.47% std::__basic_file::open 9ms 0.12% 58.24% 112ms 1.47% std::vector::_M_realloc_insert 0 0% 58.24% 111ms 1.45% __fopen_internal (inline) 7ms 0.092% 58.33% 110ms 1.44% AbstractTetrahedralElement::RefreshJacobian 109ms 1.43% 59.76% 109ms 1.43% incircle 1ms 0.013% 59.77% 107ms 1.40% _IO_new_file_fopen 12ms 0.16% 59.93% 106ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 28ms 0.37% 60.30% 106ms 1.39% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.079% 60.37% 105ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.37% 104ms 1.36% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 60.39% 104ms 1.36% __GI__IO_file_open 103ms 1.35% 61.74% 103ms 1.35% std::_Rb_tree_insert_and_rebalance 2ms 0.026% 61.76% 103ms 1.35% std::basic_filebuf::overflow 2ms 0.026% 61.79% 102ms 1.34% std::basic_filebuf::_M_terminate_output 101ms 1.32% 63.11% 101ms 1.32% std::_Rb_tree_increment 2ms 0.026% 63.14% 101ms 1.32% std::basic_filebuf::_M_convert_to_external 46ms 0.6% 63.74% 99ms 1.30% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 63.75% 99ms 1.30% std::__basic_file::xsputn 66ms 0.86% 64.62% 98ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 4ms 0.052% 64.67% 97ms 1.27% Node::~Node 96ms 1.26% 65.93% 97ms 1.27% __GI___libc_write 34ms 0.45% 66.37% 97ms 1.27% boost::numeric::ublas::indexing_vector_assign 2ms 0.026% 66.40% 92ms 1.21% std::operator<< (inline) 87ms 1.14% 67.54% 88ms 1.15% __libc_open64 1ms 0.013% 67.55% 87ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.51% 68.06% 87ms 1.14% AbstractElement::GetNodeLocation 86ms 1.13% 69.19% 86ms 1.13% [libchaste_cell_based.so] 4ms 0.052% 69.24% 85ms 1.11% std::filesystem::status 3ms 0.039% 69.28% 84ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 81ms 1.06% 70.34% 81ms 1.06% __GI___fstatat64 46ms 0.6% 70.95% 81ms 1.06% std::basic_filebuf::xsputn 79ms 1.03% 71.98% 79ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 71.98% 77ms 1.01% std::_Rb_tree::_M_destroy_node (inline) 0 0% 71.98% 77ms 1.01% std::__new_allocator::destroy (inline) 0 0% 71.98% 77ms 1.01% std::allocator_traits::destroy (inline) 1ms 0.013% 71.99% 72ms 0.94% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 71.99% 71ms 0.93% Cell::GetCellId 0 0% 71.99% 71ms 0.93% std::filesystem::create_directory 3ms 0.039% 72.03% 70ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 72.03% 70ms 0.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.03% 70ms 0.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 70ms 0.92% 72.95% 70ms 0.92% std::vector::size (inline) 0 0% 72.95% 68ms 0.89% AbstractCellPopulation::GetLocationIndexUsingCell 46ms 0.6% 73.55% 68ms 0.89% malloc_consolidate 59ms 0.77% 74.33% 66ms 0.86% vertexsort 49ms 0.64% 74.97% 64ms 0.84% AbstractElement::GetNodeGlobalIndex 63ms 0.83% 75.79% 63ms 0.83% Node::GetIndex 59ms 0.77% 76.57% 59ms 0.77% boost::numeric::ublas::c_vector::operator() (partial-inline) 59ms 0.77% 77.34% 59ms 0.77% counterclockwise 0 0% 77.34% 59ms 0.77% tcache_get (inline) 59ms 0.77% 78.11% 59ms 0.77% tcache_get_n (inline) 55ms 0.72% 78.83% 55ms 0.72% [libchaste_mesh.so] 2ms 0.026% 78.86% 55ms 0.72% std::_Vector_base::_M_deallocate (inline) 44ms 0.58% 79.43% 55ms 0.72% std::num_put::do_put 8ms 0.1% 79.54% 54ms 0.71% CellPropertyCollection::AddProperty 53ms 0.69% 80.23% 53ms 0.69% __memcpy_avx_unaligned_erms 50ms 0.65% 80.89% 53ms 0.69% boost::detail::shared_count::shared_count (inline) 33ms 0.43% 81.32% 52ms 0.68% std::basic_streambuf::xsputn 3ms 0.039% 81.36% 51ms 0.67% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 81.37% 50ms 0.65% Node::ConstructNodeAttributes (inline) 0 0% 81.37% 49ms 0.64% Node::ClearAppliedForce 27ms 0.35% 81.73% 49ms 0.64% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.026% 81.75% 49ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.75% 48ms 0.63% boost::numeric::ublas::norm_2 (inline) 10ms 0.13% 81.88% 48ms 0.63% boost::numeric::ublas::vector_norm_2::apply (inline) 22ms 0.29% 82.17% 47ms 0.62% AbstractTetrahedralMesh::GetElement 0 0% 82.17% 47ms 0.62% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 13ms 0.17% 82.34% 45ms 0.59% AbstractCellCycleModel::GetAge 0 0% 82.34% 45ms 0.59% std::map::map (inline) 0 0% 82.34% 45ms 0.59% std::vector::vector (inline) 44ms 0.58% 82.92% 44ms 0.58% std::ostream::sentry::sentry 0 0% 82.92% 43ms 0.56% CellPropertyCollection::~CellPropertyCollection (inline) 13ms 0.17% 83.09% 43ms 0.56% Inverse 42ms 0.55% 83.64% 42ms 0.55% boost::shared_ptr::operator-> (inline) 0 0% 83.64% 42ms 0.55% std::_Vector_base::_Vector_base (inline) 2ms 0.026% 83.67% 41ms 0.54% BoundaryNodeWriter::Visit 0 0% 83.67% 41ms 0.54% FileFinder::GetAbsolutePath[abi:cxx11] 2ms 0.026% 83.69% 41ms 0.54% NodeAttributes::NodeAttributes 41ms 0.54% 84.23% 41ms 0.54% [libstdc++.so.6.0.33] 0 0% 84.23% 41ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 84.23% 41ms 0.54% std::map::find (inline) 0 0% 84.23% 40ms 0.52% AbstractCentreBasedCellPopulation::CreateCellPair 40ms 0.52% 84.75% 40ms 0.52% Node::IsDeleted 0 0% 84.75% 40ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)