File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6727ms, 84.83% of 7930ms total Dropped 601 nodes (cum <= 39.65ms) flat flat% sum% cum cum% 0 0% 0% 7894ms 99.55% __libc_start_call_main 0 0% 0% 7894ms 99.55% __libc_start_main_impl 0 0% 0% 7894ms 99.55% _start 0 0% 0% 7880ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7880ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7880ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7880ms 99.37% main 0 0% 0% 7843ms 98.90% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7843ms 98.90% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7843ms 98.90% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7839ms 98.85% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3392ms 42.77% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.038% 2894ms 36.49% MeshBasedCellPopulation::Update 1ms 0.013% 0.05% 2824ms 35.61% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.063% 1613ms 20.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.063% 1463ms 18.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.088% 1426ms 17.98% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.076% 0.16% 1401ms 17.67% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.16% 1392ms 17.55% MutableMesh::ReMesh 17ms 0.21% 0.38% 1240ms 15.64% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.42% 1.80% 1022ms 12.89% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.076% 1.88% 1011ms 12.75% AbstractTwoBodyInteractionForce::AddForceContribution 422ms 5.32% 7.20% 963ms 12.14% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.21% 923ms 11.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 39ms 0.49% 7.70% 883ms 11.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 280ms 3.53% 11.24% 880ms 11.10% __dynamic_cast 10ms 0.13% 11.36% 863ms 10.88% CellPopulationElementWriter::Visit 15ms 0.19% 11.55% 854ms 10.77% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.33% 11.88% 787ms 9.92% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.076% 11.95% 777ms 9.80% MeshBasedCellPopulation::AcceptCellWriter 11ms 0.14% 12.09% 735ms 9.27% TetrahedralMesh::ImportFromMesher 3ms 0.038% 12.13% 668ms 8.42% AbstractCellProperty::IsSubType (inline) 58ms 0.73% 12.86% 584ms 7.36% std::map::operator[] (partial-inline) 1ms 0.013% 12.88% 578ms 7.29% std::ostream::operator<< (inline) 88ms 1.11% 13.98% 575ms 7.25% std::ostream::_M_insert 50ms 0.63% 14.62% 572ms 7.21% operator new 9ms 0.11% 14.73% 557ms 7.02% std::set::insert (inline) 9ms 0.11% 14.84% 548ms 6.91% std::_Rb_tree::_M_insert_unique 27ms 0.34% 15.18% 534ms 6.73% std::_Rb_tree::find (inline) 8ms 0.1% 15.28% 519ms 6.54% Cell::GetCellProliferativeType 34ms 0.43% 15.71% 515ms 6.49% std::__new_allocator::allocate (inline) 155ms 1.95% 17.67% 514ms 6.48% __GI___libc_malloc 0 0% 17.67% 512ms 6.46% std::allocator_traits::allocate (inline) 0 0% 17.67% 511ms 6.44% triangulate 493ms 6.22% 23.88% 493ms 6.22% __strcmp_avx2 6ms 0.076% 23.96% 490ms 6.18% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.96% 486ms 6.13% std::_Rb_tree::lower_bound (inline) 0 0% 23.96% 486ms 6.13% std::map::lower_bound (inline) 6ms 0.076% 24.04% 480ms 6.05% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.04% 480ms 6.05% std::set::count (inline) 0 0% 24.04% 459ms 5.79% delaunay 3ms 0.038% 24.07% 458ms 5.78% divconqdelaunay 197ms 2.48% 26.56% 443ms 5.59% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.56% 426ms 5.37% std::_Rb_tree::_M_create_node (inline) 23ms 0.29% 26.85% 411ms 5.18% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.85% 403ms 5.08% std::_Rb_tree::_Alloc_node::operator() (inline) 89ms 1.12% 27.97% 386ms 4.87% std::_Rb_tree::_M_erase 22ms 0.28% 28.25% 382ms 4.82% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.25% 381ms 4.80% std::_Rb_tree::_M_get_node (inline) 0 0% 28.25% 375ms 4.73% std::set::~set (inline) 11ms 0.14% 28.39% 365ms 4.60% std::less::operator() (inline) 6ms 0.076% 28.46% 358ms 4.51% std::set::set (inline) 354ms 4.46% 32.93% 354ms 4.46% std::operator< (inline) 16ms 0.2% 33.13% 349ms 4.40% std::_Rb_tree::_M_insert_ (inline) 5ms 0.063% 33.19% 346ms 4.36% Cell::GetMutationState 4ms 0.05% 33.24% 342ms 4.31% Cell::ReadyToDivide 1ms 0.013% 33.25% 335ms 4.22% NodeLocationWriter::Visit 0 0% 33.25% 323ms 4.07% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 33.28% 321ms 4.05% AbstractCellBasedWriter::OpenOutputFileForAppend 34ms 0.43% 33.71% 321ms 4.05% std::_Rb_tree::_M_copy (inline) 317ms 4.00% 37.70% 317ms 4.00% std::_Rb_tree::_S_right (inline) 1ms 0.013% 37.72% 315ms 3.97% OutputFileHandler::OpenOutputFile 103ms 1.30% 39.02% 301ms 3.80% __GI___libc_free 3ms 0.038% 39.05% 299ms 3.77% Element::Element 22ms 0.28% 39.33% 297ms 3.75% std::num_put::_M_insert_float 2ms 0.025% 39.36% 295ms 3.72% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 39.38% 293ms 3.69% AbstractCentreBasedCellPopulation::GetDampingConstant 93ms 1.17% 40.55% 280ms 3.53% std::_Rb_tree::_M_clone_node (inline) 189ms 2.38% 42.94% 278ms 3.51% _int_malloc 10ms 0.13% 43.06% 273ms 3.44% std::__new_allocator::deallocate (inline) 4ms 0.05% 43.11% 271ms 3.42% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 43.11% 270ms 3.40% std::allocator_traits::deallocate (inline) 0 0% 43.11% 265ms 3.34% std::_Rb_tree::_M_drop_node (inline) 5ms 0.063% 43.18% 262ms 3.30% AbstractCellProperty::IsType (inline) 0 0% 43.18% 255ms 3.22% Cell::HasCellProperty (inline) 8ms 0.1% 43.28% 255ms 3.22% CellPropertyCollection::HasProperty 2ms 0.025% 43.30% 246ms 3.10% CellProliferativeTypesWriter::VisitCell 7ms 0.088% 43.39% 233ms 2.94% divconqrecurse 72ms 0.91% 44.30% 225ms 2.84% mergehulls 0 0% 44.30% 225ms 2.84% std::_Rb_tree::_M_put_node (inline) 7ms 0.088% 44.39% 224ms 2.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.05% 44.44% 220ms 2.77% std::__cxx11::collate::do_transform 14ms 0.18% 44.62% 212ms 2.67% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 44.65% 206ms 2.60% ___vsnprintf 1ms 0.013% 44.67% 203ms 2.56% __vsnprintf_internal (inline) 30ms 0.38% 45.04% 198ms 2.50% __printf_buffer 169ms 2.13% 47.18% 198ms 2.50% _int_free 4ms 0.05% 47.23% 197ms 2.48% Element::RegisterWithNodes (inline) 20ms 0.25% 47.48% 193ms 2.43% TetrahedralMesh::Clear 4ms 0.05% 47.53% 192ms 2.42% Node::AddElement 80ms 1.01% 48.54% 190ms 2.40% std::_Rb_tree::_M_get_insert_unique_pos (inline) 6ms 0.076% 48.61% 187ms 2.36% MeshBasedCellPopulation::SpringsEnd (inline) 56ms 0.71% 49.32% 181ms 2.28% AbstractCellProperty::IsSame 1ms 0.013% 49.33% 159ms 2.01% __printf_fp_spec (inline) 12ms 0.15% 49.48% 158ms 1.99% __printf_fp_l_buffer 8ms 0.1% 49.58% 150ms 1.89% AbstractTetrahedralElement::CalculateJacobian 2ms 0.025% 49.61% 149ms 1.88% std::basic_filebuf::close 0 0% 49.61% 148ms 1.87% AbstractCellBasedWriter::CloseFile 0 0% 49.61% 148ms 1.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 49.62% 148ms 1.87% std::basic_ofstream::close (inline) 30ms 0.38% 50.00% 147ms 1.85% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.00% 144ms 1.82% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 50.01% 144ms 1.82% std::filesystem::permissions 1ms 0.013% 50.03% 143ms 1.80% OutputFileHandler::CommonConstructor 0 0% 50.03% 143ms 1.80% OutputFileHandler::OutputFileHandler 0 0% 50.03% 143ms 1.80% std::basic_ofstream::basic_ofstream (inline) 142ms 1.79% 51.82% 142ms 1.79% __GI_fchmodat 0 0% 51.82% 138ms 1.74% std::basic_filebuf::open 0 0% 51.82% 138ms 1.74% std::basic_ofstream::open (inline) 0 0% 51.82% 137ms 1.73% OutputFileHandler::MakeFoldersAndReturnFullPath 48ms 0.61% 52.42% 137ms 1.73% std::__ostream_insert 84ms 1.06% 53.48% 136ms 1.72% __printf_fp_buffer_1 3ms 0.038% 53.52% 136ms 1.72% boost::numeric::ublas::vector_assign (inline) 0 0% 53.52% 134ms 1.69% alternateaxes 5ms 0.063% 53.58% 133ms 1.68% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 53.61% 133ms 1.68% std::_Vector_base::_M_allocate (inline) 115ms 1.45% 55.06% 133ms 1.68% vertexmedian 18ms 0.23% 55.28% 129ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 34ms 0.43% 55.71% 127ms 1.60% std::num_put::_M_insert_int 24ms 0.3% 56.02% 125ms 1.58% std::type_info::operator== (inline) 0 0% 56.02% 124ms 1.56% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.063% 56.08% 124ms 1.56% std::vector::push_back (inline) 13ms 0.16% 56.24% 121ms 1.53% AbstractTetrahedralElement::RefreshJacobian 19ms 0.24% 56.48% 120ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 120ms 1.51% 57.99% 120ms 1.51% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 58.03% 118ms 1.49% AbstractTetrahedralElement::CalculateInverseJacobian 117ms 1.48% 59.51% 117ms 1.48% std::_Rb_tree_increment 0 0% 59.51% 115ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 6ms 0.076% 59.58% 114ms 1.44% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.05% 59.63% 114ms 1.44% std::operator<< (inline) 8ms 0.1% 59.74% 114ms 1.44% std::vector::_M_realloc_insert 11ms 0.14% 59.87% 113ms 1.42% Node::~Node 0 0% 59.87% 112ms 1.41% _IO_new_fopen 0 0% 59.87% 112ms 1.41% __fopen_internal (inline) 5ms 0.063% 59.94% 112ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 59.94% 112ms 1.41% std::__basic_file::open 2ms 0.025% 59.96% 109ms 1.37% _IO_new_file_fopen 65ms 0.82% 60.78% 108ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 60.81% 107ms 1.35% std::basic_filebuf::overflow 1ms 0.013% 60.82% 106ms 1.34% std::basic_filebuf::_M_terminate_output 0 0% 60.82% 105ms 1.32% __GI__IO_file_open 105ms 1.32% 62.14% 105ms 1.32% __GI___libc_write 0 0% 62.14% 105ms 1.32% std::__basic_file::xsputn 0 0% 62.14% 105ms 1.32% std::basic_filebuf::_M_convert_to_external 8ms 0.1% 62.24% 102ms 1.29% boost::detail::shared_count::~shared_count (inline) 0 0% 62.24% 102ms 1.29% boost::shared_ptr::~shared_ptr (inline) 30ms 0.38% 62.62% 100ms 1.26% boost::numeric::ublas::indexing_vector_assign 46ms 0.58% 63.20% 96ms 1.21% AbstractElement::GetNodeLocation 96ms 1.21% 64.41% 96ms 1.21% incircle 95ms 1.20% 65.61% 95ms 1.20% __libc_open64 90ms 1.13% 66.75% 92ms 1.16% boost::detail::sp_counted_base::release 44ms 0.55% 67.30% 92ms 1.16% boost::shared_ptr::shared_ptr (inline) 60ms 0.76% 68.06% 87ms 1.10% std::basic_streambuf::xsputn 3ms 0.038% 68.10% 86ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 68.11% 86ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 86ms 1.08% 69.19% 86ms 1.08% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 85ms 1.07% 70.26% 85ms 1.07% [libchaste_cell_based.so] 51ms 0.64% 70.91% 80ms 1.01% std::basic_filebuf::xsputn 68ms 0.86% 71.77% 75ms 0.95% vertexsort 3ms 0.038% 71.80% 73ms 0.92% std::filesystem::status 2ms 0.025% 71.83% 72ms 0.91% AbstractCellPopulation::GetLocationIndexUsingCell 71ms 0.9% 72.72% 71ms 0.9% __GI___fstatat64 0 0% 72.72% 70ms 0.88% Cell::GetCellId 0 0% 72.72% 70ms 0.88% tcache_get (inline) 70ms 0.88% 73.61% 70ms 0.88% tcache_get_n (inline) 67ms 0.84% 74.45% 67ms 0.84% Node::GetIndex 0 0% 74.45% 65ms 0.82% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 74.45% 65ms 0.82% std::filesystem::create_directory 0 0% 74.45% 64ms 0.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.45% 64ms 0.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 45ms 0.57% 75.02% 63ms 0.79% malloc_consolidate 62ms 0.78% 75.80% 62ms 0.78% Node::IsDeleted 7ms 0.088% 75.89% 61ms 0.77% CellPropertyCollection::AddProperty 0 0% 75.89% 61ms 0.77% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 5ms 0.063% 75.95% 61ms 0.77% TetrahedralMesh::EdgeIterator::GetNodeB 48ms 0.61% 76.56% 60ms 0.76% AbstractElement::GetNodeGlobalIndex 0 0% 76.56% 60ms 0.76% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 58ms 0.73% 77.29% 58ms 0.73% __memcpy_avx_unaligned_erms 46ms 0.58% 77.87% 56ms 0.71% std::num_put::do_put 6ms 0.076% 77.94% 55ms 0.69% Node::ConstructNodeAttributes (inline) 0 0% 77.94% 54ms 0.68% std::vector::vector (inline) 53ms 0.67% 78.61% 53ms 0.67% std::vector::size (inline) 52ms 0.66% 79.27% 52ms 0.66% counterclockwise 1ms 0.013% 79.28% 51ms 0.64% Node::ClearAppliedForce 0 0% 79.28% 50ms 0.63% std::_Vector_base::_Vector_base (inline) 33ms 0.42% 79.70% 49ms 0.62% AbstractTetrahedralMesh::GetElement 0 0% 79.70% 49ms 0.62% boost::numeric::ublas::norm_2 (inline) 19ms 0.24% 79.94% 49ms 0.62% boost::numeric::ublas::vector_norm_2::apply (inline) 1ms 0.013% 79.95% 49ms 0.62% std::_Vector_base::_M_create_storage (inline) 0 0% 79.95% 49ms 0.62% std::map::find (inline) 1ms 0.013% 79.96% 48ms 0.61% TetrahedralMesh::EdgeIterator::GetNodeA 47ms 0.59% 80.55% 48ms 0.61% boost::detail::shared_count::shared_count (inline) 3ms 0.038% 80.59% 48ms 0.61% std::_Vector_base::_M_deallocate (inline) 2ms 0.025% 80.62% 48ms 0.61% std::__new_allocator::construct (inline) 0 0% 80.62% 48ms 0.61% std::allocator_traits::construct (inline) 47ms 0.59% 81.21% 47ms 0.59% [libchaste_mesh.so] 22ms 0.28% 81.49% 46ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 46ms 0.58% 82.07% 46ms 0.58% [libstdc++.so.6.0.33] 46ms 0.58% 82.65% 46ms 0.58% boost::numeric::ublas::c_vector::operator() (partial-inline) 23ms 0.29% 82.94% 45ms 0.57% boost::numeric::ublas::c_matrix::operator() 0 0% 82.94% 45ms 0.57% std::_Rb_tree::_M_construct_node (inline) 16ms 0.2% 83.14% 44ms 0.55% AbstractCellCycleModel::GetAge 0 0% 83.14% 44ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 44ms 0.55% 83.69% 44ms 0.55% Node::rGetLocation 0 0% 83.69% 43ms 0.54% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 43ms 0.54% 84.24% 43ms 0.54% boost::shared_ptr::operator-> (inline) 43ms 0.54% 84.78% 43ms 0.54% std::ostream::sentry::sentry 0 0% 84.78% 42ms 0.53% BoundaryNodeWriter::Visit 0 0% 84.78% 40ms 0.5% std::_Rb_tree::_M_destroy_node (inline) 4ms 0.05% 84.83% 40ms 0.5% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.83% 40ms 0.5% std::__new_allocator::destroy (inline) 0 0% 84.83% 40ms 0.5% std::allocator_traits::destroy (inline)