File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6729ms, 85.57% of 7864ms total Dropped 575 nodes (cum <= 39.32ms) flat flat% sum% cum cum% 0 0% 0% 7831ms 99.58% __libc_start_call_main 0 0% 0% 7831ms 99.58% __libc_start_main_impl 0 0% 0% 7831ms 99.58% _start 0 0% 0% 7816ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7816ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7816ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7816ms 99.39% main 0 0% 0% 7778ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7778ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7778ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7774ms 98.86% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3378ms 42.96% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.025% 2898ms 36.85% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2842ms 36.14% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.051% 1546ms 19.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.076% 1463ms 18.60% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.038% 0.11% 1401ms 17.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.11% 1371ms 17.43% MutableMesh::ReMesh 3ms 0.038% 0.15% 1346ms 17.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.22% 0.37% 1286ms 16.35% MeshBasedCellPopulation::SpringIterator::operator++ 118ms 1.50% 1.87% 1035ms 13.16% TetrahedralMesh::EdgeIterator::operator++ 431ms 5.48% 7.35% 997ms 12.68% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.22% 7.57% 969ms 12.32% CellPropertyCollection::GetPropertiesType (inline) 267ms 3.40% 10.96% 917ms 11.66% __dynamic_cast 5ms 0.064% 11.02% 916ms 11.65% CellPopulationElementWriter::Visit 3ms 0.038% 11.06% 909ms 11.56% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.013% 11.08% 908ms 11.55% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 36ms 0.46% 11.53% 809ms 10.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.038% 11.57% 780ms 9.92% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.051% 11.62% 755ms 9.60% AbstractCellProperty::IsSubType (inline) 36ms 0.46% 12.08% 744ms 9.46% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.23% 713ms 9.07% TetrahedralMesh::ImportFromMesher 56ms 0.71% 12.95% 613ms 7.80% std::map::operator[] (partial-inline) 2ms 0.025% 12.97% 572ms 7.27% std::ostream::operator<< (inline) 77ms 0.98% 13.95% 568ms 7.22% std::ostream::_M_insert 2ms 0.025% 13.98% 559ms 7.11% Cell::GetCellProliferativeType 29ms 0.37% 14.34% 555ms 7.06% operator new 29ms 0.37% 14.71% 550ms 6.99% std::_Rb_tree::find (inline) 8ms 0.1% 14.81% 533ms 6.78% std::set::insert (inline) 12ms 0.15% 14.97% 525ms 6.68% std::_Rb_tree::_M_insert_unique 182ms 2.31% 17.28% 519ms 6.60% __GI___libc_malloc 518ms 6.59% 23.87% 518ms 6.59% __strcmp_avx2 0 0% 23.87% 517ms 6.57% std::_Rb_tree::lower_bound (inline) 0 0% 23.87% 517ms 6.57% std::map::lower_bound (inline) 0 0% 23.87% 498ms 6.33% std::set::count (inline) 23ms 0.29% 24.16% 490ms 6.23% std::__new_allocator::allocate (inline) 0 0% 24.16% 486ms 6.18% std::allocator_traits::allocate (inline) 1ms 0.013% 24.17% 485ms 6.17% triangulate 4ms 0.051% 24.22% 471ms 5.99% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.038% 24.26% 470ms 5.98% AbstractCellBasedSimulation::DoCellBirth 208ms 2.64% 26.91% 469ms 5.96% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.91% 423ms 5.38% delaunay 2ms 0.025% 26.93% 422ms 5.37% divconqdelaunay 0 0% 26.93% 422ms 5.37% std::_Rb_tree::_M_create_node (inline) 33ms 0.42% 27.35% 418ms 5.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.35% 399ms 5.07% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.35% 392ms 4.98% std::set::~set (inline) 16ms 0.2% 27.56% 388ms 4.93% std::less::operator() (inline) 4ms 0.051% 27.61% 386ms 4.91% Cell::GetMutationState 89ms 1.13% 28.74% 385ms 4.90% std::_Rb_tree::_M_erase 0 0% 28.74% 383ms 4.87% std::_Rb_tree::_M_get_node (inline) 372ms 4.73% 33.47% 372ms 4.73% std::operator< (inline) 14ms 0.18% 33.65% 358ms 4.55% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.025% 33.67% 349ms 4.44% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.67% 347ms 4.41% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.025% 33.70% 347ms 4.41% NodeLocationWriter::Visit 342ms 4.35% 38.05% 342ms 4.35% std::_Rb_tree::_S_right (inline) 8ms 0.1% 38.15% 328ms 4.17% AbstractCellPopulation::IsCellAttachedToLocationIndex 25ms 0.32% 38.47% 328ms 4.17% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 38.50% 324ms 4.12% std::set::set (inline) 32ms 0.41% 38.91% 317ms 4.03% std::_Rb_tree::_M_copy (inline) 4ms 0.051% 38.96% 312ms 3.97% Cell::ReadyToDivide 26ms 0.33% 39.29% 307ms 3.90% std::num_put::_M_insert_float 1ms 0.013% 39.31% 301ms 3.83% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.31% 299ms 3.80% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 39.31% 297ms 3.78% OutputFileHandler::OpenOutputFile 95ms 1.21% 40.51% 296ms 3.76% __GI___libc_free 6ms 0.076% 40.59% 293ms 3.73% Element::Element 94ms 1.20% 41.79% 282ms 3.59% std::_Rb_tree::_M_clone_node (inline) 4ms 0.051% 41.84% 278ms 3.54% CellProliferativeTypesWriter::VisitCell 0 0% 41.84% 265ms 3.37% std::_Rb_tree::_M_drop_node (inline) 169ms 2.15% 43.99% 262ms 3.33% _int_malloc 6ms 0.076% 44.06% 258ms 3.28% std::__new_allocator::deallocate (inline) 0 0% 44.06% 253ms 3.22% std::allocator_traits::deallocate (inline) 11ms 0.14% 44.20% 243ms 3.09% divconqrecurse 10ms 0.13% 44.33% 232ms 2.95% CellPropertyCollection::HasProperty 0 0% 44.33% 231ms 2.94% Cell::HasCellProperty (inline) 61ms 0.78% 45.10% 230ms 2.92% mergehulls 12ms 0.15% 45.26% 224ms 2.85% AbstractCellProperty::IsType (inline) 6ms 0.076% 45.33% 222ms 2.82% std::__cxx11::collate::do_transform 23ms 0.29% 45.63% 221ms 2.81% TetrahedralMesh::Clear 13ms 0.17% 45.79% 216ms 2.75% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.038% 45.83% 211ms 2.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.83% 211ms 2.68% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 45.85% 206ms 2.62% ___vsnprintf 10ms 0.13% 45.98% 204ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 45.98% 204ms 2.59% __vsnprintf_internal (inline) 173ms 2.20% 48.18% 201ms 2.56% _int_free 29ms 0.37% 48.55% 200ms 2.54% __printf_buffer 5ms 0.064% 48.61% 199ms 2.53% Element::RegisterWithNodes (inline) 1ms 0.013% 48.63% 192ms 2.44% Node::AddElement 75ms 0.95% 49.58% 185ms 2.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 20ms 0.25% 49.83% 170ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 46ms 0.58% 50.42% 168ms 2.14% AbstractCellProperty::IsSame 10ms 0.13% 50.55% 165ms 2.10% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.55% 164ms 2.09% OutputFileHandler::CommonConstructor 0 0% 50.55% 164ms 2.09% OutputFileHandler::OutputFileHandler 13ms 0.17% 50.71% 163ms 2.07% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 50.71% 163ms 2.07% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 50.72% 158ms 2.01% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.1% 50.83% 156ms 1.98% __printf_fp_l_buffer 0 0% 50.83% 156ms 1.98% __printf_fp_spec (inline) 1ms 0.013% 50.84% 149ms 1.89% boost::numeric::ublas::vector_assign (inline) 122ms 1.55% 52.39% 146ms 1.86% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 52.39% 146ms 1.86% std::basic_ofstream::basic_ofstream (inline) 76ms 0.97% 53.36% 145ms 1.84% __printf_fp_buffer_1 2ms 0.025% 53.38% 143ms 1.82% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 53.40% 142ms 1.81% std::basic_ofstream::open (inline) 1ms 0.013% 53.41% 141ms 1.79% std::basic_filebuf::open 5ms 0.064% 53.47% 140ms 1.78% Node::~Node 4ms 0.051% 53.52% 140ms 1.78% boost::numeric::ublas::c_vector::c_vector (inline) 58ms 0.74% 54.26% 136ms 1.73% std::__ostream_insert 16ms 0.2% 54.46% 132ms 1.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 54.48% 132ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.23% 54.70% 132ms 1.68% AbstractTetrahedralElement::RefreshJacobian 48ms 0.61% 55.32% 130ms 1.65% std::num_put::_M_insert_int 9ms 0.11% 55.43% 124ms 1.58% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 55.43% 123ms 1.56% FilesystemPermissions::SetFilePermissions (inline) 123ms 1.56% 56.99% 123ms 1.56% __GI_fchmodat 0 0% 56.99% 123ms 1.56% std::filesystem::permissions 0 0% 56.99% 122ms 1.55% AbstractCellPopulation::CloseRoundRobinWritersFiles 27ms 0.34% 57.34% 122ms 1.55% std::type_info::operator== (inline) 0 0% 57.34% 121ms 1.54% AbstractCellBasedWriter::CloseFile 1ms 0.013% 57.35% 121ms 1.54% std::basic_ofstream::close (inline) 120ms 1.53% 58.88% 120ms 1.53% std::_Rb_tree_increment 0 0% 58.88% 120ms 1.53% std::basic_filebuf::close 4ms 0.051% 58.93% 120ms 1.53% std::operator<< (inline) 9ms 0.11% 59.04% 116ms 1.48% boost::detail::shared_count::~shared_count (inline) 38ms 0.48% 59.52% 116ms 1.48% boost::numeric::ublas::indexing_vector_assign 0 0% 59.52% 116ms 1.48% boost::shared_ptr::~shared_ptr (inline) 108ms 1.37% 60.90% 108ms 1.37% incircle 105ms 1.34% 62.23% 106ms 1.35% boost::detail::sp_counted_base::release 1ms 0.013% 62.25% 106ms 1.35% std::__basic_file::open 0 0% 62.25% 105ms 1.34% _IO_new_fopen 0 0% 62.25% 105ms 1.34% __fopen_internal (inline) 2ms 0.025% 62.27% 105ms 1.34% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 62.28% 104ms 1.32% _IO_new_file_fopen 57ms 0.72% 63.01% 103ms 1.31% AbstractElement::GetNodeLocation 0 0% 63.01% 102ms 1.30% __GI__IO_file_open 4ms 0.051% 63.06% 102ms 1.30% alternateaxes 2ms 0.025% 63.08% 101ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 63.10% 100ms 1.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 99ms 1.26% 64.36% 99ms 1.26% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 64.36% 99ms 1.26% std::vector::push_back (inline) 89ms 1.13% 65.49% 98ms 1.25% vertexmedian 10ms 0.13% 65.62% 96ms 1.22% std::vector::_M_realloc_insert 94ms 1.20% 66.81% 94ms 1.20% std::_Rb_tree_insert_and_rebalance 5ms 0.064% 66.87% 93ms 1.18% AbstractTetrahedralElement::AbstractTetrahedralElement 91ms 1.16% 68.03% 91ms 1.16% __libc_open64 90ms 1.14% 69.18% 90ms 1.14% __GI___fstatat64 0 0% 69.18% 89ms 1.13% Cell::GetCellId 1ms 0.013% 69.19% 89ms 1.13% std::basic_filebuf::_M_convert_to_external 0 0% 69.19% 89ms 1.13% std::basic_filebuf::_M_terminate_output 0 0% 69.19% 89ms 1.13% std::basic_filebuf::overflow 87ms 1.11% 70.30% 88ms 1.12% __GI___libc_write 43ms 0.55% 70.84% 88ms 1.12% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 70.85% 88ms 1.12% std::__basic_file::xsputn 0 0% 70.85% 88ms 1.12% std::filesystem::status 3ms 0.038% 70.89% 85ms 1.08% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.89% 83ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.89% 83ms 1.06% std::filesystem::create_directory 82ms 1.04% 71.94% 82ms 1.04% [libchaste_cell_based.so] 47ms 0.6% 72.53% 79ms 1.00% std::basic_filebuf::xsputn 53ms 0.67% 73.21% 75ms 0.95% malloc_consolidate 11ms 0.14% 73.35% 73ms 0.93% CellPropertyCollection::AddProperty 63ms 0.8% 74.15% 70ms 0.89% vertexsort 54ms 0.69% 74.83% 69ms 0.88% std::basic_streambuf::xsputn 0 0% 74.83% 68ms 0.86% tcache_get (inline) 68ms 0.86% 75.70% 68ms 0.86% tcache_get_n (inline) 3ms 0.038% 75.74% 66ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 66ms 0.84% 76.58% 66ms 0.84% [libchaste_mesh.so] 1ms 0.013% 76.59% 65ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeB 64ms 0.81% 77.40% 64ms 0.81% Node::GetIndex 2ms 0.025% 77.43% 58ms 0.74% Node::ClearAppliedForce 2ms 0.025% 77.45% 58ms 0.74% Node::ConstructNodeAttributes (inline) 0 0% 77.45% 58ms 0.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.45% 58ms 0.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 49ms 0.62% 78.08% 57ms 0.72% AbstractElement::GetNodeGlobalIndex 57ms 0.72% 78.80% 57ms 0.72% counterclockwise 55ms 0.7% 79.50% 55ms 0.7% boost::shared_ptr::operator-> (inline) 29ms 0.37% 79.87% 54ms 0.69% AbstractTetrahedralMesh::GetElement 0 0% 79.87% 54ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.87% 54ms 0.69% std::__new_allocator::destroy (inline) 0 0% 79.87% 54ms 0.69% std::allocator_traits::destroy (inline) 42ms 0.53% 80.40% 54ms 0.69% std::num_put::do_put 53ms 0.67% 81.08% 53ms 0.67% __memcpy_avx_unaligned_erms 52ms 0.66% 81.74% 52ms 0.66% [libstdc++.so.6.0.33] 50ms 0.64% 82.38% 50ms 0.64% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.38% 49ms 0.62% std::map::find (inline) 15ms 0.19% 82.57% 46ms 0.58% AbstractCellCycleModel::GetAge 0 0% 82.57% 46ms 0.58% AbstractCentreBasedCellPopulation::CreateCellPair 6ms 0.076% 82.64% 46ms 0.58% std::_Vector_base::_M_deallocate (inline) 0 0% 82.64% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 43ms 0.55% 83.19% 45ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 83.19% 44ms 0.56% AbstractCentreBasedCellPopulation::IsMarkedSpring 44ms 0.56% 83.75% 44ms 0.56% std::vector::size (inline) 23ms 0.29% 84.04% 43ms 0.55% boost::numeric::ublas::c_matrix::operator() 43ms 0.55% 84.59% 43ms 0.55% std::ostream::sentry::sentry 0 0% 84.59% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 11ms 0.14% 84.73% 42ms 0.53% NodeAttributes::NodeAttributes 0 0% 84.73% 42ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 84.74% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 84.74% 42ms 0.53% std::allocator_traits::construct (inline) 0 0% 84.74% 41ms 0.52% BoundaryNodeWriter::Visit 0 0% 84.74% 41ms 0.52% boost::numeric::ublas::norm_2 (inline) 41ms 0.52% 85.26% 41ms 0.52% boost::numeric::ublas::same_impl_ex 12ms 0.15% 85.41% 41ms 0.52% boost::numeric::ublas::vector_norm_2::apply (inline) 12ms 0.15% 85.57% 40ms 0.51% Inverse 0 0% 85.57% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 85.57% 40ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 0 0% 85.57% 40ms 0.51% std::vector::vector (inline)