File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6685ms, 84.73% of 7890ms total Dropped 568 nodes (cum <= 39.45ms) flat flat% sum% cum cum% 0 0% 0% 7856ms 99.57% __libc_start_call_main 0 0% 0% 7856ms 99.57% __libc_start_main_impl 0 0% 0% 7856ms 99.57% _start 0 0% 0% 7842ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7842ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7842ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7842ms 99.39% main 0 0% 0% 7805ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7805ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7805ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7804ms 98.91% AbstractCellBasedSimulation::Solve 0 0% 0% 3355ms 42.52% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2924ms 37.06% AbstractCellPopulation::WriteResultsToFiles 4ms 0.051% 0.063% 2862ms 36.27% MeshBasedCellPopulation::Update 0 0% 0.063% 1520ms 19.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.076% 1419ms 17.98% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.076% 1391ms 17.63% MutableMesh::ReMesh 0 0% 0.076% 1377ms 17.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.051% 0.13% 1315ms 16.67% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.38% 1225ms 15.53% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.43% 1.81% 1024ms 12.98% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.076% 1.89% 944ms 11.96% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.038% 1.93% 942ms 11.94% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 12ms 0.15% 2.08% 939ms 11.90% CellPropertyCollection::GetPropertiesType (inline) 270ms 3.42% 5.50% 929ms 11.77% __dynamic_cast 433ms 5.49% 10.99% 919ms 11.65% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.1% 11.09% 891ms 11.29% CellPopulationElementWriter::Visit 45ms 0.57% 11.66% 827ms 10.48% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 1ms 0.013% 11.67% 800ms 10.14% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.051% 11.72% 745ms 9.44% AbstractCellProperty::IsSubType (inline) 21ms 0.27% 11.99% 691ms 8.76% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 12.10% 690ms 8.75% TetrahedralMesh::ImportFromMesher 5ms 0.063% 12.17% 631ms 8.00% std::ostream::operator<< (inline) 87ms 1.10% 13.27% 624ms 7.91% std::ostream::_M_insert 40ms 0.51% 13.78% 586ms 7.43% operator new 7ms 0.089% 13.87% 580ms 7.35% std::set::insert (inline) 15ms 0.19% 14.06% 573ms 7.26% std::_Rb_tree::_M_insert_unique 1ms 0.013% 14.07% 559ms 7.08% Cell::GetCellProliferativeType 2ms 0.025% 14.09% 545ms 6.91% triangulate 42ms 0.53% 14.63% 542ms 6.87% std::map::operator[] (partial-inline) 196ms 2.48% 17.11% 541ms 6.86% __GI___libc_malloc 524ms 6.64% 23.75% 524ms 6.64% __strcmp_avx2 36ms 0.46% 24.21% 524ms 6.64% std::__new_allocator::allocate (inline) 20ms 0.25% 24.46% 521ms 6.60% std::_Rb_tree::find (inline) 0 0% 24.46% 518ms 6.57% std::allocator_traits::allocate (inline) 7ms 0.089% 24.55% 498ms 6.31% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.038% 24.59% 483ms 6.12% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.59% 478ms 6.06% std::set::count (inline) 0 0% 24.59% 475ms 6.02% delaunay 1ms 0.013% 24.60% 473ms 5.99% divconqdelaunay 219ms 2.78% 27.38% 467ms 5.92% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.38% 459ms 5.82% std::_Rb_tree::_M_create_node (inline) 0 0% 27.38% 450ms 5.70% std::_Rb_tree::lower_bound (inline) 0 0% 27.38% 450ms 5.70% std::map::lower_bound (inline) 0 0% 27.38% 435ms 5.51% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.38% 418ms 5.30% std::_Rb_tree::_M_get_node (inline) 32ms 0.41% 27.78% 409ms 5.18% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.78% 383ms 4.85% std::set::~set (inline) 84ms 1.06% 28.85% 377ms 4.78% std::_Rb_tree::_M_erase 1ms 0.013% 28.86% 376ms 4.77% NodeLocationWriter::Visit 4ms 0.051% 28.91% 369ms 4.68% Cell::GetMutationState 19ms 0.24% 29.15% 355ms 4.50% std::_Rb_tree::_Rb_tree (partial-inline) 23ms 0.29% 29.44% 353ms 4.47% std::_Rb_tree::_M_insert_ (inline) 9ms 0.11% 29.56% 350ms 4.44% std::less::operator() (inline) 341ms 4.32% 33.88% 341ms 4.32% std::operator< (inline) 7ms 0.089% 33.97% 335ms 4.25% Cell::ReadyToDivide 28ms 0.35% 34.32% 335ms 4.25% std::num_put::_M_insert_float 0 0% 34.32% 326ms 4.13% std::set::set (inline) 122ms 1.55% 35.87% 303ms 3.84% __GI___libc_free 0 0% 35.87% 301ms 3.81% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 27ms 0.34% 36.21% 300ms 3.80% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 36.22% 297ms 3.76% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.025% 36.25% 294ms 3.73% Element::Element 14ms 0.18% 36.43% 293ms 3.71% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 36.44% 291ms 3.69% OutputFileHandler::OpenOutputFile 286ms 3.62% 40.06% 286ms 3.62% std::_Rb_tree::_S_right (inline) 1ms 0.013% 40.08% 284ms 3.60% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 40.09% 283ms 3.59% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.051% 40.14% 281ms 3.56% divconqrecurse 82ms 1.04% 41.18% 271ms 3.43% mergehulls 0 0% 41.18% 271ms 3.43% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 41.19% 270ms 3.42% CellProliferativeTypesWriter::VisitCell 73ms 0.93% 42.12% 266ms 3.37% std::_Rb_tree::_M_clone_node (inline) 13ms 0.16% 42.28% 263ms 3.33% std::__new_allocator::deallocate (inline) 2ms 0.025% 42.31% 262ms 3.32% std::__cxx11::collate::do_transform 0 0% 42.31% 259ms 3.28% std::allocator_traits::deallocate (inline) 164ms 2.08% 44.39% 255ms 3.23% _int_malloc 3ms 0.038% 44.42% 249ms 3.16% ___vsnprintf 3ms 0.038% 44.46% 246ms 3.12% AbstractCellProperty::IsType (inline) 0 0% 44.46% 246ms 3.12% __vsnprintf_internal (inline) 8ms 0.1% 44.56% 244ms 3.09% CellPropertyCollection::HasProperty 0 0% 44.56% 241ms 3.05% Cell::HasCellProperty (inline) 42ms 0.53% 45.10% 237ms 3.00% __printf_buffer 7ms 0.089% 45.18% 221ms 2.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.18% 215ms 2.72% std::_Rb_tree::_M_put_node (inline) 5ms 0.063% 45.25% 208ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 79ms 1.00% 46.25% 205ms 2.60% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.038% 46.29% 204ms 2.59% Element::RegisterWithNodes (inline) 3ms 0.038% 46.32% 200ms 2.53% Node::AddElement 17ms 0.22% 46.54% 195ms 2.47% TetrahedralMesh::Clear 51ms 0.65% 47.19% 191ms 2.42% AbstractCellProperty::IsSame 149ms 1.89% 49.07% 181ms 2.29% _int_free 2ms 0.025% 49.10% 179ms 2.27% __printf_fp_spec (inline) 6ms 0.076% 49.18% 177ms 2.24% __printf_fp_l_buffer 6ms 0.076% 49.25% 169ms 2.14% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.16% 49.42% 162ms 2.05% AbstractTetrahedralElement::CalculateJacobian 98ms 1.24% 50.66% 162ms 2.05% __printf_fp_buffer_1 0 0% 50.66% 153ms 1.94% AbstractCellBasedWriter::CloseFile 0 0% 50.66% 153ms 1.94% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.66% 153ms 1.94% std::basic_ofstream::close (inline) 1ms 0.013% 50.67% 152ms 1.93% std::basic_filebuf::close 1ms 0.013% 50.68% 151ms 1.91% OutputFileHandler::CommonConstructor 0 0% 50.68% 151ms 1.91% OutputFileHandler::OutputFileHandler 30ms 0.38% 51.06% 148ms 1.88% TetrahedralMesh::EdgesEnd (partial-inline) 5ms 0.063% 51.13% 146ms 1.85% boost::numeric::ublas::vector_assign (inline) 0 0% 51.13% 145ms 1.84% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.13% 143ms 1.81% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.051% 51.18% 143ms 1.81% boost::numeric::ublas::c_vector::c_vector (inline) 26ms 0.33% 51.51% 140ms 1.77% std::num_put::_M_insert_int 30ms 0.38% 51.89% 140ms 1.77% std::type_info::operator== (inline) 0 0% 51.89% 138ms 1.75% std::basic_ofstream::basic_ofstream (inline) 4ms 0.051% 51.94% 137ms 1.74% AbstractTetrahedralElement::CalculateInverseJacobian 62ms 0.79% 52.72% 137ms 1.74% std::__ostream_insert 0 0% 52.72% 133ms 1.69% std::basic_filebuf::open 0 0% 52.72% 133ms 1.69% std::basic_ofstream::open (inline) 131ms 1.66% 54.39% 131ms 1.66% incircle 13ms 0.16% 54.55% 129ms 1.63% AbstractTetrahedralElement::RefreshJacobian 11ms 0.14% 54.69% 125ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.038% 54.73% 122ms 1.55% alternateaxes 0 0% 54.73% 121ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 54.74% 121ms 1.53% std::filesystem::permissions 120ms 1.52% 56.26% 120ms 1.52% __GI_fchmodat 0 0% 56.26% 119ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 106ms 1.34% 57.60% 119ms 1.51% vertexmedian 1ms 0.013% 57.62% 115ms 1.46% std::basic_filebuf::_M_terminate_output 19ms 0.24% 57.86% 114ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 57.87% 114ms 1.44% std::basic_filebuf::overflow 2ms 0.025% 57.90% 114ms 1.44% std::operator<< (inline) 2ms 0.025% 57.92% 113ms 1.43% std::basic_filebuf::_M_convert_to_external 110ms 1.39% 59.32% 111ms 1.41% __GI___libc_write 26ms 0.33% 59.65% 111ms 1.41% boost::numeric::ublas::indexing_vector_assign 0 0% 59.65% 111ms 1.41% std::__basic_file::xsputn 9ms 0.11% 59.76% 110ms 1.39% boost::detail::shared_count::~shared_count (inline) 0 0% 59.76% 110ms 1.39% boost::shared_ptr::~shared_ptr (inline) 5ms 0.063% 59.82% 108ms 1.37% Node::~Node 43ms 0.54% 60.37% 106ms 1.34% boost::shared_ptr::shared_ptr (inline) 8ms 0.1% 60.47% 105ms 1.33% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 60.48% 104ms 1.32% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 58ms 0.74% 61.22% 103ms 1.31% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 103ms 1.31% 62.52% 103ms 1.31% std::_Rb_tree_increment 0 0% 62.52% 102ms 1.29% _IO_new_fopen 1ms 0.013% 62.53% 102ms 1.29% __fopen_internal (inline) 102ms 1.29% 63.83% 102ms 1.29% std::_Rb_tree_insert_and_rebalance 0 0% 63.83% 102ms 1.29% std::__basic_file::open 42ms 0.53% 64.36% 101ms 1.28% AbstractElement::GetNodeLocation 0 0% 64.36% 100ms 1.27% std::_Vector_base::_M_allocate (inline) 3ms 0.038% 64.40% 98ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 64.40% 98ms 1.24% _IO_new_file_fopen 3ms 0.038% 64.44% 98ms 1.24% __GI__IO_file_open 98ms 1.24% 65.68% 98ms 1.24% boost::detail::sp_counted_base::release 5ms 0.063% 65.74% 97ms 1.23% AbstractTetrahedralElement::AbstractTetrahedralElement 61ms 0.77% 66.51% 93ms 1.18% std::basic_filebuf::xsputn 5ms 0.063% 66.58% 93ms 1.18% std::vector::push_back (inline) 0 0% 66.58% 91ms 1.15% Cell::GetCellId 91ms 1.15% 67.73% 91ms 1.15% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 87ms 1.10% 68.83% 88ms 1.12% __libc_open64 6ms 0.076% 68.91% 85ms 1.08% std::vector::_M_realloc_insert 3ms 0.038% 68.95% 83ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.051% 69.00% 79ms 1.00% CellPropertyCollection::AddProperty 58ms 0.74% 69.73% 79ms 1.00% std::basic_streambuf::xsputn 0 0% 69.73% 79ms 1.00% tcache_get (inline) 79ms 1.00% 70.74% 79ms 1.00% tcache_get_n (inline) 2ms 0.025% 70.76% 78ms 0.99% std::filesystem::status 76ms 0.96% 71.72% 76ms 0.96% [libchaste_cell_based.so] 74ms 0.94% 72.66% 74ms 0.94% __GI___fstatat64 5ms 0.063% 72.72% 71ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 72.72% 70ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 48ms 0.61% 73.33% 70ms 0.89% malloc_consolidate 1ms 0.013% 73.35% 70ms 0.89% std::filesystem::create_directory 66ms 0.84% 74.18% 68ms 0.86% vertexsort 50ms 0.63% 74.82% 64ms 0.81% std::num_put::do_put 0 0% 74.82% 63ms 0.8% AbstractCentreBasedCellPopulation::CreateCellPair 59ms 0.75% 75.56% 63ms 0.8% boost::detail::shared_count::shared_count (inline) 62ms 0.79% 76.35% 62ms 0.79% Node::GetIndex 1ms 0.013% 76.36% 62ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 76.36% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.36% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 61ms 0.77% 77.14% 61ms 0.77% std::vector::size (inline) 59ms 0.75% 77.88% 59ms 0.75% boost::numeric::ublas::c_vector::operator() (partial-inline) 34ms 0.43% 78.31% 58ms 0.74% boost::numeric::ublas::c_matrix::operator() (partial-inline) 57ms 0.72% 79.04% 57ms 0.72% counterclockwise 40ms 0.51% 79.54% 56ms 0.71% AbstractElement::GetNodeGlobalIndex 56ms 0.71% 80.25% 56ms 0.71% __memcpy_avx_unaligned_erms 0 0% 80.25% 56ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.25% 56ms 0.71% std::__new_allocator::destroy (inline) 0 0% 80.25% 56ms 0.71% std::allocator_traits::destroy (inline) 0 0% 80.25% 55ms 0.7% BoundaryNodeWriter::Visit 1ms 0.013% 80.27% 52ms 0.66% Node::ClearAppliedForce 3ms 0.038% 80.30% 52ms 0.66% Node::ConstructNodeAttributes (inline) 52ms 0.66% 80.96% 52ms 0.66% [libchaste_mesh.so] 52ms 0.66% 81.62% 52ms 0.66% [libstdc++.so.6.0.33] 0 0% 81.62% 50ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 81.62% 50ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.62% 48ms 0.61% boost::numeric::ublas::norm_2 (inline) 16ms 0.2% 81.83% 48ms 0.61% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 81.83% 47ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 15ms 0.19% 82.02% 46ms 0.58% AbstractCellCycleModel::GetAge 30ms 0.38% 82.40% 46ms 0.58% AbstractTetrahedralMesh::GetElement 46ms 0.58% 82.98% 46ms 0.58% std::ostream::sentry::sentry 19ms 0.24% 83.22% 45ms 0.57% AbstractTetrahedralMesh::GetNumAllElements 4ms 0.051% 83.27% 45ms 0.57% std::_Vector_base::_M_deallocate (inline) 44ms 0.56% 83.83% 44ms 0.56% boost::shared_ptr::operator-> (inline) 3ms 0.038% 83.87% 44ms 0.56% std::__new_allocator::construct (inline) 0 0% 83.87% 44ms 0.56% std::allocator_traits::construct (inline) 0 0% 83.87% 42ms 0.53% std::vector::vector (inline) 41ms 0.52% 84.39% 41ms 0.52% Node::IsDeleted 0 0% 84.39% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.39% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 27ms 0.34% 84.73% 40ms 0.51% CellPropertyCollection::GetProperty 0 0% 84.73% 40ms 0.51% std::_Vector_base::_Vector_base (inline) 0 0% 84.73% 40ms 0.51% std::map::find (inline)