File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6488ms, 83.49% of 7771ms total Dropped 554 nodes (cum <= 38.85ms) flat flat% sum% cum cum% 0 0% 0% 7733ms 99.51% __libc_start_call_main 0 0% 0% 7733ms 99.51% __libc_start_main_impl 0 0% 0% 7733ms 99.51% _start 0 0% 0% 7717ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7717ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7717ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7717ms 99.31% main 0 0% 0% 7682ms 98.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7682ms 98.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7682ms 98.85% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7679ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0% 3299ms 42.45% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2904ms 37.37% AbstractCellPopulation::WriteResultsToFiles 3ms 0.039% 0.039% 2852ms 36.70% MeshBasedCellPopulation::Update 1ms 0.013% 0.051% 1468ms 18.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1425ms 18.34% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.064% 1355ms 17.44% MutableMesh::ReMesh 0 0% 0.064% 1301ms 16.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.077% 0.14% 1238ms 15.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.39% 1236ms 15.91% MeshBasedCellPopulation::SpringIterator::operator++ 114ms 1.47% 1.85% 1006ms 12.95% TetrahedralMesh::EdgeIterator::operator++ 471ms 6.06% 7.91% 985ms 12.68% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.12% 8.03% 978ms 12.59% CellPopulationElementWriter::Visit 5ms 0.064% 8.09% 893ms 11.49% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.064% 8.16% 858ms 11.04% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.013% 8.17% 844ms 10.86% AbstractTwoBodyInteractionForce::AddForceContribution 231ms 2.97% 11.14% 819ms 10.54% __dynamic_cast 26ms 0.33% 11.48% 762ms 9.81% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.039% 11.52% 762ms 9.81% MeshBasedCellPopulation::AcceptCellWriter 45ms 0.58% 12.10% 758ms 9.75% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 3ms 0.039% 12.13% 653ms 8.40% AbstractCellProperty::IsSubType (inline) 12ms 0.15% 12.29% 644ms 8.29% TetrahedralMesh::ImportFromMesher 58ms 0.75% 13.04% 640ms 8.24% std::map::operator[] (partial-inline) 2ms 0.026% 13.06% 579ms 7.45% std::ostream::operator<< (inline) 84ms 1.08% 14.14% 575ms 7.40% std::ostream::_M_insert 1ms 0.013% 14.16% 570ms 7.33% triangulate 30ms 0.39% 14.54% 557ms 7.17% operator new 6ms 0.077% 14.62% 530ms 6.82% Cell::GetCellProliferativeType 0 0% 14.62% 527ms 6.78% std::_Rb_tree::lower_bound (inline) 0 0% 14.62% 527ms 6.78% std::map::lower_bound (inline) 190ms 2.44% 17.06% 520ms 6.69% __GI___libc_malloc 24ms 0.31% 17.37% 514ms 6.61% std::_Rb_tree::find (inline) 40ms 0.51% 17.89% 510ms 6.56% std::__new_allocator::allocate (inline) 1ms 0.013% 17.90% 509ms 6.55% delaunay 0 0% 17.90% 507ms 6.52% divconqdelaunay 0 0% 17.90% 506ms 6.51% std::allocator_traits::allocate (inline) 8ms 0.1% 18.00% 484ms 6.23% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.039% 18.04% 478ms 6.15% std::set::insert (inline) 7ms 0.09% 18.13% 475ms 6.11% std::_Rb_tree::_M_insert_unique 0 0% 18.13% 470ms 6.05% std::set::count (inline) 454ms 5.84% 23.97% 454ms 5.84% __strcmp_avx2 36ms 0.46% 24.44% 441ms 5.67% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.077% 24.51% 434ms 5.58% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.51% 430ms 5.53% std::_Rb_tree::_M_create_node (inline) 211ms 2.72% 27.23% 422ms 5.43% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.23% 412ms 5.30% std::set::~set (inline) 0 0% 27.23% 404ms 5.20% std::_Rb_tree::_Alloc_node::operator() (inline) 87ms 1.12% 28.35% 401ms 5.16% std::_Rb_tree::_M_erase 0 0% 28.35% 394ms 5.07% std::_Rb_tree::_M_get_node (inline) 16ms 0.21% 28.55% 379ms 4.88% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.026% 28.58% 360ms 4.63% NodeLocationWriter::Visit 9ms 0.12% 28.70% 356ms 4.58% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.077% 28.77% 354ms 4.56% std::set::set (inline) 5ms 0.064% 28.84% 350ms 4.50% Cell::GetMutationState 11ms 0.14% 28.98% 345ms 4.44% std::less::operator() (inline) 334ms 4.30% 33.28% 334ms 4.30% std::operator< (inline) 38ms 0.49% 33.77% 326ms 4.20% std::_Rb_tree::_M_copy (inline) 29ms 0.37% 34.14% 320ms 4.12% std::num_put::_M_insert_float 3ms 0.039% 34.18% 316ms 4.07% MeshBasedCellPopulation::GetDampingConstant 2ms 0.026% 34.20% 313ms 4.03% AbstractCentreBasedCellPopulation::GetDampingConstant 309ms 3.98% 38.18% 309ms 3.98% std::_Rb_tree::_S_right (inline) 0 0% 38.18% 305ms 3.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.18% 303ms 3.90% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.18% 301ms 3.87% OutputFileHandler::OpenOutputFile 119ms 1.53% 39.71% 297ms 3.82% __GI___libc_free 10ms 0.13% 39.84% 296ms 3.81% std::_Rb_tree::_M_insert_ (inline) 5ms 0.064% 39.90% 291ms 3.74% Cell::ReadyToDivide 0 0% 39.90% 291ms 3.74% std::_Rb_tree::_M_drop_node (inline) 74ms 0.95% 40.86% 282ms 3.63% std::_Rb_tree::_M_clone_node (inline) 12ms 0.15% 41.01% 269ms 3.46% std::__new_allocator::deallocate (inline) 0 0% 41.01% 264ms 3.40% std::allocator_traits::deallocate (inline) 13ms 0.17% 41.18% 263ms 3.38% divconqrecurse 5ms 0.064% 41.24% 245ms 3.15% CellProliferativeTypesWriter::VisitCell 163ms 2.10% 43.34% 244ms 3.14% _int_malloc 78ms 1.00% 44.34% 242ms 3.11% mergehulls 2ms 0.026% 44.37% 241ms 3.10% Element::Element 2ms 0.026% 44.40% 241ms 3.10% std::__cxx11::collate::do_transform 2ms 0.026% 44.42% 232ms 2.99% ___vsnprintf 0 0% 44.42% 230ms 2.96% __vsnprintf_internal (inline) 9ms 0.12% 44.54% 229ms 2.95% CellPropertyCollection::HasProperty 0 0% 44.54% 229ms 2.95% std::_Rb_tree::_M_put_node (inline) 0 0% 44.54% 228ms 2.93% Cell::HasCellProperty (inline) 28ms 0.36% 44.90% 223ms 2.87% __printf_buffer 1ms 0.013% 44.91% 215ms 2.77% AbstractCellProperty::IsType (inline) 16ms 0.21% 45.12% 200ms 2.57% TetrahedralMesh::Clear 7ms 0.09% 45.21% 194ms 2.50% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.051% 45.26% 188ms 2.42% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.077% 45.34% 180ms 2.32% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 156ms 2.01% 47.34% 178ms 2.29% _int_free 1ms 0.013% 47.36% 174ms 2.24% __printf_fp_spec (inline) 9ms 0.12% 47.47% 173ms 2.23% __printf_fp_l_buffer 69ms 0.89% 48.36% 172ms 2.21% std::_Rb_tree::_M_get_insert_unique_pos (inline) 40ms 0.51% 48.87% 161ms 2.07% AbstractCellProperty::IsSame 37ms 0.48% 49.35% 158ms 2.03% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 49.35% 155ms 1.99% std::basic_ofstream::basic_ofstream (inline) 11ms 0.14% 49.49% 154ms 1.98% AbstractTetrahedralElement::CalculateJacobian 76ms 0.98% 50.47% 152ms 1.96% __printf_fp_buffer_1 0 0% 50.47% 150ms 1.93% std::basic_ofstream::open (inline) 4ms 0.051% 50.52% 149ms 1.92% Element::RegisterWithNodes (inline) 1ms 0.013% 50.53% 149ms 1.92% std::basic_filebuf::open 1ms 0.013% 50.55% 145ms 1.87% OutputFileHandler::CommonConstructor 0 0% 50.55% 145ms 1.87% OutputFileHandler::OutputFileHandler 1ms 0.013% 50.56% 144ms 1.85% Node::AddElement 1ms 0.013% 50.57% 139ms 1.79% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 50.57% 138ms 1.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.57% 136ms 1.75% AbstractCellBasedWriter::CloseFile 1ms 0.013% 50.59% 136ms 1.75% std::basic_ofstream::close (inline) 56ms 0.72% 51.31% 135ms 1.74% std::__ostream_insert 1ms 0.013% 51.32% 135ms 1.74% std::basic_filebuf::close 11ms 0.14% 51.46% 131ms 1.69% std::_Rb_tree_const_iterator::operator++ (inline) 34ms 0.44% 51.90% 131ms 1.69% std::num_put::_M_insert_int 22ms 0.28% 52.18% 129ms 1.66% MeshBasedCellPopulation::SpringIterator::SpringIterator 10ms 0.13% 52.31% 129ms 1.66% Node::~Node 127ms 1.63% 53.94% 127ms 1.63% std::_Rb_tree_increment 2ms 0.026% 53.97% 126ms 1.62% boost::numeric::ublas::vector_assign (inline) 0 0% 53.97% 121ms 1.56% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 53.98% 121ms 1.56% alternateaxes 27ms 0.35% 54.33% 121ms 1.56% std::type_info::operator== (inline) 10ms 0.13% 54.46% 120ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.46% 120ms 1.54% FilesystemPermissions::SetFilePermissions (inline) 120ms 1.54% 56.00% 120ms 1.54% __GI_fchmodat 0 0% 56.00% 120ms 1.54% std::filesystem::permissions 113ms 1.45% 57.46% 120ms 1.54% vertexmedian 3ms 0.039% 57.50% 119ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 57.50% 117ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 57.51% 115ms 1.48% std::__basic_file::open 3ms 0.039% 57.55% 114ms 1.47% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 57.55% 114ms 1.47% _IO_new_fopen 0 0% 57.55% 114ms 1.47% __fopen_internal (inline) 14ms 0.18% 57.73% 113ms 1.45% AbstractTetrahedralElement::RefreshJacobian 71ms 0.91% 58.64% 113ms 1.45% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 58.65% 113ms 1.45% std::_Vector_base::_M_allocate (inline) 3ms 0.039% 58.69% 113ms 1.45% std::operator<< (inline) 2ms 0.026% 58.72% 111ms 1.43% _IO_new_file_fopen 50ms 0.64% 59.36% 110ms 1.42% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 59.37% 109ms 1.40% __GI__IO_file_open 7ms 0.09% 59.46% 109ms 1.40% boost::detail::shared_count::~shared_count (inline) 0 0% 59.46% 109ms 1.40% boost::shared_ptr::~shared_ptr (inline) 4ms 0.051% 59.52% 106ms 1.36% std::vector::push_back (inline) 92ms 1.18% 60.70% 102ms 1.31% vertexsort 100ms 1.29% 61.99% 101ms 1.30% boost::detail::sp_counted_base::release 101ms 1.30% 63.29% 101ms 1.30% incircle 1ms 0.013% 63.30% 99ms 1.27% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.12% 63.42% 97ms 1.25% std::vector::_M_realloc_insert 95ms 1.22% 64.64% 95ms 1.22% std::_Rb_tree_insert_and_rebalance 0 0% 64.64% 95ms 1.22% std::basic_filebuf::_M_terminate_output 2ms 0.026% 64.66% 94ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 30ms 0.39% 65.05% 94ms 1.21% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 65.06% 94ms 1.21% std::basic_filebuf::overflow 63ms 0.81% 65.87% 94ms 1.21% std::basic_streambuf::xsputn 92ms 1.18% 67.06% 93ms 1.20% __GI___libc_write 93ms 1.20% 68.25% 93ms 1.20% __libc_open64 0 0% 68.25% 93ms 1.20% std::__basic_file::xsputn 0 0% 68.25% 93ms 1.20% std::basic_filebuf::_M_convert_to_external 90ms 1.16% 69.41% 90ms 1.16% [libchaste_cell_based.so] 4ms 0.051% 69.46% 89ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 87ms 1.12% 70.58% 87ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.077% 70.66% 83ms 1.07% TetrahedralMesh::EdgeIterator::GetNodeB 31ms 0.4% 71.06% 81ms 1.04% AbstractElement::GetNodeLocation 0 0% 71.06% 78ms 1.00% tcache_get (inline) 78ms 1.00% 72.06% 78ms 1.00% tcache_get_n (inline) 1ms 0.013% 72.08% 76ms 0.98% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 72.08% 75ms 0.97% std::filesystem::create_directory 0 0% 72.08% 74ms 0.95% AbstractCellPopulation::GetLocationIndexUsingCell 74ms 0.95% 73.03% 74ms 0.95% std::vector::size (inline) 1ms 0.013% 73.04% 72ms 0.93% std::filesystem::status 71ms 0.91% 73.95% 71ms 0.91% __GI___fstatat64 71ms 0.91% 74.87% 71ms 0.91% __memcpy_avx_unaligned_erms 11ms 0.14% 75.01% 68ms 0.88% CellPropertyCollection::AddProperty 52ms 0.67% 75.68% 68ms 0.88% malloc_consolidate 40ms 0.51% 76.19% 68ms 0.88% std::basic_filebuf::xsputn 1ms 0.013% 76.21% 66ms 0.85% Cell::GetCellId 63ms 0.81% 77.02% 63ms 0.81% Node::GetIndex 63ms 0.81% 77.83% 63ms 0.81% counterclockwise 0 0% 77.83% 62ms 0.8% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.83% 62ms 0.8% std::__new_allocator::destroy (inline) 0 0% 77.83% 62ms 0.8% std::allocator_traits::destroy (inline) 50ms 0.64% 78.47% 61ms 0.78% AbstractElement::GetNodeGlobalIndex 32ms 0.41% 78.88% 61ms 0.78% AbstractTetrahedralMesh::GetElement 60ms 0.77% 79.66% 60ms 0.77% boost::detail::shared_count::shared_count (inline) 56ms 0.72% 80.38% 56ms 0.72% [libchaste_mesh.so] 2ms 0.026% 80.40% 54ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.40% 53ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 51ms 0.66% 81.06% 51ms 0.66% boost::numeric::ublas::c_vector::operator() (inline) 4ms 0.051% 81.11% 49ms 0.63% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 81.11% 48ms 0.62% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 30ms 0.39% 81.50% 48ms 0.62% boost::numeric::ublas::c_matrix::operator() (partial-inline) 41ms 0.53% 82.02% 48ms 0.62% std::num_put::do_put 10ms 0.13% 82.15% 46ms 0.59% AbstractTetrahedralMesh::GetNumAllElements 46ms 0.59% 82.74% 46ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 82.74% 44ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 82.74% 42ms 0.54% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 82.76% 42ms 0.54% Node::ClearAppliedForce 1ms 0.013% 82.77% 42ms 0.54% Node::ConstructNodeAttributes (inline) 0 0% 82.77% 42ms 0.54% std::vector::vector (inline) 3ms 0.039% 82.81% 41ms 0.53% std::__new_allocator::construct (inline) 0 0% 82.81% 41ms 0.53% std::allocator_traits::construct (inline) 0 0% 82.81% 40ms 0.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.81% 40ms 0.51% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 82.81% 39ms 0.5% BoundaryNodeWriter::Visit 14ms 0.18% 82.99% 39ms 0.5% Determinant (inline) 39ms 0.5% 83.49% 39ms 0.5% Node::IsDeleted 0 0% 83.49% 39ms 0.5% std::_Vector_base::_M_create_storage (inline) 0 0% 83.49% 39ms 0.5% std::_Vector_base::_Vector_base (inline)