File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6803ms, 84.90% of 8013ms total Dropped 585 nodes (cum <= 40.06ms) flat flat% sum% cum cum% 0 0% 0% 7976ms 99.54% __libc_start_call_main 0 0% 0% 7976ms 99.54% __libc_start_main_impl 0 0% 0% 7976ms 99.54% _start 0 0% 0% 7958ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7958ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7958ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7958ms 99.31% main 0 0% 0% 7914ms 98.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7914ms 98.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7914ms 98.76% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7911ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3432ms 42.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2970ms 37.06% MeshBasedCellPopulation::Update 1ms 0.012% 0.012% 2886ms 36.02% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.012% 1582ms 19.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.025% 1463ms 18.26% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.05% 1455ms 18.16% MutableMesh::ReMesh 0 0% 0.05% 1411ms 17.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.037% 0.087% 1367ms 17.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.17% 0.26% 1247ms 15.56% MeshBasedCellPopulation::SpringIterator::operator++ 99ms 1.24% 1.50% 1003ms 12.52% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.52% 983ms 12.27% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.037% 1.56% 954ms 11.91% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 409ms 5.10% 6.66% 948ms 11.83% std::_Rb_tree::_M_lower_bound (inline) 279ms 3.48% 10.15% 942ms 11.76% __dynamic_cast 6ms 0.075% 10.22% 910ms 11.36% CellPropertyCollection::GetPropertiesType (inline) 33ms 0.41% 10.63% 895ms 11.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.17% 10.81% 887ms 11.07% CellPopulationElementWriter::Visit 6ms 0.075% 10.88% 812ms 10.13% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.35% 11.23% 756ms 9.43% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.037% 11.27% 728ms 9.09% AbstractCellProperty::IsSubType (inline) 10ms 0.12% 11.39% 705ms 8.80% TetrahedralMesh::ImportFromMesher 0 0% 11.39% 597ms 7.45% std::ostream::operator<< (inline) 66ms 0.82% 12.22% 596ms 7.44% std::map::operator[] (partial-inline) 92ms 1.15% 13.37% 594ms 7.41% std::ostream::_M_insert 43ms 0.54% 13.90% 584ms 7.29% operator new 3ms 0.037% 13.94% 573ms 7.15% triangulate 9ms 0.11% 14.05% 536ms 6.69% std::set::insert (inline) 534ms 6.66% 20.72% 534ms 6.66% __strcmp_avx2 6ms 0.075% 20.79% 530ms 6.61% Cell::GetCellProliferativeType 8ms 0.1% 20.89% 528ms 6.59% std::_Rb_tree::_M_insert_unique 21ms 0.26% 21.15% 525ms 6.55% std::_Rb_tree::find (inline) 192ms 2.40% 23.55% 524ms 6.54% __GI___libc_malloc 29ms 0.36% 23.91% 520ms 6.49% std::__new_allocator::allocate (inline) 0 0% 23.91% 514ms 6.41% std::allocator_traits::allocate (inline) 2ms 0.025% 23.94% 512ms 6.39% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.94% 508ms 6.34% delaunay 3ms 0.037% 23.97% 508ms 6.34% divconqdelaunay 218ms 2.72% 26.69% 491ms 6.13% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.69% 479ms 5.98% std::set::count (inline) 0 0% 26.69% 476ms 5.94% std::_Rb_tree::lower_bound (inline) 0 0% 26.69% 476ms 5.94% std::map::lower_bound (inline) 3ms 0.037% 26.73% 448ms 5.59% AbstractCellBasedSimulation::DoCellBirth 38ms 0.47% 27.21% 448ms 5.59% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.21% 439ms 5.48% std::_Rb_tree::_M_create_node (inline) 0 0% 27.21% 418ms 5.22% std::set::~set (inline) 0 0% 27.21% 414ms 5.17% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.21% 410ms 5.12% std::_Rb_tree::_M_get_node (inline) 93ms 1.16% 28.37% 406ms 5.07% std::_Rb_tree::_M_erase 2ms 0.025% 28.39% 370ms 4.62% Cell::GetMutationState 20ms 0.25% 28.64% 362ms 4.52% std::_Rb_tree::_Rb_tree (partial-inline) 10ms 0.12% 28.77% 362ms 4.52% std::less::operator() (inline) 352ms 4.39% 33.16% 352ms 4.39% std::operator< (inline) 0 0% 33.16% 339ms 4.23% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 33.18% 338ms 4.22% NodeLocationWriter::Visit 0 0% 33.18% 337ms 4.21% AbstractCellBasedWriter::OpenOutputFileForAppend 334ms 4.17% 37.35% 334ms 4.17% std::_Rb_tree::_S_right (inline) 0 0% 37.35% 332ms 4.14% OutputFileHandler::OpenOutputFile 6ms 0.075% 37.43% 328ms 4.09% std::set::set (inline) 23ms 0.29% 37.71% 324ms 4.04% std::_Rb_tree::_M_insert_ (inline) 42ms 0.52% 38.24% 315ms 3.93% std::_Rb_tree::_M_copy (inline) 22ms 0.27% 38.51% 308ms 3.84% std::num_put::_M_insert_float 4ms 0.05% 38.56% 306ms 3.82% Element::Element 6ms 0.075% 38.64% 304ms 3.79% Cell::ReadyToDivide 7ms 0.087% 38.72% 300ms 3.74% AbstractCellPopulation::IsCellAttachedToLocationIndex 82ms 1.02% 39.75% 300ms 3.74% __GI___libc_free 6ms 0.075% 39.82% 297ms 3.71% divconqrecurse 3ms 0.037% 39.86% 289ms 3.61% MeshBasedCellPopulation::GetDampingConstant 0 0% 39.86% 288ms 3.59% std::_Rb_tree::_M_drop_node (inline) 4ms 0.05% 39.91% 286ms 3.57% AbstractCentreBasedCellPopulation::GetDampingConstant 80ms 1% 40.91% 283ms 3.53% mergehulls 10ms 0.12% 41.03% 274ms 3.42% std::__new_allocator::deallocate (inline) 0 0% 41.03% 271ms 3.38% std::allocator_traits::deallocate (inline) 76ms 0.95% 41.98% 268ms 3.34% std::_Rb_tree::_M_clone_node (inline) 163ms 2.03% 44.02% 265ms 3.31% _int_malloc 3ms 0.037% 44.05% 262ms 3.27% CellProliferativeTypesWriter::VisitCell 9ms 0.11% 44.17% 260ms 3.24% std::__cxx11::collate::do_transform 13ms 0.16% 44.33% 245ms 3.06% ___vsnprintf 4ms 0.05% 44.38% 244ms 3.05% AbstractCellProperty::IsType (inline) 4ms 0.05% 44.43% 242ms 3.02% CellPropertyCollection::HasProperty 0 0% 44.43% 240ms 3.00% Cell::HasCellProperty (inline) 0 0% 44.43% 240ms 3.00% std::_Rb_tree::_M_put_node (inline) 0 0% 44.43% 232ms 2.90% __vsnprintf_internal (inline) 28ms 0.35% 44.78% 229ms 2.86% __printf_buffer 183ms 2.28% 47.06% 218ms 2.72% _int_free 3ms 0.037% 47.10% 209ms 2.61% Element::RegisterWithNodes (inline) 11ms 0.14% 47.24% 203ms 2.53% TetrahedralMesh::Clear 2ms 0.025% 47.26% 202ms 2.52% Node::AddElement 9ms 0.11% 47.37% 201ms 2.51% MeshBasedCellPopulation::SpringsEnd (inline) 67ms 0.84% 48.21% 197ms 2.46% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.05% 48.26% 195ms 2.43% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.05% 48.31% 189ms 2.36% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.05% 48.36% 189ms 2.36% __printf_fp_l_buffer 0 0% 48.36% 189ms 2.36% __printf_fp_spec (inline) 34ms 0.42% 48.78% 183ms 2.28% AbstractCellProperty::IsSame 98ms 1.22% 50.01% 178ms 2.22% __printf_fp_buffer_1 40ms 0.5% 50.51% 174ms 2.17% TetrahedralMesh::EdgesEnd (partial-inline) 17ms 0.21% 50.72% 165ms 2.06% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.72% 163ms 2.03% std::basic_ofstream::basic_ofstream (inline) 3ms 0.037% 50.76% 160ms 2.00% std::basic_filebuf::open 0 0% 50.76% 160ms 2.00% std::basic_ofstream::open (inline) 0 0% 50.76% 156ms 1.95% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.087% 50.84% 150ms 1.87% AbstractTetrahedralElement::CalculateInverseJacobian 35ms 0.44% 51.28% 149ms 1.86% std::type_info::operator== (inline) 0 0% 51.28% 147ms 1.83% OutputFileHandler::CommonConstructor 0 0% 51.28% 147ms 1.83% OutputFileHandler::OutputFileHandler 29ms 0.36% 51.64% 147ms 1.83% std::num_put::_M_insert_int 5ms 0.062% 51.70% 145ms 1.81% boost::numeric::ublas::vector_assign (inline) 3ms 0.037% 51.74% 143ms 1.78% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.012% 51.75% 142ms 1.77% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.75% 140ms 1.75% AbstractCellBasedWriter::CloseFile 0 0% 51.75% 140ms 1.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.012% 51.77% 140ms 1.75% std::basic_filebuf::close 0 0% 51.77% 140ms 1.75% std::basic_ofstream::close (inline) 0 0% 51.77% 136ms 1.70% FilesystemPermissions::SetFilePermissions (inline) 9ms 0.11% 51.88% 136ms 1.70% Node::~Node 136ms 1.70% 53.58% 136ms 1.70% __GI_fchmodat 0 0% 53.58% 136ms 1.70% std::filesystem::permissions 102ms 1.27% 54.85% 135ms 1.68% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 133ms 1.66% 56.51% 133ms 1.66% incircle 13ms 0.16% 56.67% 131ms 1.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.012% 56.68% 124ms 1.55% _IO_new_fopen 1ms 0.012% 56.70% 123ms 1.54% _IO_new_file_fopen 0 0% 56.70% 123ms 1.54% __fopen_internal (inline) 0 0% 56.70% 123ms 1.54% std::__basic_file::open 1ms 0.012% 56.71% 122ms 1.52% __GI__IO_file_open 42ms 0.52% 57.23% 120ms 1.50% std::__ostream_insert 2ms 0.025% 57.26% 119ms 1.49% alternateaxes 7ms 0.087% 57.34% 119ms 1.49% boost::detail::shared_count::~shared_count (inline) 0 0% 57.34% 119ms 1.49% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 57.37% 117ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 104ms 1.30% 58.67% 117ms 1.46% vertexmedian 16ms 0.2% 58.87% 116ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 13ms 0.16% 59.03% 115ms 1.44% AbstractTetrahedralElement::RefreshJacobian 113ms 1.41% 60.44% 113ms 1.41% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 54ms 0.67% 61.11% 110ms 1.37% boost::shared_ptr::shared_ptr (inline) 107ms 1.34% 62.45% 108ms 1.35% __libc_open64 100ms 1.25% 63.70% 105ms 1.31% boost::detail::sp_counted_base::release 0 0% 63.70% 104ms 1.30% std::_Vector_base::_M_allocate (inline) 5ms 0.062% 63.76% 103ms 1.29% AbstractTetrahedralElement::AbstractTetrahedralElement 103ms 1.29% 65.04% 103ms 1.29% [libchaste_cell_based.so] 5ms 0.062% 65.11% 101ms 1.26% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.012% 65.12% 101ms 1.26% std::__basic_file::xsputn 0 0% 65.12% 101ms 1.26% std::basic_filebuf::_M_convert_to_external 0 0% 65.12% 101ms 1.26% std::basic_filebuf::_M_terminate_output 0 0% 65.12% 101ms 1.26% std::basic_filebuf::overflow 99ms 1.24% 66.35% 100ms 1.25% __GI___libc_write 5ms 0.062% 66.42% 97ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 97ms 1.21% 67.63% 97ms 1.21% std::_Rb_tree_increment 58ms 0.72% 68.35% 97ms 1.21% std::basic_filebuf::xsputn 0 0% 68.35% 96ms 1.20% std::operator<< (inline) 23ms 0.29% 68.64% 95ms 1.19% boost::numeric::ublas::indexing_vector_assign 0 0% 68.64% 94ms 1.17% Cell::GetCellId 7ms 0.087% 68.73% 92ms 1.15% std::vector::push_back (inline) 90ms 1.12% 69.85% 90ms 1.12% std::_Rb_tree_insert_and_rebalance 4ms 0.05% 69.90% 88ms 1.10% TetrahedralMesh::EdgeIterator::GetNodeA 32ms 0.4% 70.30% 87ms 1.09% AbstractElement::GetNodeLocation 2ms 0.025% 70.32% 86ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.32% 83ms 1.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.32% 83ms 1.04% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 60ms 0.75% 71.07% 81ms 1.01% malloc_consolidate 74ms 0.92% 72.00% 81ms 1.01% vertexsort 4ms 0.05% 72.05% 80ms 1% std::vector::_M_realloc_insert 2ms 0.025% 72.07% 78ms 0.97% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 72.07% 77ms 0.96% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 72.08% 77ms 0.96% std::filesystem::create_directory 72ms 0.9% 72.98% 72ms 0.9% __GI___fstatat64 0 0% 72.98% 70ms 0.87% std::filesystem::status 54ms 0.67% 73.66% 69ms 0.86% AbstractElement::GetNodeGlobalIndex 3ms 0.037% 73.69% 69ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 44ms 0.55% 74.24% 69ms 0.86% std::basic_streambuf::xsputn 68ms 0.85% 75.09% 68ms 0.85% __memcpy_avx_unaligned_erms 68ms 0.85% 75.94% 68ms 0.85% counterclockwise 9ms 0.11% 76.05% 65ms 0.81% CellPropertyCollection::AddProperty 65ms 0.81% 76.86% 65ms 0.81% std::vector::size (inline) 0 0% 76.86% 62ms 0.77% Node::ClearAppliedForce 0 0% 76.86% 62ms 0.77% Node::ConstructNodeAttributes (inline) 0 0% 76.86% 62ms 0.77% tcache_get (inline) 62ms 0.77% 77.64% 62ms 0.77% tcache_get_n (inline) 0 0% 77.64% 60ms 0.75% boost::numeric::ublas::norm_2 (inline) 23ms 0.29% 77.92% 60ms 0.75% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 77.92% 59ms 0.74% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 58ms 0.72% 78.65% 58ms 0.72% Node::GetIndex 32ms 0.4% 79.05% 58ms 0.72% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.05% 57ms 0.71% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 55ms 0.69% 79.73% 56ms 0.7% boost::detail::shared_count::shared_count (inline) 56ms 0.7% 80.43% 56ms 0.7% boost::shared_ptr::operator-> (inline) 55ms 0.69% 81.12% 55ms 0.69% [libstdc++.so.6.0.33] 5ms 0.062% 81.18% 54ms 0.67% std::_Rb_tree::_M_emplace_hint_unique 25ms 0.31% 81.49% 51ms 0.64% AbstractTetrahedralMesh::GetElement 14ms 0.17% 81.67% 51ms 0.64% Determinant (inline) 0 0% 81.67% 50ms 0.62% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.012% 81.68% 48ms 0.6% BoundaryNodeWriter::Visit 0 0% 81.68% 48ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 48ms 0.6% 82.28% 48ms 0.6% [libchaste_mesh.so] 48ms 0.6% 82.88% 48ms 0.6% boost::numeric::ublas::c_vector::operator() 0 0% 82.88% 48ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.88% 48ms 0.6% std::__new_allocator::destroy (inline) 0 0% 82.88% 48ms 0.6% std::allocator_traits::destroy (inline) 37ms 0.46% 83.34% 48ms 0.6% std::num_put::do_put 0 0% 83.34% 47ms 0.59% AbstractCentreBasedCellPopulation::IsMarkedSpring 5ms 0.062% 83.40% 47ms 0.59% NodeAttributes::NodeAttributes 46ms 0.57% 83.98% 46ms 0.57% Node::rGetLocation 0 0% 83.98% 44ms 0.55% std::vector::vector (inline) 8ms 0.1% 84.08% 43ms 0.54% Inverse 0 0% 84.08% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 24ms 0.3% 84.38% 42ms 0.52% hack_digit 42ms 0.52% 84.90% 42ms 0.52% unlink_chunk