File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6723ms, 84.42% of 7964ms total Dropped 566 nodes (cum <= 39.82ms) flat flat% sum% cum cum% 0 0% 0% 7928ms 99.55% __libc_start_call_main 0 0% 0% 7928ms 99.55% __libc_start_main_impl 0 0% 0% 7928ms 99.55% _start 0 0% 0% 7912ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7912ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7912ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7912ms 99.35% main 0 0% 0% 7874ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7874ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7873ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7872ms 98.84% AbstractCellBasedSimulation::Solve 0 0% 0% 3411ms 42.83% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2878ms 36.14% MeshBasedCellPopulation::Update 2ms 0.025% 0.05% 2871ms 36.05% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.05% 1579ms 19.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.063% 1436ms 18.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.063% 1425ms 17.89% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.075% 1382ms 17.35% MutableMesh::ReMesh 8ms 0.1% 0.18% 1378ms 17.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.35% 1263ms 15.86% MeshBasedCellPopulation::SpringIterator::operator++ 107ms 1.34% 1.70% 1026ms 12.88% TetrahedralMesh::EdgeIterator::operator++ 465ms 5.84% 7.53% 949ms 11.92% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.075% 7.61% 946ms 11.88% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.025% 7.63% 909ms 11.41% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.76% 892ms 11.20% CellPopulationElementWriter::Visit 282ms 3.54% 11.30% 890ms 11.18% __dynamic_cast 9ms 0.11% 11.41% 886ms 11.13% CellPropertyCollection::GetPropertiesType (inline) 35ms 0.44% 11.85% 818ms 10.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.063% 11.92% 761ms 9.56% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 12.29% 732ms 9.19% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 12.43% 710ms 8.92% TetrahedralMesh::ImportFromMesher 7ms 0.088% 12.52% 693ms 8.70% AbstractCellProperty::IsSubType (inline) 0 0% 12.52% 602ms 7.56% std::ostream::operator<< (inline) 97ms 1.22% 13.74% 601ms 7.55% std::ostream::_M_insert 36ms 0.45% 14.19% 568ms 7.13% operator new 47ms 0.59% 14.78% 562ms 7.06% std::map::operator[] (partial-inline) 5ms 0.063% 14.84% 551ms 6.92% std::set::insert (inline) 10ms 0.13% 14.97% 546ms 6.86% std::_Rb_tree::_M_insert_unique 20ms 0.25% 15.22% 528ms 6.63% std::_Rb_tree::find (inline) 175ms 2.20% 17.42% 522ms 6.55% __GI___libc_malloc 516ms 6.48% 23.90% 516ms 6.48% __strcmp_avx2 1ms 0.013% 23.91% 515ms 6.47% AbstractCellBasedSimulation::DoCellBirth 2ms 0.025% 23.93% 515ms 6.47% triangulate 25ms 0.31% 24.25% 506ms 6.35% std::__new_allocator::allocate (inline) 0 0% 24.25% 504ms 6.33% std::allocator_traits::allocate (inline) 8ms 0.1% 24.35% 501ms 6.29% Cell::GetCellProliferativeType 4ms 0.05% 24.40% 484ms 6.08% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.40% 474ms 5.95% std::set::count (inline) 0 0% 24.40% 466ms 5.85% std::_Rb_tree::lower_bound (inline) 0 0% 24.40% 466ms 5.85% std::map::lower_bound (inline) 0 0% 24.40% 452ms 5.68% delaunay 1ms 0.013% 24.41% 451ms 5.66% divconqdelaunay 205ms 2.57% 26.98% 435ms 5.46% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.98% 433ms 5.44% std::_Rb_tree::_M_create_node (inline) 0 0% 26.98% 409ms 5.14% std::_Rb_tree::_Alloc_node::operator() (inline) 34ms 0.43% 27.41% 402ms 5.05% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.41% 394ms 4.95% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 27.44% 391ms 4.91% Cell::GetMutationState 0 0% 27.44% 376ms 4.72% std::set::~set (inline) 1ms 0.013% 27.45% 375ms 4.71% NodeLocationWriter::Visit 80ms 1.00% 28.45% 368ms 4.62% std::_Rb_tree::_M_erase 25ms 0.31% 28.77% 362ms 4.55% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.075% 28.84% 347ms 4.36% Cell::ReadyToDivide 24ms 0.3% 29.14% 347ms 4.36% std::_Rb_tree::_M_insert_ (inline) 10ms 0.13% 29.27% 346ms 4.34% std::less::operator() (inline) 20ms 0.25% 29.52% 339ms 4.26% std::num_put::_M_insert_float 336ms 4.22% 33.74% 336ms 4.22% std::operator< (inline) 1ms 0.013% 33.75% 335ms 4.21% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.75% 333ms 4.18% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 33.75% 329ms 4.13% std::set::set (inline) 1ms 0.013% 33.76% 323ms 4.06% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.76% 322ms 4.04% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.76% 316ms 3.97% OutputFileHandler::OpenOutputFile 115ms 1.44% 35.21% 309ms 3.88% __GI___libc_free 7ms 0.088% 35.30% 302ms 3.79% Element::Element 28ms 0.35% 35.65% 296ms 3.72% std::_Rb_tree::_M_copy (inline) 293ms 3.68% 39.33% 293ms 3.68% std::_Rb_tree::_S_right (inline) 11ms 0.14% 39.47% 284ms 3.57% AbstractCellPopulation::IsCellAttachedToLocationIndex 8ms 0.1% 39.57% 276ms 3.47% CellPropertyCollection::HasProperty 0 0% 39.57% 274ms 3.44% Cell::HasCellProperty (inline) 172ms 2.16% 41.73% 268ms 3.37% _int_malloc 1ms 0.013% 41.74% 265ms 3.33% AbstractCellProperty::IsType (inline) 0 0% 41.74% 263ms 3.30% std::_Rb_tree::_M_drop_node (inline) 72ms 0.9% 42.64% 262ms 3.29% std::_Rb_tree::_M_clone_node (inline) 2ms 0.025% 42.67% 261ms 3.28% std::__cxx11::collate::do_transform 8ms 0.1% 42.77% 260ms 3.26% divconqrecurse 8ms 0.1% 42.87% 256ms 3.21% std::__new_allocator::deallocate (inline) 0 0% 42.87% 250ms 3.14% std::allocator_traits::deallocate (inline) 2ms 0.025% 42.89% 249ms 3.13% ___vsnprintf 0 0% 42.89% 247ms 3.10% __vsnprintf_internal (inline) 34ms 0.43% 43.32% 245ms 3.08% __printf_buffer 80ms 1.00% 44.32% 242ms 3.04% mergehulls 1ms 0.013% 44.34% 236ms 2.96% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 44.37% 215ms 2.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 44.37% 212ms 2.66% std::_Rb_tree::_M_put_node (inline) 9ms 0.11% 44.49% 210ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 46ms 0.58% 45.07% 203ms 2.55% AbstractCellProperty::IsSame 10ms 0.13% 45.19% 203ms 2.55% TetrahedralMesh::Clear 5ms 0.063% 45.25% 199ms 2.50% Element::RegisterWithNodes (inline) 7ms 0.088% 45.34% 196ms 2.46% __printf_fp_l_buffer 0 0% 45.34% 196ms 2.46% __printf_fp_spec (inline) 167ms 2.10% 47.44% 194ms 2.44% _int_free 3ms 0.038% 47.48% 192ms 2.41% Node::AddElement 54ms 0.68% 48.15% 189ms 2.37% std::_Rb_tree::_M_get_insert_unique_pos (inline) 101ms 1.27% 49.42% 180ms 2.26% __printf_fp_buffer_1 5ms 0.063% 49.49% 173ms 2.17% boost::numeric::ublas::vector_assign (inline) 6ms 0.075% 49.56% 169ms 2.12% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 49.56% 166ms 2.08% std::basic_ofstream::basic_ofstream (inline) 20ms 0.25% 49.81% 165ms 2.07% AbstractTetrahedralElement::CalculateJacobian 4ms 0.05% 49.86% 161ms 2.02% std::basic_filebuf::open 0 0% 49.86% 161ms 2.02% std::basic_ofstream::open (inline) 5ms 0.063% 49.92% 157ms 1.97% boost::numeric::ublas::c_vector::c_vector (inline) 41ms 0.51% 50.44% 157ms 1.97% std::type_info::operator== (inline) 37ms 0.46% 50.90% 151ms 1.90% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 50.92% 148ms 1.86% OutputFileHandler::CommonConstructor 0 0% 50.92% 148ms 1.86% OutputFileHandler::OutputFileHandler 1ms 0.013% 50.93% 144ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 64ms 0.8% 51.73% 141ms 1.77% std::__ostream_insert 1ms 0.013% 51.75% 136ms 1.71% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.75% 135ms 1.70% AbstractCellBasedWriter::CloseFile 2ms 0.025% 51.77% 135ms 1.70% std::basic_filebuf::close 0 0% 51.77% 135ms 1.70% std::basic_ofstream::close (inline) 15ms 0.19% 51.96% 133ms 1.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 51.96% 132ms 1.66% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 51.98% 132ms 1.66% TetrahedralMesh::RefreshJacobianCachedData 46ms 0.58% 52.56% 131ms 1.64% boost::numeric::ublas::indexing_vector_assign 0 0% 52.56% 122ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 52.57% 122ms 1.53% std::filesystem::permissions 121ms 1.52% 54.09% 121ms 1.52% __GI_fchmodat 3ms 0.038% 54.13% 121ms 1.52% std::operator<< (inline) 33ms 0.41% 54.55% 119ms 1.49% std::num_put::_M_insert_int 1ms 0.013% 54.56% 118ms 1.48% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.11% 54.67% 118ms 1.48% Node::~Node 2ms 0.025% 54.70% 118ms 1.48% std::__basic_file::open 0 0% 54.70% 117ms 1.47% _IO_new_fopen 0 0% 54.70% 117ms 1.47% __fopen_internal (inline) 0 0% 54.70% 116ms 1.46% _IO_new_file_fopen 1ms 0.013% 54.71% 115ms 1.44% __GI__IO_file_open 15ms 0.19% 54.90% 115ms 1.44% boost::detail::shared_count::~shared_count (inline) 0 0% 54.90% 115ms 1.44% boost::shared_ptr::~shared_ptr (inline) 18ms 0.23% 55.12% 113ms 1.42% AbstractTetrahedralElement::RefreshJacobian 113ms 1.42% 56.54% 113ms 1.42% [libchaste_cell_based.so] 2ms 0.025% 56.57% 112ms 1.41% alternateaxes 112ms 1.41% 57.97% 112ms 1.41% std::_Rb_tree_insert_and_rebalance 8ms 0.1% 58.07% 111ms 1.39% std::_Rb_tree_const_iterator::operator++ (inline) 111ms 1.39% 59.47% 111ms 1.39% std::_Rb_tree_increment 0 0% 59.47% 110ms 1.38% std::_Vector_base::_M_allocate (inline) 103ms 1.29% 60.76% 110ms 1.38% vertexmedian 64ms 0.8% 61.56% 108ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 20ms 0.25% 61.82% 107ms 1.34% MeshBasedCellPopulation::SpringIterator::SpringIterator 49ms 0.62% 62.43% 107ms 1.34% boost::shared_ptr::shared_ptr (inline) 2ms 0.025% 62.46% 106ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 62.47% 105ms 1.32% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.038% 62.51% 105ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 105ms 1.32% 63.82% 105ms 1.32% incircle 101ms 1.27% 65.09% 103ms 1.29% __libc_open64 5ms 0.063% 65.16% 102ms 1.28% std::vector::push_back (inline) 1ms 0.013% 65.17% 100ms 1.26% std::basic_filebuf::_M_terminate_output 4ms 0.05% 65.22% 99ms 1.24% std::basic_filebuf::overflow 98ms 1.23% 66.45% 98ms 1.23% boost::detail::sp_counted_base::release 1ms 0.013% 66.46% 95ms 1.19% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 66.49% 94ms 1.18% std::__basic_file::xsputn 13ms 0.16% 66.65% 93ms 1.17% std::vector::_M_realloc_insert 92ms 1.16% 67.81% 92ms 1.16% __GI___libc_write 1ms 0.013% 67.82% 89ms 1.12% AbstractCellPopulation::GetLocationIndexUsingCell 56ms 0.7% 68.52% 86ms 1.08% std::basic_filebuf::xsputn 84ms 1.05% 69.58% 84ms 1.05% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 7ms 0.088% 69.66% 83ms 1.04% TetrahedralMesh::EdgeIterator::GetNodeA 82ms 1.03% 70.69% 82ms 1.03% Node::GetIndex 0 0% 70.69% 81ms 1.02% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.69% 81ms 1.02% std::filesystem::create_directory 1ms 0.013% 70.71% 81ms 1.02% std::filesystem::status 30ms 0.38% 71.08% 80ms 1.00% AbstractElement::GetNodeLocation 78ms 0.98% 72.06% 78ms 0.98% __GI___fstatat64 51ms 0.64% 72.70% 78ms 0.98% malloc_consolidate 0 0% 72.70% 73ms 0.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.70% 73ms 0.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 55ms 0.69% 73.39% 73ms 0.92% std::basic_streambuf::xsputn 0 0% 73.39% 73ms 0.92% tcache_get (inline) 73ms 0.92% 74.31% 73ms 0.92% tcache_get_n (inline) 68ms 0.85% 75.16% 71ms 0.89% vertexsort 70ms 0.88% 76.04% 70ms 0.88% std::vector::size (inline) 3ms 0.038% 76.08% 68ms 0.85% CellPropertyCollection::AddProperty 4ms 0.05% 76.13% 67ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeB 49ms 0.62% 76.75% 64ms 0.8% AbstractElement::GetNodeGlobalIndex 62ms 0.78% 77.52% 62ms 0.78% boost::shared_ptr::operator-> (inline) 0 0% 77.52% 61ms 0.77% Cell::GetCellId 61ms 0.77% 78.29% 61ms 0.77% __memcpy_avx_unaligned_erms 1ms 0.013% 78.30% 58ms 0.73% Node::ClearAppliedForce 2ms 0.025% 78.33% 58ms 0.73% Node::ConstructNodeAttributes (inline) 56ms 0.7% 79.03% 58ms 0.73% boost::detail::shared_count::shared_count (inline) 58ms 0.73% 79.76% 58ms 0.73% boost::numeric::ublas::c_vector::operator() 33ms 0.41% 80.17% 57ms 0.72% AbstractTetrahedralMesh::GetElement 56ms 0.7% 80.88% 56ms 0.7% counterclockwise 54ms 0.68% 81.55% 54ms 0.68% Node::IsDeleted 38ms 0.48% 82.03% 52ms 0.65% std::num_put::do_put 0 0% 82.03% 51ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.03% 51ms 0.64% std::__new_allocator::destroy (inline) 0 0% 82.03% 51ms 0.64% std::allocator_traits::destroy (inline) 20ms 0.25% 82.28% 50ms 0.63% AbstractCellCycleModel::GetAge 1ms 0.013% 82.30% 49ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.30% 47ms 0.59% boost::numeric::ublas::norm_2 (inline) 12ms 0.15% 82.45% 47ms 0.59% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 82.45% 47ms 0.59% std::map::find (inline) 0 0% 82.45% 47ms 0.59% std::vector::vector (inline) 0 0% 82.45% 45ms 0.57% BoundaryNodeWriter::Visit 26ms 0.33% 82.77% 45ms 0.57% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.013% 82.79% 44ms 0.55% NodeAttributes::NodeAttributes 19ms 0.24% 83.02% 43ms 0.54% Determinant (inline) 43ms 0.54% 83.56% 43ms 0.54% [libchaste_mesh.so] 1ms 0.013% 83.58% 43ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 83.58% 43ms 0.54% std::_Vector_base::_Vector_base (inline) 14ms 0.18% 83.75% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 18ms 0.23% 83.98% 42ms 0.53% NodeAttributes::AddAppliedForceContribution 3ms 0.038% 84.02% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 84.02% 42ms 0.53% std::allocator_traits::construct (inline) 28ms 0.35% 84.37% 41ms 0.51% hack_digit 4ms 0.05% 84.42% 41ms 0.51% std::_Vector_base::_M_deallocate (inline)