File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6376ms, 84.48% of 7547ms total Dropped 552 nodes (cum <= 37.73ms) flat flat% sum% cum cum% 0 0% 0% 7511ms 99.52% __libc_start_call_main 0 0% 0% 7511ms 99.52% __libc_start_main_impl 0 0% 0% 7511ms 99.52% _start 0 0% 0% 7497ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7497ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7497ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7497ms 99.34% main 0 0% 0% 7461ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7461ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7461ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7457ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3207ms 42.49% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.04% 0.053% 2746ms 36.39% MeshBasedCellPopulation::Update 0 0% 0.053% 2734ms 36.23% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.053% 1506ms 19.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.066% 1372ms 18.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.027% 0.093% 1364ms 18.07% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.093% 1343ms 17.80% MutableMesh::ReMesh 7ms 0.093% 0.19% 1324ms 17.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 12ms 0.16% 0.34% 1179ms 15.62% MeshBasedCellPopulation::SpringIterator::operator++ 114ms 1.51% 1.86% 968ms 12.83% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.066% 1.92% 924ms 12.24% AbstractTwoBodyInteractionForce::AddForceContribution 247ms 3.27% 5.19% 922ms 12.22% __dynamic_cast 1ms 0.013% 5.21% 915ms 12.12% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.15% 5.35% 915ms 12.12% CellPopulationElementWriter::Visit 426ms 5.64% 11.00% 885ms 11.73% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.16% 11.16% 879ms 11.65% CellPropertyCollection::GetPropertiesType (inline) 32ms 0.42% 11.58% 813ms 10.77% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.027% 11.61% 763ms 10.11% MeshBasedCellPopulation::AcceptCellWriter 37ms 0.49% 12.10% 737ms 9.77% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.093% 12.19% 690ms 9.14% AbstractCellProperty::IsSubType (inline) 6ms 0.08% 12.27% 681ms 9.02% TetrahedralMesh::ImportFromMesher 1ms 0.013% 12.28% 591ms 7.83% std::ostream::operator<< (inline) 93ms 1.23% 13.52% 588ms 7.79% std::ostream::_M_insert 31ms 0.41% 13.93% 577ms 7.65% operator new 43ms 0.57% 14.50% 549ms 7.27% std::__new_allocator::allocate (inline) 0 0% 14.50% 543ms 7.19% std::allocator_traits::allocate (inline) 174ms 2.31% 16.80% 539ms 7.14% __GI___libc_malloc 35ms 0.46% 17.27% 535ms 7.09% std::map::operator[] (partial-inline) 3ms 0.04% 17.30% 527ms 6.98% Cell::GetCellProliferativeType 527ms 6.98% 24.29% 527ms 6.98% __strcmp_avx2 9ms 0.12% 24.41% 523ms 6.93% std::set::insert (inline) 225ms 2.98% 27.39% 515ms 6.82% __cxxabiv1::__si_class_type_info::__do_dyncast 11ms 0.15% 27.53% 514ms 6.81% std::_Rb_tree::_M_insert_unique 2ms 0.027% 27.56% 499ms 6.61% triangulate 2ms 0.027% 27.59% 480ms 6.36% LegacyCellProliferativeTypesWriter::VisitCell 24ms 0.32% 27.91% 477ms 6.32% std::_Rb_tree::find (inline) 0 0% 27.91% 452ms 5.99% std::_Rb_tree::lower_bound (inline) 0 0% 27.91% 452ms 5.99% std::map::lower_bound (inline) 4ms 0.053% 27.96% 448ms 5.94% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.96% 438ms 5.80% std::_Rb_tree::_M_create_node (inline) 0 0% 27.96% 437ms 5.79% std::set::count (inline) 0 0% 27.96% 432ms 5.72% delaunay 1ms 0.013% 27.97% 430ms 5.70% divconqdelaunay 0 0% 27.97% 415ms 5.50% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.97% 410ms 5.43% std::_Rb_tree::_M_get_node (inline) 32ms 0.42% 28.40% 398ms 5.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.40% 374ms 4.96% std::set::~set (inline) 3ms 0.04% 28.44% 372ms 4.93% Cell::GetMutationState 3ms 0.04% 28.47% 367ms 4.86% NodeLocationWriter::Visit 76ms 1.01% 29.48% 362ms 4.80% std::_Rb_tree::_M_erase 17ms 0.23% 29.71% 360ms 4.77% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.027% 29.73% 329ms 4.36% std::set::set (inline) 15ms 0.2% 29.93% 328ms 4.35% std::_Rb_tree::_M_insert_ (inline) 27ms 0.36% 30.29% 327ms 4.33% std::num_put::_M_insert_float 12ms 0.16% 30.45% 319ms 4.23% std::less::operator() (inline) 30ms 0.4% 30.85% 318ms 4.21% std::_Rb_tree::_M_copy (inline) 7ms 0.093% 30.94% 314ms 4.16% Cell::ReadyToDivide 2ms 0.027% 30.97% 311ms 4.12% MeshBasedCellPopulation::GetDampingConstant 0 0% 30.97% 309ms 4.09% AbstractCentreBasedCellPopulation::GetDampingConstant 307ms 4.07% 35.03% 307ms 4.07% std::operator< (inline) 1ms 0.013% 35.05% 301ms 3.99% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.053% 35.10% 295ms 3.91% Element::Element 98ms 1.30% 36.40% 291ms 3.86% __GI___libc_free 74ms 0.98% 37.38% 282ms 3.74% std::_Rb_tree::_M_clone_node (inline) 282ms 3.74% 41.12% 282ms 3.74% std::_Rb_tree::_S_right (inline) 179ms 2.37% 43.49% 264ms 3.50% _int_malloc 0 0% 43.49% 263ms 3.48% std::_Rb_tree::_M_drop_node (inline) 2ms 0.027% 43.51% 262ms 3.47% CellProliferativeTypesWriter::VisitCell 13ms 0.17% 43.69% 260ms 3.45% std::__new_allocator::deallocate (inline) 0 0% 43.69% 255ms 3.38% std::allocator_traits::deallocate (inline) 5ms 0.066% 43.75% 252ms 3.34% std::__cxx11::collate::do_transform 3ms 0.04% 43.79% 242ms 3.21% ___vsnprintf 3ms 0.04% 43.83% 240ms 3.18% AbstractCellProperty::IsType (inline) 0 0% 43.83% 239ms 3.17% __vsnprintf_internal (inline) 18ms 0.24% 44.07% 237ms 3.14% divconqrecurse 36ms 0.48% 44.55% 233ms 3.09% __printf_buffer 4ms 0.053% 44.60% 231ms 3.06% CellPropertyCollection::HasProperty 0 0% 44.60% 230ms 3.05% Cell::HasCellProperty (inline) 58ms 0.77% 45.37% 213ms 2.82% mergehulls 0 0% 45.37% 212ms 2.81% std::_Rb_tree::_M_put_node (inline) 5ms 0.066% 45.44% 208ms 2.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 13ms 0.17% 45.61% 200ms 2.65% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 164ms 2.17% 47.78% 192ms 2.54% _int_free 10ms 0.13% 47.91% 185ms 2.45% __printf_fp_l_buffer 0 0% 47.91% 185ms 2.45% __printf_fp_spec (inline) 5ms 0.066% 47.98% 184ms 2.44% Element::RegisterWithNodes (inline) 10ms 0.13% 48.11% 184ms 2.44% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.04% 48.15% 176ms 2.33% Node::AddElement 58ms 0.77% 48.92% 175ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 10ms 0.13% 49.05% 173ms 2.29% AbstractTetrahedralElement::CalculateJacobian 95ms 1.26% 50.31% 171ms 2.27% __printf_fp_buffer_1 49ms 0.65% 50.96% 170ms 2.25% AbstractCellProperty::IsSame 15ms 0.2% 51.16% 168ms 2.23% TetrahedralMesh::Clear 0 0% 51.16% 162ms 2.15% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 45ms 0.6% 51.76% 162ms 2.15% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.76% 161ms 2.13% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 51.76% 157ms 2.08% OutputFileHandler::OpenOutputFile 0 0% 51.76% 153ms 2.03% std::basic_ofstream::basic_ofstream (inline) 3ms 0.04% 51.80% 150ms 1.99% std::basic_filebuf::open 0 0% 51.80% 150ms 1.99% std::basic_ofstream::open (inline) 0 0% 51.80% 149ms 1.97% OutputFileHandler::CommonConstructor 0 0% 51.80% 149ms 1.97% OutputFileHandler::OutputFileHandler 1ms 0.013% 51.81% 146ms 1.93% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 51.82% 146ms 1.93% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.027% 51.85% 143ms 1.89% boost::numeric::ublas::vector_assign (inline) 10ms 0.13% 51.98% 136ms 1.80% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 51.99% 134ms 1.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 52.01% 134ms 1.78% std::_Vector_base::_M_allocate (inline) 0 0% 52.01% 132ms 1.75% AbstractCellBasedWriter::CloseFile 4ms 0.053% 52.06% 132ms 1.75% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 52.06% 132ms 1.75% std::basic_ofstream::close (inline) 1ms 0.013% 52.07% 131ms 1.74% std::basic_filebuf::close 46ms 0.61% 52.68% 130ms 1.72% std::__ostream_insert 24ms 0.32% 53.00% 129ms 1.71% AbstractTetrahedralElement::RefreshJacobian 5ms 0.066% 53.07% 123ms 1.63% std::vector::push_back (inline) 1ms 0.013% 53.08% 121ms 1.60% _IO_new_fopen 0 0% 53.08% 121ms 1.60% std::__basic_file::open 28ms 0.37% 53.45% 121ms 1.60% std::num_put::_M_insert_int 27ms 0.36% 53.81% 121ms 1.60% std::type_info::operator== (inline) 1ms 0.013% 53.82% 120ms 1.59% __fopen_internal (inline) 1ms 0.013% 53.84% 118ms 1.56% _IO_new_file_fopen 2ms 0.027% 53.86% 118ms 1.56% std::operator<< (inline) 13ms 0.17% 54.03% 117ms 1.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 54.03% 116ms 1.54% __GI__IO_file_open 1ms 0.013% 54.05% 114ms 1.51% alternateaxes 11ms 0.15% 54.19% 114ms 1.51% std::vector::_M_realloc_insert 0 0% 54.19% 113ms 1.50% AbstractTetrahedralElement::AbstractTetrahedralElement 54ms 0.72% 54.91% 113ms 1.50% boost::shared_ptr::shared_ptr (inline) 12ms 0.16% 55.07% 112ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 111ms 1.47% 56.54% 111ms 1.47% std::_Rb_tree_insert_and_rebalance 101ms 1.34% 57.88% 111ms 1.47% vertexmedian 0 0% 57.88% 110ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.093% 57.97% 110ms 1.46% boost::detail::shared_count::~shared_count (inline) 0 0% 57.97% 110ms 1.46% boost::shared_ptr::~shared_ptr (inline) 27ms 0.36% 58.33% 105ms 1.39% boost::numeric::ublas::indexing_vector_assign 66ms 0.87% 59.20% 104ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 102ms 1.35% 60.55% 104ms 1.38% __libc_open64 102ms 1.35% 61.91% 103ms 1.36% boost::detail::sp_counted_base::release 16ms 0.21% 62.12% 100ms 1.33% std::_Rb_tree_const_iterator::operator++ (inline) 96ms 1.27% 63.39% 96ms 1.27% incircle 95ms 1.26% 64.65% 95ms 1.26% [libchaste_cell_based.so] 93ms 1.23% 65.88% 93ms 1.23% std::_Rb_tree_increment 45ms 0.6% 66.48% 91ms 1.21% AbstractElement::GetNodeLocation 5ms 0.066% 66.54% 88ms 1.17% Node::~Node 88ms 1.17% 67.71% 88ms 1.17% __GI___fstatat64 1ms 0.013% 67.72% 88ms 1.17% std::filesystem::status 9ms 0.12% 67.84% 87ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 67.84% 87ms 1.15% tcache_get (inline) 87ms 1.15% 68.99% 87ms 1.15% tcache_get_n (inline) 2ms 0.027% 69.02% 85ms 1.13% std::basic_filebuf::_M_terminate_output 2ms 0.027% 69.05% 85ms 1.13% std::basic_filebuf::overflow 47ms 0.62% 69.67% 85ms 1.13% std::basic_filebuf::xsputn 83ms 1.10% 70.77% 83ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 70.78% 83ms 1.10% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 70.80% 82ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 70.81% 82ms 1.09% std::__basic_file::xsputn 78ms 1.03% 71.84% 80ms 1.06% __GI___libc_write 1ms 0.013% 71.86% 74ms 0.98% std::filesystem::create_directory 51ms 0.68% 72.53% 72ms 0.95% malloc_consolidate 52ms 0.69% 73.22% 71ms 0.94% std::basic_streambuf::xsputn 64ms 0.85% 74.07% 71ms 0.94% vertexsort 10ms 0.13% 74.20% 66ms 0.87% CellPropertyCollection::AddProperty 66ms 0.87% 75.08% 66ms 0.87% std::vector::size (inline) 2ms 0.027% 75.10% 65ms 0.86% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.053% 75.16% 65ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 75.16% 63ms 0.83% Cell::GetCellId 4ms 0.053% 75.21% 63ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeB 25ms 0.33% 75.54% 62ms 0.82% AbstractTetrahedralMesh::GetElement 0 0% 75.54% 62ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.54% 62ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 60ms 0.8% 76.33% 60ms 0.8% [libchaste_mesh.so] 59ms 0.78% 77.12% 59ms 0.78% boost::detail::shared_count::shared_count (inline) 43ms 0.57% 77.69% 58ms 0.77% AbstractElement::GetNodeGlobalIndex 57ms 0.76% 78.44% 57ms 0.76% Node::GetIndex 54ms 0.72% 79.16% 54ms 0.72% counterclockwise 0 0% 79.16% 54ms 0.72% std::vector::vector (inline) 44ms 0.58% 79.74% 53ms 0.7% std::num_put::do_put 0 0% 79.74% 51ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.053% 79.79% 51ms 0.68% Node::ConstructNodeAttributes (inline) 51ms 0.68% 80.47% 51ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 80.47% 51ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.47% 51ms 0.68% std::__new_allocator::destroy (inline) 0 0% 80.47% 51ms 0.68% std::allocator_traits::destroy (inline) 50ms 0.66% 81.13% 50ms 0.66% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 81.13% 50ms 0.66% std::_Vector_base::_M_create_storage (inline) 0 0% 81.13% 50ms 0.66% std::_Vector_base::_Vector_base (inline) 0 0% 81.13% 49ms 0.65% Node::ClearAppliedForce 29ms 0.38% 81.52% 49ms 0.65% hack_digit 4ms 0.053% 81.57% 48ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.57% 47ms 0.62% boost::numeric::ublas::norm_2 (inline) 16ms 0.21% 81.78% 47ms 0.62% boost::numeric::ublas::vector_norm_2::apply (inline) 28ms 0.37% 82.15% 46ms 0.61% boost::numeric::ublas::c_matrix::operator() (partial-inline) 45ms 0.6% 82.75% 45ms 0.6% __memcpy_avx_unaligned_erms 3ms 0.04% 82.79% 45ms 0.6% std::_Vector_base::_M_deallocate (inline) 18ms 0.24% 83.03% 44ms 0.58% AbstractCellCycleModel::GetAge 20ms 0.27% 83.29% 44ms 0.58% Determinant (inline) 0 0% 83.29% 43ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 43ms 0.57% 83.86% 43ms 0.57% [libstdc++.so.6.0.33] 0 0% 83.86% 42ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.86% 41ms 0.54% BoundaryNodeWriter::Visit 3ms 0.04% 83.90% 41ms 0.54% std::__basic_file::close 40ms 0.53% 84.43% 40ms 0.53% Node::rGetLocation 4ms 0.053% 84.48% 39ms 0.52% NodeAttributes::NodeAttributes 0 0% 84.48% 38ms 0.5% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 84.48% 38ms 0.5% _IO_new_fclose