File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6442ms, 84.82% of 7595ms total Dropped 540 nodes (cum <= 37.98ms) flat flat% sum% cum cum% 0 0% 0% 7561ms 99.55% __libc_start_call_main 0 0% 0% 7561ms 99.55% __libc_start_main_impl 0 0% 0% 7561ms 99.55% _start 0 0% 0% 7547ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7547ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7547ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7547ms 99.37% main 0 0% 0% 7512ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7512ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7512ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7509ms 98.87% AbstractCellBasedSimulation::Solve 0 0% 0% 3283ms 43.23% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.026% 2823ms 37.17% MeshBasedCellPopulation::Update 1ms 0.013% 0.039% 2721ms 35.83% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.053% 1494ms 19.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.026% 0.079% 1400ms 18.43% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.092% 1363ms 17.95% MutableMesh::ReMesh 0 0% 0.092% 1355ms 17.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.11% 0.2% 1292ms 17.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.22% 0.42% 1206ms 15.88% MeshBasedCellPopulation::SpringIterator::operator++ 117ms 1.54% 1.96% 995ms 13.10% TetrahedralMesh::EdgeIterator::operator++ 434ms 5.71% 7.68% 951ms 12.52% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.69% 938ms 12.35% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.026% 7.72% 890ms 11.72% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.16% 7.87% 890ms 11.72% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.13% 8.01% 881ms 11.60% CellPopulationElementWriter::Visit 236ms 3.11% 11.11% 852ms 11.22% __dynamic_cast 3ms 0.039% 11.15% 787ms 10.36% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.39% 11.55% 776ms 10.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 24ms 0.32% 11.86% 739ms 9.73% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.11% 11.97% 698ms 9.19% TetrahedralMesh::ImportFromMesher 10ms 0.13% 12.10% 678ms 8.93% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.11% 605ms 7.97% std::ostream::operator<< (inline) 97ms 1.28% 13.39% 603ms 7.94% std::ostream::_M_insert 41ms 0.54% 13.93% 586ms 7.72% std::map::operator[] (partial-inline) 44ms 0.58% 14.51% 567ms 7.47% operator new 3ms 0.039% 14.55% 559ms 7.36% std::set::insert (inline) 5ms 0.066% 14.61% 556ms 7.32% std::_Rb_tree::_M_insert_unique 156ms 2.05% 16.67% 521ms 6.86% __GI___libc_malloc 38ms 0.5% 17.17% 513ms 6.75% std::__new_allocator::allocate (inline) 511ms 6.73% 23.90% 511ms 6.73% __strcmp_avx2 8ms 0.11% 24.00% 508ms 6.69% Cell::GetCellProliferativeType 0 0% 24.00% 508ms 6.69% std::allocator_traits::allocate (inline) 0 0% 24.00% 507ms 6.68% std::_Rb_tree::lower_bound (inline) 0 0% 24.00% 507ms 6.68% std::map::lower_bound (inline) 5ms 0.066% 24.07% 495ms 6.52% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.026% 24.09% 484ms 6.37% triangulate 20ms 0.26% 24.36% 481ms 6.33% std::_Rb_tree::find (inline) 4ms 0.053% 24.41% 447ms 5.89% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.41% 434ms 5.71% std::set::count (inline) 24ms 0.32% 24.73% 432ms 5.69% std::_Rb_tree::~_Rb_tree (inline) 191ms 2.51% 27.24% 431ms 5.67% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.24% 431ms 5.67% std::_Rb_tree::_M_create_node (inline) 0 0% 27.24% 419ms 5.52% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.24% 416ms 5.48% delaunay 1ms 0.013% 27.25% 416ms 5.48% divconqdelaunay 0 0% 27.25% 407ms 5.36% std::set::~set (inline) 70ms 0.92% 28.18% 401ms 5.28% std::_Rb_tree::_M_erase 0 0% 28.18% 391ms 5.15% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 28.19% 387ms 5.10% Cell::GetMutationState 2ms 0.026% 28.22% 362ms 4.77% NodeLocationWriter::Visit 21ms 0.28% 28.49% 362ms 4.77% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.26% 28.76% 342ms 4.50% std::_Rb_tree::_M_insert_ (inline) 13ms 0.17% 28.93% 339ms 4.46% std::less::operator() (inline) 5ms 0.066% 28.99% 333ms 4.38% std::set::set (inline) 326ms 4.29% 33.29% 326ms 4.29% std::_Rb_tree::_S_right (inline) 326ms 4.29% 37.58% 326ms 4.29% std::operator< (inline) 1ms 0.013% 37.59% 316ms 4.16% MeshBasedCellPopulation::GetDampingConstant 23ms 0.3% 37.89% 316ms 4.16% std::num_put::_M_insert_float 11ms 0.14% 38.04% 315ms 4.15% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.039% 38.08% 315ms 4.15% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 38.08% 315ms 4.15% std::_Rb_tree::_M_drop_node (inline) 5ms 0.066% 38.14% 312ms 4.11% Cell::ReadyToDivide 31ms 0.41% 38.55% 311ms 4.09% std::_Rb_tree::_M_copy (inline) 5ms 0.066% 38.62% 310ms 4.08% Element::Element 120ms 1.58% 40.20% 306ms 4.03% __GI___libc_free 215ms 2.83% 43.03% 306ms 4.03% _int_malloc 11ms 0.14% 43.17% 286ms 3.77% std::__new_allocator::deallocate (inline) 0 0% 43.17% 284ms 3.74% std::allocator_traits::deallocate (inline) 83ms 1.09% 44.27% 277ms 3.65% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.27% 259ms 3.41% CellProliferativeTypesWriter::VisitCell 0 0% 44.27% 251ms 3.30% Cell::HasCellProperty (inline) 4ms 0.053% 44.32% 250ms 3.29% CellPropertyCollection::HasProperty 4ms 0.053% 44.37% 249ms 3.28% std::__cxx11::collate::do_transform 3ms 0.039% 44.41% 247ms 3.25% AbstractCellProperty::IsType (inline) 7ms 0.092% 44.50% 246ms 3.24% divconqrecurse 0 0% 44.50% 244ms 3.21% std::_Rb_tree::_M_put_node (inline) 2ms 0.026% 44.53% 234ms 3.08% ___vsnprintf 0 0% 44.53% 232ms 3.05% __vsnprintf_internal (inline) 40ms 0.53% 45.06% 231ms 3.04% __printf_buffer 67ms 0.88% 45.94% 227ms 2.99% mergehulls 77ms 1.01% 46.95% 209ms 2.75% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.066% 47.02% 208ms 2.74% Element::RegisterWithNodes (inline) 2ms 0.026% 47.04% 202ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.053% 47.10% 200ms 2.63% Node::AddElement 7ms 0.092% 47.19% 197ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.21% 47.40% 191ms 2.51% TetrahedralMesh::Clear 156ms 2.05% 49.45% 186ms 2.45% _int_free 44ms 0.58% 50.03% 183ms 2.41% AbstractCellProperty::IsSame 1ms 0.013% 50.05% 172ms 2.26% __printf_fp_spec (inline) 9ms 0.12% 50.16% 171ms 2.25% __printf_fp_l_buffer 4ms 0.053% 50.22% 169ms 2.23% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 50.23% 168ms 2.21% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 50.23% 167ms 2.20% AbstractCellBasedWriter::OpenOutputFileForAppend 13ms 0.17% 50.40% 165ms 2.17% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.40% 165ms 2.17% OutputFileHandler::OpenOutputFile 0 0% 50.40% 161ms 2.12% std::basic_ofstream::basic_ofstream (inline) 37ms 0.49% 50.89% 156ms 2.05% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.89% 156ms 2.05% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.89% 155ms 2.04% std::basic_filebuf::open 0 0% 50.89% 155ms 2.04% std::basic_ofstream::open (inline) 100ms 1.32% 52.21% 154ms 2.03% __printf_fp_buffer_1 9ms 0.12% 52.32% 146ms 1.92% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.12% 52.44% 142ms 1.87% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.44% 142ms 1.87% OutputFileHandler::CommonConstructor 0 0% 52.44% 142ms 1.87% OutputFileHandler::OutputFileHandler 1ms 0.013% 52.46% 139ms 1.83% boost::numeric::ublas::vector_assign (inline) 29ms 0.38% 52.84% 139ms 1.83% std::type_info::operator== (inline) 0 0% 52.84% 136ms 1.79% OutputFileHandler::MakeFoldersAndReturnFullPath 13ms 0.17% 53.01% 132ms 1.74% std::_Rb_tree_const_iterator::operator++ (inline) 29ms 0.38% 53.39% 128ms 1.69% std::num_put::_M_insert_int 0 0% 53.39% 126ms 1.66% AbstractCellPopulation::CloseRoundRobinWritersFiles 17ms 0.22% 53.61% 126ms 1.66% AbstractTetrahedralElement::RefreshJacobian 7ms 0.092% 53.71% 126ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 53.71% 126ms 1.66% boost::shared_ptr::~shared_ptr (inline) 0 0% 53.71% 125ms 1.65% AbstractCellBasedWriter::CloseFile 0 0% 53.71% 125ms 1.65% std::__basic_file::open 0 0% 53.71% 125ms 1.65% std::basic_filebuf::close 0 0% 53.71% 125ms 1.65% std::basic_ofstream::close (inline) 0 0% 53.71% 124ms 1.63% _IO_new_fopen 0 0% 53.71% 124ms 1.63% __fopen_internal (inline) 124ms 1.63% 55.34% 124ms 1.63% std::_Rb_tree_increment 0 0% 55.34% 120ms 1.58% _IO_new_file_fopen 25ms 0.33% 55.67% 119ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.14% 55.81% 119ms 1.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.026% 55.84% 119ms 1.57% __GI__IO_file_open 1ms 0.013% 55.85% 118ms 1.55% std::_Vector_base::_M_allocate (inline) 0 0% 55.85% 117ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.16% 56.01% 116ms 1.53% Node::~Node 115ms 1.51% 57.52% 116ms 1.53% boost::detail::sp_counted_base::release 83ms 1.09% 58.62% 115ms 1.51% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.039% 58.66% 115ms 1.51% alternateaxes 112ms 1.47% 60.13% 112ms 1.47% std::_Rb_tree_insert_and_rebalance 101ms 1.33% 61.46% 112ms 1.47% vertexmedian 39ms 0.51% 61.97% 106ms 1.40% std::__ostream_insert 34ms 0.45% 62.42% 105ms 1.38% boost::numeric::ublas::indexing_vector_assign 4ms 0.053% 62.48% 104ms 1.37% AbstractTetrahedralElement::AbstractTetrahedralElement 102ms 1.34% 63.82% 102ms 1.34% [libchaste_cell_based.so] 101ms 1.33% 65.15% 101ms 1.33% incircle 98ms 1.29% 66.44% 99ms 1.30% __libc_open64 43ms 0.57% 67.00% 95ms 1.25% AbstractElement::GetNodeLocation 4ms 0.053% 67.06% 92ms 1.21% std::vector::push_back (inline) 1ms 0.013% 67.07% 91ms 1.20% std::basic_filebuf::_M_terminate_output 3ms 0.039% 67.11% 90ms 1.18% std::operator<< (inline) 2ms 0.026% 67.14% 89ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 4ms 0.053% 67.19% 89ms 1.17% std::__basic_file::xsputn 0 0% 67.19% 89ms 1.17% std::basic_filebuf::_M_convert_to_external 0 0% 67.19% 89ms 1.17% std::basic_filebuf::overflow 33ms 0.43% 67.62% 86ms 1.13% boost::shared_ptr::shared_ptr (inline) 85ms 1.12% 68.74% 85ms 1.12% __GI___libc_write 1ms 0.013% 68.76% 85ms 1.12% std::filesystem::status 84ms 1.11% 69.86% 84ms 1.11% __GI___fstatat64 9ms 0.12% 69.98% 84ms 1.11% std::vector::_M_realloc_insert 1ms 0.013% 69.99% 83ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 58ms 0.76% 70.76% 83ms 1.09% std::basic_streambuf::xsputn 1ms 0.013% 70.77% 82ms 1.08% Cell::GetCellId 58ms 0.76% 71.53% 77ms 1.01% malloc_consolidate 0 0% 71.53% 73ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 71.53% 72ms 0.95% std::filesystem::create_directory 0 0% 71.53% 71ms 0.93% std::_Rb_tree::_M_destroy_node (inline) 0 0% 71.53% 71ms 0.93% std::__new_allocator::destroy (inline) 0 0% 71.53% 71ms 0.93% std::allocator_traits::destroy (inline) 6ms 0.079% 71.61% 70ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeB 70ms 0.92% 72.53% 70ms 0.92% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 70ms 0.92% 73.46% 70ms 0.92% [libchaste_mesh.so] 43ms 0.57% 74.02% 70ms 0.92% std::basic_filebuf::xsputn 52ms 0.68% 74.71% 68ms 0.9% AbstractElement::GetNodeGlobalIndex 9ms 0.12% 74.83% 67ms 0.88% CellPropertyCollection::AddProperty 63ms 0.83% 75.66% 63ms 0.83% __memcpy_avx_unaligned_erms 0 0% 75.66% 60ms 0.79% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 60ms 0.79% 76.45% 60ms 0.79% Node::GetIndex 0 0% 76.45% 60ms 0.79% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 28ms 0.37% 76.81% 59ms 0.78% AbstractTetrahedralMesh::GetElement 0 0% 76.81% 59ms 0.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.81% 59ms 0.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 59ms 0.78% 77.59% 59ms 0.78% std::vector::size (inline) 5ms 0.066% 77.66% 58ms 0.76% Node::ConstructNodeAttributes (inline) 57ms 0.75% 78.41% 57ms 0.75% counterclockwise 0 0% 78.41% 57ms 0.75% std::vector::vector (inline) 0 0% 78.41% 56ms 0.74% tcache_get (inline) 56ms 0.74% 79.14% 56ms 0.74% tcache_get_n (inline) 3ms 0.039% 79.18% 55ms 0.72% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 79.18% 55ms 0.72% std::_Vector_base::_Vector_base (inline) 34ms 0.45% 79.63% 54ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.63% 54ms 0.71% std::_Vector_base::_M_create_storage (inline) 0 0% 79.63% 53ms 0.7% Node::ClearAppliedForce 53ms 0.7% 80.33% 53ms 0.7% boost::detail::shared_count::shared_count (inline) 53ms 0.7% 81.03% 53ms 0.7% std::ostream::sentry::sentry 0 0% 81.03% 49ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 49ms 0.65% 81.67% 49ms 0.65% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 81.67% 48ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 47ms 0.62% 82.29% 47ms 0.62% Node::IsDeleted 0 0% 82.29% 45ms 0.59% BoundaryNodeWriter::Visit 38ms 0.5% 82.79% 45ms 0.59% vertexsort 44ms 0.58% 83.37% 44ms 0.58% boost::shared_ptr::operator-> (inline) 6ms 0.079% 83.45% 44ms 0.58% std::_Vector_base::_M_deallocate (inline) 0 0% 83.45% 42ms 0.55% AbstractCentreBasedCellPopulation::IsMarkedSpring 31ms 0.41% 83.86% 42ms 0.55% std::num_put::do_put 2ms 0.026% 83.88% 41ms 0.54% std::__new_allocator::construct (inline) 0 0% 83.88% 41ms 0.54% std::allocator_traits::construct (inline) 40ms 0.53% 84.41% 40ms 0.53% [libstdc++.so.6.0.33] 0 0% 84.41% 40ms 0.53% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 84.60% 40ms 0.53% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.60% 40ms 0.53% std::_Rb_tree::_M_construct_node (inline) 4ms 0.053% 84.65% 39ms 0.51% NodeAttributes::NodeAttributes 10ms 0.13% 84.78% 38ms 0.5% Determinant (inline) 3ms 0.039% 84.82% 38ms 0.5% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.82% 38ms 0.5% std::map::find (inline) 0 0% 84.82% 38ms 0.5% std::map::map (inline)