File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6686ms, 85.87% of 7786ms total Dropped 560 nodes (cum <= 38.93ms) flat flat% sum% cum cum% 0 0% 0% 7747ms 99.50% __libc_start_call_main 0 0% 0% 7747ms 99.50% __libc_start_main_impl 0 0% 0% 7747ms 99.50% _start 0 0% 0% 7729ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7729ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7729ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7729ms 99.27% main 0 0% 0% 7689ms 98.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7689ms 98.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7689ms 98.75% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7686ms 98.72% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3387ms 43.50% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.039% 2940ms 37.76% MeshBasedCellPopulation::Update 2ms 0.026% 0.064% 2722ms 34.96% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.064% 1566ms 20.11% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.064% 1479ms 19.00% MutableMesh::ReMesh 0 0% 0.064% 1406ms 18.06% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.077% 1404ms 18.03% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.12% 0.19% 1351ms 17.35% AbstractNumericalMethod::ComputeForcesIncludingDamping 26ms 0.33% 0.53% 1216ms 15.62% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.026% 0.55% 965ms 12.39% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 119ms 1.53% 2.08% 964ms 12.38% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.013% 2.09% 954ms 12.25% AbstractTwoBodyInteractionForce::AddForceContribution 405ms 5.20% 7.30% 937ms 12.03% std::_Rb_tree::_M_lower_bound (inline) 221ms 2.84% 10.13% 904ms 11.61% __dynamic_cast 11ms 0.14% 10.27% 877ms 11.26% CellPropertyCollection::GetPropertiesType (inline) 14ms 0.18% 10.45% 864ms 11.10% CellPopulationElementWriter::Visit 40ms 0.51% 10.97% 840ms 10.79% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.077% 11.05% 815ms 10.47% MeshBasedCellPopulation::AcceptCellWriter 11ms 0.14% 11.19% 755ms 9.70% TetrahedralMesh::ImportFromMesher 29ms 0.37% 11.56% 750ms 9.63% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 11.57% 685ms 8.80% AbstractCellProperty::IsSubType (inline) 101ms 1.30% 12.87% 592ms 7.60% std::ostream::_M_insert 0 0% 12.87% 592ms 7.60% std::ostream::operator<< (inline) 24ms 0.31% 13.18% 574ms 7.37% operator new 38ms 0.49% 13.67% 571ms 7.33% std::map::operator[] (partial-inline) 4ms 0.051% 13.72% 547ms 7.03% std::set::insert (inline) 6ms 0.077% 13.79% 545ms 7.00% triangulate 8ms 0.1% 13.90% 543ms 6.97% std::_Rb_tree::_M_insert_unique 542ms 6.96% 20.86% 542ms 6.96% __strcmp_avx2 3ms 0.039% 20.90% 537ms 6.90% LegacyCellProliferativeTypesWriter::VisitCell 192ms 2.47% 23.36% 536ms 6.88% __GI___libc_malloc 30ms 0.39% 23.75% 517ms 6.64% std::__new_allocator::allocate (inline) 0 0% 23.75% 516ms 6.63% std::allocator_traits::allocate (inline) 234ms 3.01% 26.75% 506ms 6.50% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.23% 26.98% 493ms 6.33% std::_Rb_tree::find (inline) 7ms 0.09% 27.07% 489ms 6.28% Cell::GetCellProliferativeType 0 0% 27.07% 483ms 6.20% std::_Rb_tree::lower_bound (inline) 0 0% 27.07% 483ms 6.20% std::map::lower_bound (inline) 0 0% 27.07% 474ms 6.09% delaunay 1ms 0.013% 27.09% 474ms 6.09% divconqdelaunay 0 0% 27.09% 437ms 5.61% std::set::count (inline) 9ms 0.12% 27.20% 434ms 5.57% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.20% 424ms 5.45% std::_Rb_tree::_M_create_node (inline) 37ms 0.48% 27.68% 408ms 5.24% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.68% 400ms 5.14% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.064% 27.74% 392ms 5.03% Cell::GetMutationState 0 0% 27.74% 384ms 4.93% std::_Rb_tree::_M_get_node (inline) 0 0% 27.74% 376ms 4.83% std::set::~set (inline) 75ms 0.96% 28.71% 365ms 4.69% std::_Rb_tree::_M_erase 10ms 0.13% 28.83% 347ms 4.46% std::less::operator() (inline) 0 0% 28.83% 344ms 4.42% NodeLocationWriter::Visit 30ms 0.39% 29.22% 340ms 4.37% std::_Rb_tree::_M_insert_ (inline) 337ms 4.33% 33.55% 337ms 4.33% std::operator< (inline) 9ms 0.12% 33.66% 336ms 4.32% Element::Element 20ms 0.26% 33.92% 332ms 4.26% std::_Rb_tree::_Rb_tree (partial-inline) 319ms 4.10% 38.02% 319ms 4.10% std::_Rb_tree::_S_right (inline) 2ms 0.026% 38.04% 314ms 4.03% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 38.06% 311ms 3.99% AbstractCentreBasedCellPopulation::GetDampingConstant 82ms 1.05% 39.11% 300ms 3.85% __GI___libc_free 27ms 0.35% 39.46% 299ms 3.84% std::num_put::_M_insert_float 4ms 0.051% 39.51% 296ms 3.80% std::set::set (inline) 0 0% 39.51% 284ms 3.65% std::_Rb_tree::_M_drop_node (inline) 27ms 0.35% 39.85% 283ms 3.63% std::_Rb_tree::_M_copy (inline) 5ms 0.064% 39.92% 275ms 3.53% Cell::ReadyToDivide 9ms 0.12% 40.03% 273ms 3.51% divconqrecurse 10ms 0.13% 40.16% 271ms 3.48% AbstractCellPopulation::IsCellAttachedToLocationIndex 179ms 2.30% 42.46% 270ms 3.47% _int_malloc 11ms 0.14% 42.60% 266ms 3.42% std::__new_allocator::deallocate (inline) 77ms 0.99% 43.59% 259ms 3.33% mergehulls 0 0% 43.59% 258ms 3.31% std::allocator_traits::deallocate (inline) 4ms 0.051% 43.64% 251ms 3.22% AbstractCellProperty::IsType (inline) 68ms 0.87% 44.52% 245ms 3.15% std::_Rb_tree::_M_clone_node (inline) 7ms 0.09% 44.61% 244ms 3.13% std::__cxx11::collate::do_transform 7ms 0.09% 44.70% 239ms 3.07% CellPropertyCollection::HasProperty 0 0% 44.70% 237ms 3.04% Cell::HasCellProperty (inline) 1ms 0.013% 44.71% 232ms 2.98% CellProliferativeTypesWriter::VisitCell 0 0% 44.71% 230ms 2.95% ___vsnprintf 0 0% 44.71% 230ms 2.95% __vsnprintf_internal (inline) 34ms 0.44% 45.15% 226ms 2.90% __printf_buffer 0 0% 45.15% 225ms 2.89% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 45.21% 215ms 2.76% Element::RegisterWithNodes (inline) 183ms 2.35% 47.56% 215ms 2.76% _int_free 15ms 0.19% 47.75% 208ms 2.67% TetrahedralMesh::Clear 4ms 0.051% 47.80% 206ms 2.65% Node::AddElement 7ms 0.09% 47.89% 195ms 2.50% MeshBasedCellPopulation::SpringsEnd (inline) 64ms 0.82% 48.72% 195ms 2.50% std::_Rb_tree::_M_get_insert_unique_pos (inline) 40ms 0.51% 49.23% 189ms 2.43% AbstractCellProperty::IsSame 0 0% 49.23% 181ms 2.32% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 49.24% 181ms 2.32% __printf_fp_spec (inline) 2ms 0.026% 49.27% 180ms 2.31% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.051% 49.32% 180ms 2.31% __printf_fp_l_buffer 2ms 0.026% 49.34% 179ms 2.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.026% 49.37% 174ms 2.23% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 49.37% 174ms 2.23% OutputFileHandler::OpenOutputFile 0 0% 49.37% 170ms 2.18% std::basic_ofstream::basic_ofstream (inline) 96ms 1.23% 50.60% 168ms 2.16% __printf_fp_buffer_1 15ms 0.19% 50.80% 164ms 2.11% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 50.81% 163ms 2.09% OutputFileHandler::OutputFileHandler 0 0% 50.81% 162ms 2.08% OutputFileHandler::CommonConstructor 1ms 0.013% 50.82% 160ms 2.05% std::basic_ofstream::open (inline) 1ms 0.013% 50.83% 159ms 2.04% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 50.83% 159ms 2.04% std::basic_filebuf::open 34ms 0.44% 51.27% 153ms 1.97% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 51.28% 152ms 1.95% TetrahedralMesh::RefreshJacobianCachedData 25ms 0.32% 51.61% 149ms 1.91% std::type_info::operator== (inline) 2ms 0.026% 51.63% 148ms 1.90% boost::numeric::ublas::vector_assign (inline) 9ms 0.12% 51.75% 145ms 1.86% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.1% 51.85% 138ms 1.77% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.21% 52.05% 137ms 1.76% boost::detail::shared_count::~shared_count (inline) 0 0% 52.05% 137ms 1.76% boost::shared_ptr::~shared_ptr (inline) 0 0% 52.05% 135ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 52.07% 133ms 1.71% AbstractCellBasedWriter::CloseFile 0 0% 52.07% 133ms 1.71% std::basic_filebuf::close 10ms 0.13% 52.20% 132ms 1.70% Node::~Node 0 0% 52.20% 132ms 1.70% std::_Vector_base::_M_allocate (inline) 0 0% 52.20% 132ms 1.70% std::basic_ofstream::close (inline) 7ms 0.09% 52.29% 131ms 1.68% alternateaxes 59ms 0.76% 53.04% 131ms 1.68% boost::shared_ptr::shared_ptr (inline) 36ms 0.46% 53.51% 129ms 1.66% std::__ostream_insert 17ms 0.22% 53.72% 128ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 34ms 0.44% 54.16% 128ms 1.64% std::num_put::_M_insert_int 2ms 0.026% 54.19% 127ms 1.63% std::__basic_file::open 14ms 0.18% 54.37% 126ms 1.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.37% 126ms 1.62% _IO_new_fopen 0 0% 54.37% 126ms 1.62% __fopen_internal (inline) 0 0% 54.37% 124ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 120ms 1.54% 55.91% 124ms 1.59% vertexmedian 1ms 0.013% 55.92% 122ms 1.57% _IO_new_file_fopen 88ms 1.13% 57.05% 121ms 1.55% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.039% 57.09% 119ms 1.53% AbstractTetrahedralElement::AbstractTetrahedralElement 119ms 1.53% 58.62% 119ms 1.53% incircle 1ms 0.013% 58.63% 118ms 1.52% __GI__IO_file_open 17ms 0.22% 58.85% 115ms 1.48% AbstractTetrahedralElement::RefreshJacobian 39ms 0.5% 59.35% 111ms 1.43% boost::numeric::ublas::indexing_vector_assign 110ms 1.41% 60.76% 110ms 1.41% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 106ms 1.36% 62.12% 110ms 1.41% boost::detail::sp_counted_base::release 108ms 1.39% 63.51% 109ms 1.40% __libc_open64 3ms 0.039% 63.55% 109ms 1.40% std::vector::push_back (inline) 1ms 0.013% 63.56% 108ms 1.39% std::basic_filebuf::_M_terminate_output 1ms 0.013% 63.58% 106ms 1.36% std::basic_filebuf::overflow 4ms 0.051% 63.63% 105ms 1.35% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 63.63% 105ms 1.35% std::__basic_file::xsputn 0 0% 63.63% 105ms 1.35% std::basic_filebuf::_M_convert_to_external 2ms 0.026% 63.65% 103ms 1.32% std::operator<< (inline) 102ms 1.31% 64.96% 102ms 1.31% __GI___libc_write 10ms 0.13% 65.09% 100ms 1.28% std::vector::_M_realloc_insert 1ms 0.013% 65.10% 98ms 1.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 97ms 1.25% 66.35% 97ms 1.25% [libchaste_cell_based.so] 95ms 1.22% 67.57% 95ms 1.22% std::_Rb_tree_insert_and_rebalance 53ms 0.68% 68.25% 95ms 1.22% std::basic_filebuf::xsputn 8ms 0.1% 68.35% 91ms 1.17% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.026% 68.38% 89ms 1.14% std::filesystem::create_directory 38ms 0.49% 68.87% 88ms 1.13% AbstractElement::GetNodeLocation 5ms 0.064% 68.93% 88ms 1.13% TetrahedralMesh::EdgeIterator::GetNodeB 84ms 1.08% 70.01% 84ms 1.08% std::_Rb_tree_increment 66ms 0.85% 70.86% 83ms 1.07% malloc_consolidate 3ms 0.039% 70.90% 82ms 1.05% std::filesystem::status 79ms 1.01% 71.91% 79ms 1.01% __GI___fstatat64 2ms 0.026% 71.94% 78ms 1.00% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.1% 72.04% 77ms 0.99% CellPropertyCollection::AddProperty 53ms 0.68% 72.72% 74ms 0.95% AbstractElement::GetNodeGlobalIndex 68ms 0.87% 73.59% 72ms 0.92% boost::detail::shared_count::shared_count (inline) 0 0% 73.59% 70ms 0.9% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.59% 70ms 0.9% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.077% 73.67% 68ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeA 55ms 0.71% 74.38% 67ms 0.86% std::num_put::do_put 0 0% 74.38% 66ms 0.85% Cell::GetCellId 64ms 0.82% 75.20% 64ms 0.82% std::vector::size (inline) 58ms 0.74% 75.94% 64ms 0.82% vertexsort 1ms 0.013% 75.96% 63ms 0.81% tcache_get (inline) 62ms 0.8% 76.75% 62ms 0.8% tcache_get_n (inline) 59ms 0.76% 77.51% 59ms 0.76% __memcpy_avx_unaligned_erms 59ms 0.76% 78.27% 59ms 0.76% counterclockwise 0 0% 78.27% 59ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.27% 59ms 0.76% std::__new_allocator::destroy (inline) 0 0% 78.27% 59ms 0.76% std::allocator_traits::destroy (inline) 58ms 0.74% 79.01% 58ms 0.74% [libstdc++.so.6.0.33] 44ms 0.57% 79.58% 58ms 0.74% std::basic_streambuf::xsputn 41ms 0.53% 80.11% 57ms 0.73% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 80.11% 57ms 0.73% std::vector::vector (inline) 56ms 0.72% 80.82% 56ms 0.72% Node::GetIndex 0 0% 80.82% 54ms 0.69% boost::numeric::ublas::norm_2 (inline) 21ms 0.27% 81.09% 54ms 0.69% boost::numeric::ublas::vector_norm_2::apply (inline) 29ms 0.37% 81.47% 51ms 0.66% AbstractTetrahedralMesh::GetElement 11ms 0.14% 81.61% 51ms 0.66% Determinant (inline) 0 0% 81.61% 51ms 0.66% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 81.62% 50ms 0.64% Node::ClearAppliedForce 2ms 0.026% 81.65% 50ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.65% 50ms 0.64% std::_Vector_base::_M_create_storage (inline) 0 0% 81.65% 49ms 0.63% Node::ConstructNodeAttributes (inline) 0 0% 81.65% 49ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 48ms 0.62% 82.26% 48ms 0.62% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.26% 48ms 0.62% std::map::find (inline) 46ms 0.59% 82.85% 46ms 0.59% Node::rGetLocation 46ms 0.59% 83.44% 46ms 0.59% __GI___mkdir 32ms 0.41% 83.86% 46ms 0.59% hack_digit 45ms 0.58% 84.43% 45ms 0.58% Node::IsDeleted 45ms 0.58% 85.01% 45ms 0.58% boost::shared_ptr::operator-> (inline) 0 0% 85.01% 44ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 14ms 0.18% 85.19% 43ms 0.55% AbstractCellCycleModel::GetAge 0 0% 85.19% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 2ms 0.026% 85.22% 43ms 0.55% std::__new_allocator::construct (inline) 0 0% 85.22% 43ms 0.55% std::allocator_traits::construct (inline) 0 0% 85.22% 42ms 0.54% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.051% 85.27% 41ms 0.53% std::__copy_move::__copy_m (inline) 0 0% 85.27% 41ms 0.53% std::__copy_move_a (inline) 0 0% 85.27% 41ms 0.53% std::__copy_move_a1 (inline) 0 0% 85.27% 41ms 0.53% std::__copy_move_a2 (inline) 0 0% 85.27% 41ms 0.53% std::copy (inline) 0 0% 85.27% 40ms 0.51% std::_Rb_tree::_M_construct_node (inline) 8ms 0.1% 85.37% 40ms 0.51% std::_Vector_base::_M_deallocate (inline) 0 0% 85.37% 40ms 0.51% std::map::map (inline) 39ms 0.5% 85.87% 39ms 0.5% [libchaste_mesh.so] 0 0% 85.87% 39ms 0.5% _dl_init 0 0% 85.87% 39ms 0.5% call_init (inline)