File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6675ms, 85.59% of 7799ms total Dropped 559 nodes (cum <= 38.99ms) flat flat% sum% cum cum% 0 0% 0% 7763ms 99.54% __libc_start_call_main 0 0% 0% 7763ms 99.54% __libc_start_main_impl 0 0% 0% 7763ms 99.54% _start 0 0% 0% 7749ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7749ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7749ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7749ms 99.36% main 0 0% 0% 7712ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7712ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7712ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7709ms 98.85% AbstractCellBasedSimulation::Solve 0 0% 0% 3213ms 41.20% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2846ms 36.49% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.026% 2792ms 35.80% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 1642ms 21.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1471ms 18.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.026% 0.064% 1419ms 18.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.026% 0.09% 1398ms 17.93% MutableMesh::ReMesh 1ms 0.013% 0.1% 1342ms 17.21% MeshBasedCellPopulation::UpdateNodePairs 18ms 0.23% 0.33% 1186ms 15.21% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.33% 1014ms 13.00% AbstractTwoBodyInteractionForce::AddForceContribution 459ms 5.89% 6.22% 1009ms 12.94% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.12% 6.33% 994ms 12.75% CellPopulationElementWriter::Visit 2ms 0.026% 6.36% 985ms 12.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 64ms 0.82% 7.18% 945ms 12.12% AbstractCellPopulation::GetCellUsingLocationIndex 121ms 1.55% 8.73% 945ms 12.12% TetrahedralMesh::EdgeIterator::operator++ 49ms 0.63% 9.36% 918ms 11.77% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 16ms 0.21% 9.57% 874ms 11.21% CellPropertyCollection::GetPropertiesType (inline) 247ms 3.17% 12.73% 827ms 10.60% __dynamic_cast 2ms 0.026% 12.76% 801ms 10.27% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.1% 12.86% 717ms 9.19% TetrahedralMesh::ImportFromMesher 49ms 0.63% 13.49% 675ms 8.65% std::map::operator[] (partial-inline) 6ms 0.077% 13.57% 653ms 8.37% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 13.58% 617ms 7.91% std::ostream::operator<< (inline) 98ms 1.26% 14.84% 616ms 7.90% std::ostream::_M_insert 0 0% 14.84% 568ms 7.28% std::_Rb_tree::lower_bound (inline) 0 0% 14.84% 568ms 7.28% std::map::lower_bound (inline) 43ms 0.55% 15.39% 549ms 7.04% operator new 1ms 0.013% 15.40% 526ms 6.74% triangulate 5ms 0.064% 15.46% 523ms 6.71% Cell::GetCellProliferativeType 6ms 0.077% 15.54% 518ms 6.64% std::set::insert (inline) 2ms 0.026% 15.57% 512ms 6.56% std::_Rb_tree::_M_insert_unique 37ms 0.47% 16.04% 512ms 6.56% std::_Rb_tree::~_Rb_tree (inline) 173ms 2.22% 18.26% 501ms 6.42% __GI___libc_malloc 28ms 0.36% 18.62% 494ms 6.33% std::__new_allocator::allocate (inline) 0 0% 18.62% 489ms 6.27% std::allocator_traits::allocate (inline) 0 0% 18.62% 484ms 6.21% std::set::~set (inline) 5ms 0.064% 18.68% 482ms 6.18% LegacyCellProliferativeTypesWriter::VisitCell 22ms 0.28% 18.96% 478ms 6.13% std::_Rb_tree::find (inline) 93ms 1.19% 20.16% 471ms 6.04% std::_Rb_tree::_M_erase 469ms 6.01% 26.17% 469ms 6.01% __strcmp_avx2 0 0% 26.17% 466ms 5.98% delaunay 1ms 0.013% 26.18% 464ms 5.95% divconqdelaunay 0 0% 26.18% 433ms 5.55% std::_Rb_tree::_M_create_node (inline) 0 0% 26.18% 430ms 5.51% std::set::count (inline) 1ms 0.013% 26.20% 414ms 5.31% AbstractCellBasedSimulation::DoCellBirth 190ms 2.44% 28.63% 410ms 5.26% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.63% 405ms 5.19% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.63% 388ms 4.97% std::_Rb_tree::_M_get_node (inline) 2ms 0.026% 28.66% 379ms 4.86% NodeLocationWriter::Visit 6ms 0.077% 28.73% 376ms 4.82% Cell::GetMutationState 0 0% 28.73% 359ms 4.60% std::_Rb_tree::_M_drop_node (inline) 359ms 4.60% 33.34% 359ms 4.60% std::_Rb_tree::_S_right (inline) 129ms 1.65% 34.99% 355ms 4.55% __GI___libc_free 19ms 0.24% 35.24% 351ms 4.50% std::_Rb_tree::_Rb_tree (partial-inline) 12ms 0.15% 35.39% 336ms 4.31% std::__new_allocator::deallocate (inline) 0 0% 35.39% 333ms 4.27% std::allocator_traits::deallocate (inline) 1ms 0.013% 35.40% 332ms 4.26% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 35.40% 332ms 4.26% MeshBasedCellPopulation::GetDampingConstant 27ms 0.35% 35.75% 332ms 4.26% std::less::operator() (inline) 24ms 0.31% 36.06% 329ms 4.22% std::num_put::_M_insert_float 25ms 0.32% 36.38% 319ms 4.09% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 36.39% 314ms 4.03% std::set::set (inline) 4ms 0.051% 36.44% 308ms 3.95% Element::Element 305ms 3.91% 40.35% 305ms 3.91% std::operator< (inline) 39ms 0.5% 40.85% 304ms 3.90% std::_Rb_tree::_M_copy (inline) 0 0% 40.85% 296ms 3.80% std::_Rb_tree::_M_put_node (inline) 7ms 0.09% 40.94% 290ms 3.72% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.051% 40.99% 279ms 3.58% Cell::ReadyToDivide 2ms 0.026% 41.02% 268ms 3.44% CellProliferativeTypesWriter::VisitCell 77ms 0.99% 42.01% 260ms 3.33% std::_Rb_tree::_M_clone_node (inline) 183ms 2.35% 44.35% 255ms 3.27% _int_malloc 16ms 0.21% 44.56% 255ms 3.27% divconqrecurse 7ms 0.09% 44.65% 253ms 3.24% std::__cxx11::collate::do_transform 1ms 0.013% 44.66% 240ms 3.08% ___vsnprintf 0 0% 44.66% 239ms 3.06% __vsnprintf_internal (inline) 23ms 0.29% 44.95% 233ms 2.99% __printf_buffer 63ms 0.81% 45.76% 233ms 2.99% mergehulls 196ms 2.51% 48.28% 225ms 2.88% _int_free 3ms 0.038% 48.31% 221ms 2.83% AbstractCellProperty::IsType (inline) 3ms 0.038% 48.35% 212ms 2.72% CellPropertyCollection::HasProperty 0 0% 48.35% 210ms 2.69% Cell::HasCellProperty (inline) 19ms 0.24% 48.60% 201ms 2.58% TetrahedralMesh::Clear 8ms 0.1% 48.70% 198ms 2.54% __printf_fp_l_buffer 0 0% 48.70% 198ms 2.54% __printf_fp_spec (inline) 6ms 0.077% 48.78% 197ms 2.53% Element::RegisterWithNodes (inline) 64ms 0.82% 49.60% 191ms 2.45% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 49.61% 188ms 2.41% Node::AddElement 6ms 0.077% 49.69% 185ms 2.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.077% 49.76% 184ms 2.36% MeshBasedCellPopulation::SpringsEnd (inline) 106ms 1.36% 51.12% 180ms 2.31% __printf_fp_buffer_1 8ms 0.1% 51.22% 173ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 35ms 0.45% 51.67% 167ms 2.14% TetrahedralMesh::EdgesEnd (partial-inline) 15ms 0.19% 51.87% 164ms 2.10% AbstractTetrahedralElement::CalculateJacobian 45ms 0.58% 52.44% 161ms 2.06% AbstractCellProperty::IsSame 1ms 0.013% 52.46% 157ms 2.01% OutputFileHandler::OutputFileHandler 0 0% 52.46% 156ms 2.00% OutputFileHandler::CommonConstructor 6ms 0.077% 52.53% 156ms 2.00% boost::numeric::ublas::vector_assign (inline) 61ms 0.78% 53.31% 154ms 1.97% std::__ostream_insert 0 0% 53.31% 150ms 1.92% OutputFileHandler::MakeFoldersAndReturnFullPath 25ms 0.32% 53.64% 150ms 1.92% std::num_put::_M_insert_int 8ms 0.1% 53.74% 149ms 1.91% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 53.74% 147ms 1.88% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 53.74% 145ms 1.86% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 53.75% 141ms 1.81% OutputFileHandler::OpenOutputFile 0 0% 53.75% 137ms 1.76% std::basic_ofstream::basic_ofstream (inline) 0 0% 53.75% 134ms 1.72% alternateaxes 124ms 1.59% 55.34% 134ms 1.72% vertexmedian 1ms 0.013% 55.35% 133ms 1.71% std::basic_ofstream::open (inline) 0 0% 55.35% 132ms 1.69% std::basic_filebuf::open 0 0% 55.35% 131ms 1.68% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.19% 55.55% 130ms 1.67% boost::detail::shared_count::~shared_count (inline) 0 0% 55.55% 130ms 1.67% boost::shared_ptr::~shared_ptr (inline) 3ms 0.038% 55.58% 119ms 1.53% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.12% 55.70% 119ms 1.53% Node::~Node 42ms 0.54% 56.24% 119ms 1.53% boost::numeric::ublas::indexing_vector_assign 5ms 0.064% 56.30% 118ms 1.51% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.21% 56.51% 118ms 1.51% AbstractTetrahedralElement::RefreshJacobian 118ms 1.51% 58.02% 118ms 1.51% incircle 3ms 0.038% 58.06% 118ms 1.51% std::operator<< (inline) 15ms 0.19% 58.25% 116ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.28% 58.53% 116ms 1.49% std::type_info::operator== (inline) 0 0% 58.53% 115ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 109ms 1.40% 59.93% 110ms 1.41% boost::detail::sp_counted_base::release 8ms 0.1% 60.03% 110ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 109ms 1.40% 61.43% 109ms 1.40% std::_Rb_tree_increment 69ms 0.88% 62.32% 108ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 62.32% 107ms 1.37% std::__basic_file::open 1ms 0.013% 62.33% 105ms 1.35% AbstractCellBasedWriter::CloseFile 0 0% 62.33% 105ms 1.35% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 62.33% 105ms 1.35% _IO_new_fopen 1ms 0.013% 62.34% 105ms 1.35% __fopen_internal (inline) 0 0% 62.34% 104ms 1.33% std::basic_filebuf::close 0 0% 62.34% 104ms 1.33% std::basic_ofstream::close (inline) 2ms 0.026% 62.37% 104ms 1.33% std::vector::push_back (inline) 16ms 0.21% 62.57% 103ms 1.32% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 62.58% 102ms 1.31% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 62.60% 101ms 1.30% _IO_new_file_fopen 46ms 0.59% 63.19% 101ms 1.30% boost::shared_ptr::shared_ptr (inline) 0 0% 63.19% 99ms 1.27% __GI__IO_file_open 4ms 0.051% 63.24% 97ms 1.24% std::vector::_M_realloc_insert 66ms 0.85% 64.09% 93ms 1.19% std::basic_filebuf::xsputn 62ms 0.79% 64.88% 91ms 1.17% std::basic_streambuf::xsputn 88ms 1.13% 66.01% 89ms 1.14% __libc_open64 34ms 0.44% 66.44% 85ms 1.09% AbstractElement::GetNodeLocation 2ms 0.026% 66.47% 83ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 66.47% 83ms 1.06% std::__basic_file::xsputn 0 0% 66.47% 83ms 1.06% std::basic_filebuf::_M_convert_to_external 0 0% 66.47% 83ms 1.06% std::basic_filebuf::_M_terminate_output 0 0% 66.47% 83ms 1.06% std::basic_filebuf::overflow 2ms 0.026% 66.50% 83ms 1.06% std::filesystem::create_directory 81ms 1.04% 67.53% 82ms 1.05% __GI___libc_write 81ms 1.04% 68.57% 81ms 1.04% std::_Rb_tree_insert_and_rebalance 0 0% 68.57% 80ms 1.03% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 80ms 1.03% 69.60% 80ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 77ms 0.99% 70.59% 77ms 0.99% [libchaste_cell_based.so] 2ms 0.026% 70.61% 77ms 0.99% std::filesystem::status 76ms 0.97% 71.59% 76ms 0.97% __GI___fstatat64 75ms 0.96% 72.55% 75ms 0.96% __memcpy_avx_unaligned_erms 75ms 0.96% 73.51% 75ms 0.96% std::vector::size (inline) 1ms 0.013% 73.52% 72ms 0.92% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.12% 73.64% 72ms 0.92% CellPropertyCollection::AddProperty 0 0% 73.64% 71ms 0.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.64% 71ms 0.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 73.65% 70ms 0.9% Cell::GetCellId 64ms 0.82% 74.47% 70ms 0.9% vertexsort 8ms 0.1% 74.57% 69ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 51ms 0.65% 75.23% 67ms 0.86% AbstractElement::GetNodeGlobalIndex 0 0% 75.23% 66ms 0.85% tcache_get (inline) 66ms 0.85% 76.07% 66ms 0.85% tcache_get_n (inline) 0 0% 76.07% 63ms 0.81% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.07% 63ms 0.81% std::__new_allocator::destroy (inline) 0 0% 76.07% 63ms 0.81% std::allocator_traits::destroy (inline) 60ms 0.77% 76.84% 60ms 0.77% Node::GetIndex 3ms 0.038% 76.88% 58ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 46ms 0.59% 77.47% 57ms 0.73% std::num_put::do_put 55ms 0.71% 78.18% 55ms 0.71% boost::detail::shared_count::shared_count (inline) 27ms 0.35% 78.52% 54ms 0.69% boost::numeric::ublas::c_matrix::operator() (partial-inline) 54ms 0.69% 79.22% 54ms 0.69% counterclockwise 3ms 0.038% 79.25% 53ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeA 53ms 0.68% 79.93% 53ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 79.93% 52ms 0.67% boost::numeric::ublas::norm_2 (inline) 18ms 0.23% 80.16% 52ms 0.67% boost::numeric::ublas::vector_norm_2::apply (inline) 16ms 0.21% 80.37% 51ms 0.65% AbstractCellCycleModel::GetAge 2ms 0.026% 80.39% 51ms 0.65% std::__new_allocator::construct (inline) 0 0% 80.39% 51ms 0.65% std::allocator_traits::construct (inline) 1ms 0.013% 80.41% 50ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.41% 50ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 50ms 0.64% 81.05% 50ms 0.64% Node::IsDeleted 50ms 0.64% 81.69% 50ms 0.64% [libchaste_mesh.so] 49ms 0.63% 82.32% 49ms 0.63% boost::numeric::ublas::c_vector::operator() (partial-inline) 33ms 0.42% 82.74% 48ms 0.62% hack_digit 35ms 0.45% 83.19% 48ms 0.62% malloc_consolidate 18ms 0.23% 83.42% 45ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 2ms 0.026% 83.45% 45ms 0.58% Node::ConstructNodeAttributes (inline) 0 0% 83.45% 45ms 0.58% std::_Rb_tree::_M_construct_node (inline) 17ms 0.22% 83.66% 44ms 0.56% Determinant (inline) 0 0% 83.66% 44ms 0.56% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 1ms 0.013% 83.68% 44ms 0.56% Node::ClearAppliedForce 27ms 0.35% 84.02% 43ms 0.55% AbstractTetrahedralMesh::GetElement 0 0% 84.02% 43ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.53% 84.55% 41ms 0.53% AbstractElement::IsDeleted 41ms 0.53% 85.08% 41ms 0.53% Node::rGetLocation 1ms 0.013% 85.09% 39ms 0.5% BoundaryNodeWriter::Visit 39ms 0.5% 85.59% 39ms 0.5% __GI___mkdir 0 0% 85.59% 39ms 0.5% std::map::map (inline)