File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6544ms, 84.89% of 7709ms total Dropped 565 nodes (cum <= 38.55ms) flat flat% sum% cum cum% 0 0% 0% 7672ms 99.52% __libc_start_call_main 0 0% 0% 7672ms 99.52% __libc_start_main_impl 0 0% 0% 7672ms 99.52% _start 0 0% 0% 7654ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7654ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7654ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7654ms 99.29% main 0 0% 0% 7623ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7623ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7623ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7620ms 98.85% AbstractCellBasedSimulation::Solve 0 0% 0% 3633ms 47.13% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 3186ms 41.33% MeshBasedCellPopulation::Update 0 0% 0% 2549ms 33.07% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 1610ms 20.88% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0% 1519ms 19.70% MutableMesh::ReMesh 1ms 0.013% 0.013% 1433ms 18.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 30ms 0.39% 0.4% 1372ms 17.80% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.4% 1255ms 16.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.026% 0.43% 1217ms 15.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 108ms 1.40% 1.83% 1125ms 14.59% TetrahedralMesh::EdgeIterator::operator++ 12ms 0.16% 1.98% 946ms 12.27% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 471ms 6.11% 8.09% 933ms 12.10% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.052% 8.15% 920ms 11.93% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.1% 8.25% 867ms 11.25% CellPopulationElementWriter::Visit 41ms 0.53% 8.78% 853ms 11.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 12ms 0.16% 8.94% 825ms 10.70% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.13% 9.07% 777ms 10.08% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.091% 9.16% 772ms 10.01% TetrahedralMesh::ImportFromMesher 174ms 2.26% 11.42% 767ms 9.95% __dynamic_cast 2ms 0.026% 11.44% 733ms 9.51% CellPropertyCollection::GetPropertiesType (inline) 44ms 0.57% 12.01% 709ms 9.20% operator new 260ms 3.37% 15.38% 654ms 8.48% __GI___libc_malloc 11ms 0.14% 15.53% 609ms 7.90% std::__new_allocator::allocate (inline) 89ms 1.15% 16.68% 607ms 7.87% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.22% 16.90% 605ms 7.85% std::set::insert (inline) 0 0% 16.90% 602ms 7.81% std::allocator_traits::allocate (inline) 4ms 0.052% 16.95% 598ms 7.76% AbstractCellProperty::IsSubType (inline) 16ms 0.21% 17.16% 588ms 7.63% std::_Rb_tree::_M_insert_unique 0 0% 17.16% 578ms 7.50% std::set::~set (inline) 1ms 0.013% 17.17% 571ms 7.41% triangulate 8ms 0.1% 17.28% 559ms 7.25% std::_Rb_tree::find (inline) 2ms 0.026% 17.30% 530ms 6.88% std::ostream::operator<< (inline) 61ms 0.79% 18.10% 525ms 6.81% std::map::operator[] (partial-inline) 0 0% 18.10% 525ms 6.81% std::set::count (inline) 68ms 0.88% 18.98% 524ms 6.80% std::ostream::_M_insert 2ms 0.026% 19.00% 519ms 6.73% LegacyCellProliferativeTypesWriter::VisitCell 59ms 0.77% 19.77% 518ms 6.72% std::_Rb_tree::_M_erase 5ms 0.065% 19.83% 500ms 6.49% Cell::GetCellProliferativeType 0 0% 19.83% 500ms 6.49% std::_Rb_tree::_M_create_node (inline) 0 0% 19.83% 493ms 6.40% delaunay 0 0% 19.83% 491ms 6.37% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 19.85% 490ms 6.36% divconqdelaunay 481ms 6.24% 26.09% 481ms 6.24% __strcmp_evex 0 0% 26.09% 464ms 6.02% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.09% 453ms 5.88% std::_Rb_tree::_M_drop_node (inline) 2ms 0.026% 26.11% 438ms 5.68% AbstractCellBasedSimulation::DoCellBirth 23ms 0.3% 26.41% 423ms 5.49% std::_Rb_tree::_Rb_tree (partial-inline) 187ms 2.43% 28.84% 417ms 5.41% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.84% 409ms 5.31% std::_Rb_tree::lower_bound (inline) 0 0% 28.84% 409ms 5.31% std::map::lower_bound (inline) 3ms 0.039% 28.88% 392ms 5.08% std::set::set (inline) 32ms 0.42% 29.29% 388ms 5.03% std::_Rb_tree::_M_insert_ (inline) 79ms 1.02% 30.32% 370ms 4.80% __GI___libc_free 44ms 0.57% 30.89% 369ms 4.79% std::_Rb_tree::_M_copy (inline) 8ms 0.1% 30.99% 357ms 4.63% boost::detail::shared_count::~shared_count (inline) 0 0% 30.99% 357ms 4.63% boost::shared_ptr::~shared_ptr (inline) 0 0% 30.99% 343ms 4.45% NodeLocationWriter::Visit 341ms 4.42% 35.41% 342ms 4.44% boost::detail::sp_counted_base::release 16ms 0.21% 35.62% 333ms 4.32% std::__new_allocator::deallocate (inline) 0 0% 35.62% 331ms 4.29% std::allocator_traits::deallocate (inline) 6ms 0.078% 35.70% 328ms 4.25% Element::Element 5ms 0.065% 35.76% 316ms 4.10% AbstractCellPopulation::IsCellAttachedToLocationIndex 30ms 0.39% 36.15% 313ms 4.06% std::num_put::_M_insert_float 118ms 1.53% 37.68% 312ms 4.05% std::_Rb_tree::_M_clone_node (inline) 198ms 2.57% 40.25% 300ms 3.89% _int_malloc 10ms 0.13% 40.38% 295ms 3.83% divconqrecurse 0 0% 40.38% 284ms 3.68% std::_Rb_tree::_M_put_node (inline) 229ms 2.97% 43.35% 281ms 3.65% _int_free 2ms 0.026% 43.38% 279ms 3.62% Cell::GetMutationState 79ms 1.02% 44.40% 278ms 3.61% mergehulls 1ms 0.013% 44.42% 268ms 3.48% Cell::ReadyToDivide 261ms 3.39% 47.80% 261ms 3.39% std::_Rb_tree::_S_right (inline) 16ms 0.21% 48.01% 260ms 3.37% std::less::operator() (inline) 0 0% 48.01% 248ms 3.22% Cell::HasCellProperty (inline) 248ms 3.22% 51.23% 248ms 3.22% [libchaste_cell_based.so] 10ms 0.13% 51.36% 248ms 3.22% std::__cxx11::collate::do_transform 3ms 0.039% 51.39% 247ms 3.20% CellPropertyCollection::HasProperty 244ms 3.17% 54.56% 244ms 3.17% std::operator< (inline) 12ms 0.16% 54.72% 240ms 3.11% AbstractCellProperty::IsType (inline) 0 0% 54.72% 238ms 3.09% MeshBasedCellPopulation::GetDampingConstant 3ms 0.039% 54.75% 237ms 3.07% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.039% 54.79% 236ms 3.06% ___vsnprintf 1ms 0.013% 54.81% 233ms 3.02% __vsnprintf_internal (inline) 3ms 0.039% 54.84% 231ms 3.00% Element::RegisterWithNodes (inline) 27ms 0.35% 55.20% 231ms 3.00% __printf_buffer 12ms 0.16% 55.35% 227ms 2.94% Node::AddElement 0 0% 55.35% 209ms 2.71% CellProliferativeTypesWriter::VisitCell 5ms 0.065% 55.42% 199ms 2.58% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.039% 55.45% 192ms 2.49% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.026% 55.48% 189ms 2.45% TetrahedralMesh::Clear 81ms 1.05% 56.53% 184ms 2.39% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 56.53% 180ms 2.33% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 56.53% 179ms 2.32% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 56.53% 178ms 2.31% OutputFileHandler::OpenOutputFile 4ms 0.052% 56.58% 177ms 2.30% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.091% 56.67% 172ms 2.23% __printf_fp_l_buffer 0 0% 56.67% 172ms 2.23% __printf_fp_spec (inline) 0 0% 56.67% 169ms 2.19% std::_Rb_tree::_M_destroy_node (inline) 0 0% 56.67% 169ms 2.19% std::__new_allocator::destroy (inline) 0 0% 56.67% 169ms 2.19% std::allocator_traits::destroy (inline) 13ms 0.17% 56.84% 159ms 2.06% AbstractTetrahedralElement::CalculateJacobian 70ms 0.91% 57.75% 159ms 2.06% __printf_fp_buffer_1 25ms 0.32% 58.07% 154ms 2.00% AbstractCellProperty::IsSame 0 0% 58.07% 152ms 1.97% TetrahedralMesh::RefreshJacobianCachedData 22ms 0.29% 58.36% 146ms 1.89% TetrahedralMesh::EdgesEnd (partial-inline) 146ms 1.89% 60.25% 146ms 1.89% [libchaste_mesh.so] 2ms 0.026% 60.28% 140ms 1.82% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.18% 60.46% 137ms 1.78% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 60.47% 135ms 1.75% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.12% 60.59% 129ms 1.67% std::type_info::operator== (inline) 28ms 0.36% 60.95% 125ms 1.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.091% 61.05% 125ms 1.62% std::vector::push_back (inline) 50ms 0.65% 61.69% 124ms 1.61% std::__ostream_insert 3ms 0.039% 61.73% 121ms 1.57% boost::numeric::ublas::vector_assign (inline) 43ms 0.56% 62.29% 120ms 1.56% std::num_put::_M_insert_int 0 0% 62.29% 119ms 1.54% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.052% 62.34% 118ms 1.53% alternateaxes 14ms 0.18% 62.52% 115ms 1.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 115ms 1.49% 64.02% 115ms 1.49% incircle 19ms 0.25% 64.26% 113ms 1.47% AbstractTetrahedralElement::RefreshJacobian 101ms 1.31% 65.57% 113ms 1.47% vertexmedian 1ms 0.013% 65.59% 112ms 1.45% std::_Vector_base::_M_allocate (inline) 2ms 0.026% 65.61% 112ms 1.45% std::vector::_M_realloc_insert 107ms 1.39% 67.00% 107ms 1.39% [libstdc++.so.6.0.33] 3ms 0.039% 67.04% 105ms 1.36% Node::~Node 2ms 0.026% 67.06% 104ms 1.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 67.06% 104ms 1.35% std::basic_ofstream::basic_ofstream (inline) 0 0% 67.06% 101ms 1.31% std::basic_filebuf::open 0 0% 67.06% 101ms 1.31% std::basic_ofstream::open (inline) 4ms 0.052% 67.12% 100ms 1.30% AbstractTetrahedralElement::AbstractTetrahedralElement 80ms 1.04% 68.15% 100ms 1.30% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 68.17% 99ms 1.28% std::operator<< (inline) 90ms 1.17% 69.33% 90ms 1.17% std::vector::size (inline) 88ms 1.14% 70.48% 88ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 16ms 0.21% 70.68% 88ms 1.14% boost::numeric::ublas::indexing_vector_assign 15ms 0.19% 70.88% 84ms 1.09% TetrahedralMesh::EdgeIterator::GetNodeB 15ms 0.19% 71.07% 81ms 1.05% TetrahedralMesh::EdgeIterator::GetNodeA 81ms 1.05% 72.12% 81ms 1.05% std::_Rb_tree_insert_and_rebalance 54ms 0.7% 72.82% 78ms 1.01% malloc_consolidate 0 0% 72.82% 78ms 1.01% tcache_get (inline) 78ms 1.01% 73.84% 78ms 1.01% tcache_get_n (inline) 1ms 0.013% 73.85% 76ms 0.99% AbstractCellPopulation::GetLocationIndexUsingCell 29ms 0.38% 74.22% 76ms 0.99% AbstractElement::GetNodeLocation 7ms 0.091% 74.32% 73ms 0.95% CellPropertyCollection::AddProperty 5ms 0.065% 74.38% 73ms 0.95% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.27% 74.65% 72ms 0.93% AbstractElement::GetNodeGlobalIndex 2ms 0.026% 74.68% 72ms 0.93% Cell::GetCellId 48ms 0.62% 75.30% 72ms 0.93% std::basic_streambuf::xsputn 43ms 0.56% 75.86% 71ms 0.92% AbstractTetrahedralMesh::GetElement 71ms 0.92% 76.78% 71ms 0.92% counterclockwise 63ms 0.82% 77.60% 70ms 0.91% vertexsort 0 0% 77.60% 68ms 0.88% OutputFileHandler::OutputFileHandler 2ms 0.026% 77.62% 67ms 0.87% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.013% 77.64% 67ms 0.87% OutputFileHandler::CommonConstructor 0 0% 77.64% 65ms 0.84% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 77.64% 62ms 0.8% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 77.64% 62ms 0.8% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 77.64% 62ms 0.8% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 77.64% 61ms 0.79% AbstractCellBasedWriter::CloseFile 61ms 0.79% 78.43% 61ms 0.79% std::_Rb_tree::_S_left (inline) 0 0% 78.43% 61ms 0.79% std::basic_filebuf::close 0 0% 78.43% 61ms 0.79% std::basic_ofstream::close (inline) 60ms 0.78% 79.21% 60ms 0.78% std::_Rb_tree_increment 0 0% 79.21% 57ms 0.74% _IO_new_fopen 0 0% 79.21% 57ms 0.74% __fopen_internal (inline) 57ms 0.74% 79.95% 57ms 0.74% __memcpy_evex_unaligned_erms 0 0% 79.95% 57ms 0.74% std::__basic_file::open 2ms 0.026% 79.97% 55ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 13ms 0.17% 80.14% 54ms 0.7% Determinant (inline) 0 0% 80.14% 54ms 0.7% _IO_new_file_fopen 2ms 0.026% 80.17% 54ms 0.7% __GI__IO_file_open 39ms 0.51% 80.67% 53ms 0.69% boost::numeric::ublas::c_matrix::operator() 0 0% 80.67% 52ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 28ms 0.36% 81.04% 52ms 0.67% hack_digit 27ms 0.35% 81.39% 52ms 0.67% std::basic_filebuf::xsputn 2ms 0.026% 81.41% 51ms 0.66% BoundaryNodeWriter::Visit 1ms 0.013% 81.42% 50ms 0.65% std::basic_filebuf::_M_convert_to_external 0 0% 81.42% 50ms 0.65% std::basic_filebuf::_M_terminate_output 0 0% 81.42% 50ms 0.65% std::basic_filebuf::overflow 48ms 0.62% 82.05% 49ms 0.64% __GI___libc_write 0 0% 82.05% 49ms 0.64% std::map::map (inline) 49ms 0.64% 82.68% 49ms 0.64% tcache_put (inline) 48ms 0.62% 83.31% 48ms 0.62% __libc_open64 0 0% 83.31% 48ms 0.62% std::__basic_file::xsputn 0 0% 83.31% 47ms 0.61% FilesystemPermissions::SetFilePermissions (inline) 47ms 0.61% 83.91% 47ms 0.61% __GI_fchmodat 0 0% 83.91% 47ms 0.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.91% 47ms 0.61% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.91% 47ms 0.61% std::_Vector_base::_M_deallocate (inline) 0 0% 83.91% 47ms 0.61% std::filesystem::permissions 2ms 0.026% 83.94% 44ms 0.57% Node::ConstructNodeAttributes (inline) 0 0% 83.94% 44ms 0.57% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 83.94% 42ms 0.54% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.94% 42ms 0.54% Node::ClearAppliedForce 0 0% 83.94% 40ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 6ms 0.078% 84.02% 39ms 0.51% Inverse 39ms 0.51% 84.52% 39ms 0.51% boost::numeric::ublas::same_impl_ex 28ms 0.36% 84.89% 39ms 0.51% std::num_put::do_put 0 0% 84.89% 39ms 0.51% std::vector::vector (inline)