File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6624ms, 85.34% of 7762ms total Dropped 558 nodes (cum <= 38.81ms) flat flat% sum% cum cum% 0 0% 0% 7725ms 99.52% __libc_start_call_main 0 0% 0% 7725ms 99.52% __libc_start_main_impl 0 0% 0% 7725ms 99.52% _start 0 0% 0% 7706ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7706ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7706ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7706ms 99.28% main 0 0% 0% 7666ms 98.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7666ms 98.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7666ms 98.76% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7664ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3640ms 46.90% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 3185ms 41.03% MeshBasedCellPopulation::Update 1ms 0.013% 0.013% 2542ms 32.75% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.013% 1579ms 20.34% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.013% 1545ms 19.90% MutableMesh::ReMesh 1ms 0.013% 0.026% 1477ms 19.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.28% 0.31% 1361ms 17.53% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.31% 1309ms 16.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.31% 1258ms 16.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 119ms 1.53% 1.84% 1124ms 14.48% TetrahedralMesh::EdgeIterator::operator++ 18ms 0.23% 2.07% 942ms 12.14% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.052% 2.13% 925ms 11.92% AbstractTwoBodyInteractionForce::AddForceContribution 461ms 5.94% 8.06% 904ms 11.65% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.15% 8.22% 852ms 10.98% CellPopulationElementWriter::Visit 39ms 0.5% 8.72% 840ms 10.82% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 197ms 2.54% 11.26% 796ms 10.26% __dynamic_cast 9ms 0.12% 11.38% 790ms 10.18% TetrahedralMesh::ImportFromMesher 25ms 0.32% 11.70% 781ms 10.06% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.026% 11.72% 763ms 9.83% CellPropertyCollection::GetPropertiesType (inline) 12ms 0.15% 11.88% 759ms 9.78% MeshBasedCellPopulation::AcceptCellWriter 40ms 0.52% 12.39% 734ms 9.46% operator new 257ms 3.31% 15.70% 692ms 8.92% __GI___libc_malloc 13ms 0.17% 15.87% 630ms 8.12% std::__new_allocator::allocate (inline) 0 0% 15.87% 627ms 8.08% std::allocator_traits::allocate (inline) 3ms 0.039% 15.91% 626ms 8.06% AbstractCellProperty::IsSubType (inline) 9ms 0.12% 16.03% 626ms 8.06% std::set::insert (inline) 10ms 0.13% 16.16% 617ms 7.95% std::_Rb_tree::_M_insert_unique 0 0% 16.16% 571ms 7.36% triangulate 16ms 0.21% 16.36% 562ms 7.24% std::_Rb_tree::find (inline) 101ms 1.30% 17.66% 560ms 7.21% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.013% 17.68% 551ms 7.10% std::ostream::operator<< (inline) 79ms 1.02% 18.69% 546ms 7.03% std::ostream::_M_insert 0 0% 18.69% 530ms 6.83% std::set::~set (inline) 1ms 0.013% 18.71% 519ms 6.69% delaunay 0 0% 18.71% 519ms 6.69% std::set::count (inline) 2ms 0.026% 18.73% 517ms 6.66% divconqdelaunay 61ms 0.79% 19.52% 511ms 6.58% std::map::operator[] (partial-inline) 9ms 0.12% 19.63% 488ms 6.29% Cell::GetCellProliferativeType 2ms 0.026% 19.66% 483ms 6.22% LegacyCellProliferativeTypesWriter::VisitCell 480ms 6.18% 25.84% 480ms 6.18% __strcmp_evex 0 0% 25.84% 478ms 6.16% std::_Rb_tree::_M_create_node (inline) 0 0% 25.84% 462ms 5.95% std::_Rb_tree::_M_get_node (inline) 61ms 0.79% 26.63% 457ms 5.89% std::_Rb_tree::_M_erase 2ms 0.026% 26.66% 449ms 5.78% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.66% 449ms 5.78% std::_Rb_tree::_Alloc_node::operator() (inline) 20ms 0.26% 26.91% 434ms 5.59% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.039% 26.95% 408ms 5.26% std::set::set (inline) 39ms 0.5% 27.45% 404ms 5.20% std::_Rb_tree::_M_insert_ (inline) 178ms 2.29% 29.75% 401ms 5.17% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 29.75% 393ms 5.06% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.75% 388ms 5.00% std::_Rb_tree::lower_bound (inline) 0 0% 29.75% 388ms 5.00% std::map::lower_bound (inline) 35ms 0.45% 30.20% 374ms 4.82% std::_Rb_tree::_M_copy (inline) 0 0% 30.20% 371ms 4.78% NodeLocationWriter::Visit 9ms 0.12% 30.31% 345ms 4.44% boost::detail::shared_count::~shared_count (inline) 0 0% 30.31% 345ms 4.44% boost::shared_ptr::~shared_ptr (inline) 4ms 0.052% 30.37% 337ms 4.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.09% 30.46% 333ms 4.29% Element::Element 326ms 4.20% 34.66% 327ms 4.21% boost::detail::sp_counted_base::release 225ms 2.90% 37.55% 326ms 4.20% _int_malloc 133ms 1.71% 39.27% 326ms 4.20% std::_Rb_tree::_M_clone_node (inline) 66ms 0.85% 40.12% 321ms 4.14% __GI___libc_free 30ms 0.39% 40.51% 318ms 4.10% std::num_put::_M_insert_float 2ms 0.026% 40.53% 310ms 3.99% Cell::GetMutationState 13ms 0.17% 40.70% 290ms 3.74% std::less::operator() (inline) 5ms 0.064% 40.76% 285ms 3.67% Cell::ReadyToDivide 8ms 0.1% 40.87% 282ms 3.63% divconqrecurse 277ms 3.57% 44.43% 277ms 3.57% std::operator< (inline) 10ms 0.13% 44.56% 275ms 3.54% std::__new_allocator::deallocate (inline) 0 0% 44.56% 271ms 3.49% std::allocator_traits::deallocate (inline) 59ms 0.76% 45.32% 261ms 3.36% mergehulls 3ms 0.039% 45.36% 258ms 3.32% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 45.36% 258ms 3.32% MeshBasedCellPopulation::GetDampingConstant 253ms 3.26% 48.62% 253ms 3.26% std::_Rb_tree::_S_right (inline) 12ms 0.15% 48.78% 251ms 3.23% std::__cxx11::collate::do_transform 210ms 2.71% 51.48% 249ms 3.21% _int_free 231ms 2.98% 54.46% 231ms 2.98% [libchaste_cell_based.so] 1ms 0.013% 54.47% 227ms 2.92% ___vsnprintf 1ms 0.013% 54.48% 226ms 2.91% __vsnprintf_internal (inline) 2ms 0.026% 54.51% 224ms 2.89% Element::RegisterWithNodes (inline) 25ms 0.32% 54.83% 224ms 2.89% __printf_buffer 5ms 0.064% 54.90% 223ms 2.87% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 54.90% 220ms 2.83% CellProliferativeTypesWriter::VisitCell 0 0% 54.90% 220ms 2.83% std::_Rb_tree::_M_put_node (inline) 6ms 0.077% 54.97% 219ms 2.82% AbstractCellProperty::IsType (inline) 8ms 0.1% 55.08% 218ms 2.81% Node::AddElement 3ms 0.039% 55.11% 214ms 2.76% CellPropertyCollection::HasProperty 0 0% 55.11% 213ms 2.74% Cell::HasCellProperty (inline) 7ms 0.09% 55.20% 208ms 2.68% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.077% 55.28% 203ms 2.62% MeshBasedCellPopulation::SpringsEnd (inline) 72ms 0.93% 56.21% 203ms 2.62% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 56.22% 181ms 2.33% __printf_fp_spec (inline) 5ms 0.064% 56.29% 180ms 2.32% __printf_fp_l_buffer 0 0% 56.29% 173ms 2.23% std::_Rb_tree::_M_destroy_node (inline) 0 0% 56.29% 173ms 2.23% std::__new_allocator::destroy (inline) 0 0% 56.29% 173ms 2.23% std::allocator_traits::destroy (inline) 1ms 0.013% 56.30% 166ms 2.14% std::_Vector_base::_M_allocate (inline) 24ms 0.31% 56.61% 165ms 2.13% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 56.61% 165ms 2.13% TetrahedralMesh::RefreshJacobianCachedData 77ms 0.99% 57.60% 163ms 2.10% __printf_fp_buffer_1 8ms 0.1% 57.70% 157ms 2.02% AbstractTetrahedralElement::CalculateJacobian 0 0% 57.70% 155ms 2.00% TetrahedralMesh::Clear 33ms 0.43% 58.13% 153ms 1.97% AbstractCellProperty::IsSame 68ms 0.88% 59.01% 153ms 1.97% std::__ostream_insert 4ms 0.052% 59.06% 151ms 1.95% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.026% 59.08% 151ms 1.95% std::vector::push_back (inline) 0 0% 59.08% 150ms 1.93% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 59.08% 150ms 1.93% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 59.08% 147ms 1.89% OutputFileHandler::OpenOutputFile 146ms 1.88% 60.96% 146ms 1.88% [libchaste_mesh.so] 12ms 0.15% 61.12% 144ms 1.86% std::vector::_M_realloc_insert 5ms 0.064% 61.18% 142ms 1.83% alternateaxes 129ms 1.66% 62.84% 136ms 1.75% vertexmedian 6ms 0.077% 62.92% 128ms 1.65% std::operator<< (inline) 29ms 0.37% 63.30% 125ms 1.61% MeshBasedCellPopulation::SpringIterator::SpringIterator 89ms 1.15% 64.44% 125ms 1.61% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.039% 64.48% 120ms 1.55% boost::numeric::ublas::c_vector::c_vector (inline) 17ms 0.22% 64.70% 120ms 1.55% std::type_info::operator== (inline) 2ms 0.026% 64.73% 117ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.052% 64.78% 117ms 1.51% boost::numeric::ublas::vector_assign (inline) 117ms 1.51% 66.28% 117ms 1.51% incircle 6ms 0.077% 66.36% 116ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 112ms 1.44% 67.80% 112ms 1.44% std::_Rb_tree_insert_and_rebalance 7ms 0.09% 67.89% 110ms 1.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.026% 67.92% 110ms 1.42% AbstractTetrahedralElement::AbstractTetrahedralElement 28ms 0.36% 68.28% 108ms 1.39% std::num_put::_M_insert_int 16ms 0.21% 68.49% 104ms 1.34% AbstractTetrahedralElement::RefreshJacobian 1ms 0.013% 68.50% 94ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 68.51% 94ms 1.21% tcache_get (inline) 93ms 1.20% 69.71% 93ms 1.20% tcache_get_n (inline) 2ms 0.026% 69.74% 88ms 1.13% AbstractCellPopulation::GetLocationIndexUsingCell 86ms 1.11% 70.85% 86ms 1.11% [libstdc++.so.6.0.33] 0 0% 70.85% 84ms 1.08% Cell::GetCellId 0 0% 70.85% 84ms 1.08% std::basic_ofstream::basic_ofstream (inline) 84ms 1.08% 71.93% 84ms 1.08% std::vector::size (inline) 75ms 0.97% 72.89% 84ms 1.08% vertexsort 4ms 0.052% 72.95% 81ms 1.04% CellPropertyCollection::AddProperty 0 0% 72.95% 80ms 1.03% std::basic_filebuf::open 0 0% 72.95% 80ms 1.03% std::basic_ofstream::open (inline) 78ms 1.00% 73.95% 78ms 1.00% counterclockwise 11ms 0.14% 74.09% 75ms 0.97% boost::numeric::ublas::indexing_vector_assign 39ms 0.5% 74.59% 75ms 0.97% std::basic_filebuf::xsputn 32ms 0.41% 75.01% 74ms 0.95% AbstractElement::GetNodeLocation 1ms 0.013% 75.02% 74ms 0.95% Node::~Node 59ms 0.76% 75.78% 74ms 0.95% malloc_consolidate 0 0% 75.78% 70ms 0.9% OutputFileHandler::CommonConstructor 0 0% 75.78% 70ms 0.9% OutputFileHandler::OutputFileHandler 22ms 0.28% 76.06% 69ms 0.89% Determinant (inline) 0 0% 76.06% 69ms 0.89% OutputFileHandler::MakeFoldersAndReturnFullPath 26ms 0.33% 76.40% 68ms 0.88% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 76.41% 66ms 0.85% std::basic_filebuf::close 0 0% 76.41% 65ms 0.84% AbstractCellBasedWriter::CloseFile 0 0% 76.41% 65ms 0.84% AbstractCellPopulation::CloseRoundRobinWritersFiles 9ms 0.12% 76.53% 65ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.53% 65ms 0.84% std::basic_ofstream::close (inline) 64ms 0.82% 77.35% 64ms 0.82% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 4ms 0.052% 77.40% 62ms 0.8% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.40% 62ms 0.8% std::vector::vector (inline) 0 0% 77.40% 61ms 0.79% CellPropertyCollection::~CellPropertyCollection (inline) 33ms 0.43% 77.83% 61ms 0.79% boost::shared_ptr::shared_ptr (inline) 11ms 0.14% 77.97% 59ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 77.97% 59ms 0.76% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 32ms 0.41% 78.38% 58ms 0.75% AbstractTetrahedralMesh::GetElement 46ms 0.59% 78.97% 58ms 0.75% boost::numeric::ublas::c_matrix::operator() 0 0% 78.97% 58ms 0.75% std::_Vector_base::_Vector_base (inline) 9ms 0.12% 79.09% 56ms 0.72% Inverse 0 0% 79.09% 56ms 0.72% Node::ClearAppliedForce 0 0% 79.09% 56ms 0.72% Node::ConstructNodeAttributes (inline) 55ms 0.71% 79.80% 55ms 0.71% std::_Rb_tree::_S_left (inline) 4ms 0.052% 79.85% 55ms 0.71% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 79.85% 55ms 0.71% std::_Vector_base::_M_create_storage (inline) 40ms 0.52% 80.37% 55ms 0.71% std::basic_streambuf::xsputn 0 0% 80.37% 53ms 0.68% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.37% 53ms 0.68% _IO_new_fopen 0 0% 80.37% 53ms 0.68% __fopen_internal (inline) 53ms 0.68% 81.05% 53ms 0.68% std::_Rb_tree_increment 0 0% 81.05% 53ms 0.68% std::__basic_file::open 43ms 0.55% 81.60% 53ms 0.68% std::num_put::do_put 28ms 0.36% 81.96% 52ms 0.67% hack_digit 0 0% 81.96% 51ms 0.66% AbstractCentreBasedCellPopulation::CreateCellPair 51ms 0.66% 82.62% 51ms 0.66% __memcpy_avx512_unaligned_erms 0 0% 82.62% 50ms 0.64% _IO_new_file_fopen 0 0% 82.62% 50ms 0.64% __GI__IO_file_open 35ms 0.45% 83.07% 49ms 0.63% CellPropertyCollection::GetProperty 0 0% 83.07% 49ms 0.63% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 83.08% 48ms 0.62% BoundaryNodeWriter::Visit 47ms 0.61% 83.69% 48ms 0.62% __libc_open64 46ms 0.59% 84.28% 46ms 0.59% boost::numeric::ublas::same_impl_ex 0 0% 84.28% 43ms 0.55% FilesystemPermissions::SetFilePermissions (inline) 0 0% 84.28% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.28% 43ms 0.55% std::basic_filebuf::_M_terminate_output 1ms 0.013% 84.30% 43ms 0.55% std::basic_filebuf::overflow 0 0% 84.30% 43ms 0.55% std::filesystem::permissions 39ms 0.5% 84.80% 42ms 0.54% __GI___libc_write 42ms 0.54% 85.34% 42ms 0.54% __GI_fchmodat 0 0% 85.34% 42ms 0.54% std::__basic_file::xsputn 0 0% 85.34% 42ms 0.54% std::basic_filebuf::_M_convert_to_external 0 0% 85.34% 40ms 0.52% _dl_init 0 0% 85.34% 40ms 0.52% call_init (inline) 0 0% 85.34% 39ms 0.5% std::map::map (inline)