File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4584ms, 84.78% of 5407ms total Dropped 507 nodes (cum <= 27.04ms) flat flat% sum% cum cum% 0 0% 0% 5378ms 99.46% __libc_start_call_main 0 0% 0% 5378ms 99.46% __libc_start_main_impl 0 0% 0% 5378ms 99.46% _start 0 0% 0% 5362ms 99.17% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5362ms 99.17% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5362ms 99.17% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5362ms 99.17% main 0 0% 0% 5327ms 98.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5327ms 98.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5327ms 98.52% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 5325ms 98.48% AbstractCellBasedSimulation::Solve 0 0% 0% 2549ms 47.14% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2247ms 41.56% MeshBasedCellPopulation::Update 0 0% 0% 1751ms 32.38% AbstractCellPopulation::WriteResultsToFiles 1ms 0.018% 0.018% 1153ms 21.32% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.018% 1049ms 19.40% MutableMesh::ReMesh 2ms 0.037% 0.055% 1017ms 18.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.037% 0.092% 1012ms 18.72% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.018% 0.11% 901ms 16.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.11% 864ms 15.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 82ms 1.52% 1.63% 837ms 15.48% TetrahedralMesh::EdgeIterator::operator++ 343ms 6.34% 7.97% 698ms 12.91% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.15% 8.12% 668ms 12.35% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.055% 8.17% 646ms 11.95% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.055% 8.23% 596ms 11.02% CellPopulationElementWriter::Visit 28ms 0.52% 8.75% 581ms 10.75% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 20ms 0.37% 9.12% 572ms 10.58% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.11% 9.23% 542ms 10.02% MeshBasedCellPopulation::AcceptCellWriter 110ms 2.03% 11.26% 528ms 9.77% __dynamic_cast 4ms 0.074% 11.34% 527ms 9.75% TetrahedralMesh::ImportFromMesher 6ms 0.11% 11.45% 517ms 9.56% CellPropertyCollection::GetPropertiesType (inline) 36ms 0.67% 12.11% 497ms 9.19% operator new 9ms 0.17% 12.28% 464ms 8.58% std::set::insert (inline) 8ms 0.15% 12.43% 455ms 8.42% std::_Rb_tree::_M_insert_unique 160ms 2.96% 15.39% 453ms 8.38% __GI___libc_malloc 11ms 0.2% 15.59% 433ms 8.01% std::_Rb_tree::find (inline) 13ms 0.24% 15.83% 429ms 7.93% std::__new_allocator::allocate (inline) 0 0% 15.83% 422ms 7.80% std::allocator_traits::allocate (inline) 2ms 0.037% 15.87% 419ms 7.75% AbstractCellProperty::IsSubType (inline) 0 0% 15.87% 402ms 7.43% std::set::count (inline) 2ms 0.037% 15.91% 394ms 7.29% triangulate 45ms 0.83% 16.74% 393ms 7.27% std::map::operator[] (partial-inline) 1ms 0.018% 16.76% 386ms 7.14% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.018% 16.77% 383ms 7.08% std::ostream::operator<< (inline) 47ms 0.87% 17.64% 381ms 7.05% std::ostream::_M_insert 51ms 0.94% 18.59% 359ms 6.64% std::_Rb_tree::~_Rb_tree (inline) 0 0% 18.59% 352ms 6.51% std::_Rb_tree::_M_create_node (inline) 0 0% 18.59% 349ms 6.45% delaunay 1ms 0.018% 18.61% 349ms 6.45% divconqdelaunay 0 0% 18.61% 346ms 6.40% std::set::~set (inline) 343ms 6.34% 24.95% 343ms 6.34% __strcmp_evex 0 0% 24.95% 337ms 6.23% std::_Rb_tree::_M_get_node (inline) 0 0% 24.95% 327ms 6.05% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.018% 24.97% 325ms 6.01% Cell::GetCellProliferativeType 38ms 0.7% 25.67% 308ms 5.70% std::_Rb_tree::_M_erase 0 0% 25.67% 298ms 5.51% std::_Rb_tree::lower_bound (inline) 0 0% 25.67% 298ms 5.51% std::map::lower_bound (inline) 28ms 0.52% 26.19% 297ms 5.49% std::_Rb_tree::_M_insert_ (inline) 0 0% 26.19% 296ms 5.47% AbstractCellBasedSimulation::DoCellBirth 136ms 2.52% 28.70% 275ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 12ms 0.22% 28.93% 273ms 5.05% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.93% 264ms 4.88% std::_Rb_tree::_M_drop_node (inline) 0 0% 28.93% 254ms 4.70% std::set::set (inline) 3ms 0.055% 28.98% 253ms 4.68% boost::detail::shared_count::~shared_count (inline) 0 0% 28.98% 253ms 4.68% boost::shared_ptr::~shared_ptr (inline) 4ms 0.074% 29.05% 248ms 4.59% Element::Element 27ms 0.5% 29.55% 244ms 4.51% std::_Rb_tree::_M_copy (inline) 0 0% 29.55% 238ms 4.40% NodeLocationWriter::Visit 237ms 4.38% 33.94% 238ms 4.40% boost::detail::sp_counted_base::release 155ms 2.87% 36.80% 232ms 4.29% _int_malloc 54ms 1% 37.80% 231ms 4.27% __GI___libc_free 13ms 0.24% 38.04% 223ms 4.12% std::less::operator() (inline) 1ms 0.018% 38.06% 213ms 3.94% Cell::GetMutationState 16ms 0.3% 38.36% 212ms 3.92% std::num_put::_M_insert_float 210ms 3.88% 42.24% 210ms 3.88% std::operator< (inline) 3ms 0.055% 42.30% 206ms 3.81% AbstractCellPopulation::IsCellAttachedToLocationIndex 81ms 1.50% 43.80% 205ms 3.79% std::_Rb_tree::_M_clone_node (inline) 202ms 3.74% 47.53% 202ms 3.74% std::_Rb_tree::_S_right (inline) 7ms 0.13% 47.66% 197ms 3.64% divconqrecurse 3ms 0.055% 47.72% 194ms 3.59% std::__new_allocator::deallocate (inline) 0 0% 47.72% 191ms 3.53% std::allocator_traits::deallocate (inline) 5ms 0.092% 47.81% 190ms 3.51% Cell::ReadyToDivide 53ms 0.98% 48.79% 185ms 3.42% mergehulls 6ms 0.11% 48.90% 184ms 3.40% Element::RegisterWithNodes (inline) 183ms 3.38% 52.28% 183ms 3.38% [libchaste_cell_based.so] 5ms 0.092% 52.38% 178ms 3.29% AbstractCellProperty::IsType (inline) 0 0% 52.38% 177ms 3.27% Cell::HasCellProperty (inline) 2ms 0.037% 52.41% 177ms 3.27% CellPropertyCollection::HasProperty 9ms 0.17% 52.58% 176ms 3.26% Node::AddElement 148ms 2.74% 55.32% 176ms 3.26% _int_free 4ms 0.074% 55.39% 175ms 3.24% std::__cxx11::collate::do_transform 2ms 0.037% 55.43% 164ms 3.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 55.43% 164ms 3.03% MeshBasedCellPopulation::GetDampingConstant 3ms 0.055% 55.48% 163ms 3.01% ___vsnprintf 17ms 0.31% 55.80% 160ms 2.96% __printf_buffer 0 0% 55.80% 160ms 2.96% __vsnprintf_internal (inline) 4ms 0.074% 55.87% 157ms 2.90% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 55.87% 157ms 2.90% std::_Rb_tree::_M_put_node (inline) 53ms 0.98% 56.85% 150ms 2.77% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.037% 56.89% 135ms 2.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.11% 57.00% 132ms 2.44% __printf_fp_l_buffer 0 0% 57.00% 132ms 2.44% __printf_fp_spec (inline) 3ms 0.055% 57.06% 130ms 2.40% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 18ms 0.33% 57.39% 123ms 2.27% AbstractCellProperty::IsSame 0 0% 57.39% 123ms 2.27% CellProliferativeTypesWriter::VisitCell 64ms 1.18% 58.57% 122ms 2.26% __printf_fp_buffer_1 8ms 0.15% 58.72% 118ms 2.18% AbstractTetrahedralElement::CalculateJacobian 12ms 0.22% 58.94% 117ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.2% 59.15% 116ms 2.15% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.018% 59.16% 111ms 2.05% TetrahedralMesh::Clear 1ms 0.018% 59.18% 111ms 2.05% TetrahedralMesh::RefreshJacobianCachedData 0 0% 59.18% 107ms 1.98% std::_Rb_tree::_M_destroy_node (inline) 0 0% 59.18% 107ms 1.98% std::__new_allocator::destroy (inline) 0 0% 59.18% 107ms 1.98% std::allocator_traits::destroy (inline) 10ms 0.18% 59.37% 105ms 1.94% std::type_info::operator== (inline) 0 0% 59.37% 104ms 1.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 59.37% 103ms 1.90% AbstractCellBasedWriter::OpenOutputFileForAppend 4ms 0.074% 59.44% 103ms 1.90% AbstractTetrahedralElement::CalculateInverseJacobian 89ms 1.65% 61.09% 101ms 1.87% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 61.09% 98ms 1.81% OutputFileHandler::OpenOutputFile 1ms 0.018% 61.11% 93ms 1.72% alternateaxes 27ms 0.5% 61.61% 93ms 1.72% std::num_put::_M_insert_int 82ms 1.52% 63.12% 91ms 1.68% vertexmedian 89ms 1.65% 64.77% 89ms 1.65% [libchaste_mesh.so] 4ms 0.074% 64.84% 89ms 1.65% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.018% 64.86% 86ms 1.59% std::_Vector_base::_M_allocate (inline) 12ms 0.22% 65.08% 85ms 1.57% AbstractTetrahedralElement::RefreshJacobian 5ms 0.092% 65.17% 83ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.17% 83ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.037% 65.21% 83ms 1.54% boost::numeric::ublas::vector_assign (inline) 6ms 0.11% 65.32% 83ms 1.54% std::vector::push_back (inline) 80ms 1.48% 66.80% 80ms 1.48% std::_Rb_tree_insert_and_rebalance 78ms 1.44% 68.24% 78ms 1.44% incircle 32ms 0.59% 68.84% 76ms 1.41% std::__ostream_insert 3ms 0.055% 68.89% 76ms 1.41% std::vector::_M_realloc_insert 2ms 0.037% 68.93% 71ms 1.31% Node::~Node 7ms 0.13% 69.06% 69ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 69.06% 67ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.54% 69.59% 66ms 1.22% AbstractElement::GetNodeLocation 65ms 1.20% 70.80% 65ms 1.20% [libstdc++.so.6.0.33] 47ms 0.87% 71.67% 64ms 1.18% malloc_consolidate 1ms 0.018% 71.68% 63ms 1.17% std::operator<< (inline) 1ms 0.018% 71.70% 62ms 1.15% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 71.70% 56ms 1.04% std::basic_ofstream::basic_ofstream (inline) 2ms 0.037% 71.74% 55ms 1.02% std::basic_filebuf::open 0 0% 71.74% 55ms 1.02% std::basic_ofstream::open (inline) 50ms 0.92% 72.67% 55ms 1.02% vertexsort 0 0% 72.67% 54ms 1% Cell::GetCellId 1ms 0.018% 72.68% 54ms 1% OutputFileHandler::CommonConstructor 0 0% 72.68% 54ms 1% OutputFileHandler::OutputFileHandler 54ms 1% 73.68% 54ms 1% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 73.68% 54ms 1% tcache_get (inline) 54ms 1% 74.68% 54ms 1% tcache_get_n (inline) 1ms 0.018% 74.70% 52ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.037% 74.74% 52ms 0.96% CellPropertyCollection::AddProperty 35ms 0.65% 75.38% 52ms 0.96% std::basic_streambuf::xsputn 52ms 0.96% 76.35% 52ms 0.96% std::vector::size (inline) 5ms 0.092% 76.44% 50ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeB 6ms 0.11% 76.55% 50ms 0.92% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 76.55% 49ms 0.91% OutputFileHandler::MakeFoldersAndReturnFullPath 15ms 0.28% 76.83% 49ms 0.91% boost::numeric::ublas::indexing_vector_assign 0 0% 76.83% 49ms 0.91% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.018% 76.84% 48ms 0.89% Node::ClearAppliedForce 1ms 0.018% 76.86% 48ms 0.89% Node::ConstructNodeAttributes (inline) 47ms 0.87% 77.73% 47ms 0.87% counterclockwise 0 0% 77.73% 46ms 0.85% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.018% 77.75% 46ms 0.85% std::basic_filebuf::close 0 0% 77.75% 45ms 0.83% AbstractCellBasedWriter::CloseFile 0 0% 77.75% 45ms 0.83% std::basic_ofstream::close (inline) 37ms 0.68% 78.44% 43ms 0.8% std::num_put::do_put 21ms 0.39% 78.82% 41ms 0.76% hack_digit 41ms 0.76% 79.58% 41ms 0.76% std::_Rb_tree::_S_left (inline) 0 0% 79.58% 41ms 0.76% std::vector::vector (inline) 18ms 0.33% 79.91% 40ms 0.74% Determinant (inline) 21ms 0.39% 80.30% 39ms 0.72% AbstractTetrahedralMesh::GetElement 39ms 0.72% 81.02% 39ms 0.72% __memcpy_avx512_unaligned_erms 0 0% 81.02% 39ms 0.72% std::_Vector_base::_Vector_base (inline) 0 0% 81.02% 38ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.018% 81.04% 38ms 0.7% std::_Vector_base::_M_create_storage (inline) 16ms 0.3% 81.34% 37ms 0.68% AbstractElement::GetNodeGlobalIndex 3ms 0.055% 81.39% 35ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 81.39% 35ms 0.65% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 81.39% 34ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 81.39% 33ms 0.61% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 81.39% 33ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.39% 33ms 0.61% NodeAttributes::NodeAttributes 33ms 0.61% 82.00% 33ms 0.61% std::_Rb_tree_increment 0 0% 82.00% 32ms 0.59% CxxTest::RealWorldDescription::setUp 0 0% 82.00% 32ms 0.59% PetscInitialize 0 0% 82.00% 32ms 0.59% PetscSetup::setUpWorld 0 0% 82.00% 32ms 0.59% PetscSetupUtils::CommonSetup 0 0% 82.00% 32ms 0.59% PetscSetupUtils::InitialisePetsc 22ms 0.41% 82.41% 32ms 0.59% boost::shared_ptr::shared_ptr (inline) 11ms 0.2% 82.62% 32ms 0.59% std::basic_filebuf::xsputn 0 0% 82.62% 31ms 0.57% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 82.62% 31ms 0.57% BoundaryNodeWriter::Visit 31ms 0.57% 83.19% 31ms 0.57% Node::GetIndex 0 0% 83.19% 31ms 0.57% PMPI_Init_thread 0 0% 83.19% 31ms 0.57% _IO_new_fopen 0 0% 83.19% 31ms 0.57% __fopen_internal (inline) 0 0% 83.19% 31ms 0.57% ompi_mpi_init 1ms 0.018% 83.21% 31ms 0.57% std::basic_filebuf::_M_convert_to_external 0 0% 83.21% 31ms 0.57% std::basic_filebuf::_M_terminate_output 0 0% 83.21% 31ms 0.57% std::basic_filebuf::overflow 2ms 0.037% 83.24% 30ms 0.55% 24ms 0.44% 83.69% 30ms 0.55% CellPropertyCollection::GetProperty 29ms 0.54% 84.22% 30ms 0.55% __GI___libc_write 30ms 0.55% 84.78% 30ms 0.55% boost::numeric::ublas::same_impl_ex 0 0% 84.78% 30ms 0.55% std::__basic_file::open 0 0% 84.78% 30ms 0.55% std::__basic_file::xsputn 0 0% 84.78% 29ms 0.54% _IO_new_file_fopen 0 0% 84.78% 29ms 0.54% __GI__IO_file_open 0 0% 84.78% 28ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.78% 28ms 0.52% std::map::map (inline)