File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2122ms, 82.76% of 2564ms total Dropped 626 nodes (cum <= 12.82ms) flat flat% sum% cum cum% 0 0% 0% 2380ms 92.82% __libc_start_call_main 0 0% 0% 2380ms 92.82% __libc_start_main_impl 0 0% 0% 2380ms 92.82% _start 0 0% 0% 2364ms 92.20% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 2364ms 92.20% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 2364ms 92.20% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 2364ms 92.20% main 0 0% 0% 2325ms 90.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 2325ms 90.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 2325ms 90.68% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 2315ms 90.29% AbstractCellBasedSimulation::Solve 0 0% 0% 2015ms 78.59% AbstractCellPopulation::WriteResultsToFiles 22ms 0.86% 0.86% 1874ms 73.09% PottsBasedCellPopulation::WriteVtkResultsToFile 1ms 0.039% 0.9% 759ms 29.60% VertexMeshWriter::WriteFiles 0 0% 0.9% 583ms 22.74% std::ostream::operator<< (inline) 38ms 1.48% 2.38% 582ms 22.70% std::ostream::_M_insert 33ms 1.29% 3.67% 465ms 18.14% std::num_put::_M_insert_float 8ms 0.31% 3.98% 363ms 14.16% std::__cxx11::collate::do_transform 4ms 0.16% 4.13% 339ms 13.22% ___vsnprintf 0 0% 4.13% 335ms 13.07% __vsnprintf_internal (inline) 27ms 1.05% 5.19% 333ms 12.99% __printf_buffer 0 0% 5.19% 295ms 11.51% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.23% 5.42% 295ms 11.51% PottsBasedCellPopulation::UpdateCellLocations 68ms 2.65% 8.07% 273ms 10.65% __GI___libc_free 2ms 0.078% 8.15% 271ms 10.57% __printf_fp_spec (inline) 10ms 0.39% 8.54% 269ms 10.49% __printf_fp_l_buffer 132ms 5.15% 13.69% 243ms 9.48% __printf_fp_buffer_1 2ms 0.078% 13.77% 240ms 9.36% std::__new_allocator::deallocate (inline) 0 0% 13.77% 233ms 9.09% std::allocator_traits::deallocate (inline) 23ms 0.9% 14.66% 214ms 8.35% std::_Rb_tree::_Rb_tree 0 0% 14.66% 214ms 8.35% std::set::set (inline) 50ms 1.95% 16.61% 210ms 8.19% std::__new_allocator::allocate (inline) 0 0% 16.61% 210ms 8.19% std::allocator_traits::allocate (inline) 110ms 4.29% 20.90% 205ms 8.00% _int_free 16ms 0.62% 21.53% 192ms 7.49% operator new 0 0% 21.53% 185ms 7.22% std::_Rb_tree::_M_create_node (inline) 72ms 2.81% 24.34% 175ms 6.83% __GI___libc_malloc 0 0% 24.34% 175ms 6.83% std::_Rb_tree::_M_get_node (inline) 19ms 0.74% 25.08% 171ms 6.67% std::_Rb_tree::_M_copy (inline) 0 0% 25.08% 170ms 6.63% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.078% 25.16% 161ms 6.28% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 25.16% 156ms 6.08% VertexMesh::~VertexMesh 0 0% 25.16% 154ms 6.01% std::vector::~vector (inline) 33ms 1.29% 26.44% 150ms 5.85% std::_Rb_tree::_M_erase 0 0% 26.44% 148ms 5.77% clone3 0 0% 26.44% 148ms 5.77% start_thread 7ms 0.27% 26.72% 148ms 5.77% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.039% 26.76% 148ms 5.77% tbb::detail::r1::parallel_pipeline 0 0% 26.76% 146ms 5.69% tbb::detail::r1::reset 13ms 0.51% 27.26% 145ms 5.66% std::_Rb_tree::_M_clone_node (inline) 0 0% 27.26% 143ms 5.58% VertexMesh::VertexMesh 4ms 0.16% 27.42% 139ms 5.42% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 27.42% 133ms 5.19% VertexMesh::GenerateEdgesFromElements (inline) 60ms 2.34% 29.76% 133ms 5.19% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.12% 29.88% 131ms 5.11% MutableElement::BuildEdges 2ms 0.078% 29.95% 127ms 4.95% std::_Vector_base::_M_deallocate (inline) 0 0% 29.95% 121ms 4.72% std::set::~set (inline) 0 0% 29.95% 119ms 4.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 29.95% 119ms 4.64% vtkXMLWriterBase::Write 52ms 2.03% 31.98% 118ms 4.60% std::__ostream_insert 3ms 0.12% 32.10% 117ms 4.56% std::operator<< (inline) 0 0% 32.10% 117ms 4.56% vtkDemandDrivenPipeline::ProcessRequest 0 0% 32.10% 115ms 4.49% vtkStreamingDemandDrivenPipeline::ProcessRequest 3ms 0.12% 32.22% 114ms 4.45% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.12% 32.33% 114ms 4.45% EdgeHelper::GetEdgeFromNodes 0 0% 32.33% 114ms 4.45% std::_Rb_tree::_M_drop_node (inline) 0 0% 32.33% 113ms 4.41% std::_Vector_base::~_Vector_base (inline) 0 0% 32.33% 111ms 4.33% vtkCompositeDataPipeline::ExecuteData 0 0% 32.33% 111ms 4.33% vtkExecutive::CallAlgorithm 0 0% 32.33% 110ms 4.29% vtkDemandDrivenPipeline::ExecuteData 0 0% 32.33% 110ms 4.29% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 32.33% 109ms 4.25% EdgeHelper::~EdgeHelper (inline) 0 0% 32.33% 107ms 4.17% std::_Rb_tree::_M_put_node (inline) 1ms 0.039% 32.37% 106ms 4.13% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 32.37% 103ms 4.02% VtkMeshWriter::WriteFiles 0 0% 32.37% 95ms 3.71% AbstractCellProperty::IsSubType (inline) 0 0% 32.37% 95ms 3.71% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 32.37% 94ms 3.67% VertexMeshWriter::WriteVtkUsingMesh 23ms 0.9% 33.27% 94ms 3.67% __dynamic_cast 0 0% 33.27% 83ms 3.24% Cell::HasCellProperty (inline) 4ms 0.16% 33.42% 83ms 3.24% CellPropertyCollection::HasProperty 3ms 0.12% 33.54% 83ms 3.24% std::vector::push_back (inline) 38ms 1.48% 35.02% 82ms 3.20% std::basic_filebuf::xsputn 71ms 2.77% 37.79% 81ms 3.16% _int_malloc 3ms 0.12% 37.91% 79ms 3.08% _int_free_maybe_consolidate 37ms 1.44% 39.35% 79ms 3.08% malloc_consolidate 5ms 0.2% 39.55% 78ms 3.04% std::map::operator[] (partial-inline) 3ms 0.12% 39.66% 76ms 2.96% AbstractCellProperty::IsType (inline) 76ms 2.96% 42.63% 76ms 2.96% __strcmp_avx2 1ms 0.039% 42.67% 75ms 2.93% NodeLocationWriter::VisitAnyPopulation 0 0% 42.67% 72ms 2.81% AbstractCellBasedWriter::WriteDoubleAndSpace (inline) 72ms 2.81% 45.48% 72ms 2.81% __GI_sched_yield 7ms 0.27% 45.75% 71ms 2.77% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 45.75% 71ms 2.77% PottsMesh::GetMooreNeighbouringNodeIndices 32ms 1.25% 47.00% 69ms 2.69% hack_digit 21ms 0.82% 47.82% 69ms 2.69% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.039% 47.85% 67ms 2.61% Cell::GetCellProliferativeType 9ms 0.35% 48.21% 65ms 2.54% boost::numeric::ublas::c_vector::c_vector (partial-inline) 40ms 1.56% 49.77% 61ms 2.38% std::basic_streambuf::xsputn 0 0% 49.77% 60ms 2.34% NodesOnlyMesh::SetUpBoxCollection 0 0% 49.77% 59ms 2.30% NodesOnlyMesh::~NodesOnlyMesh 0 0% 49.77% 59ms 2.30% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 49.77% 59ms 2.30% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.039% 49.80% 58ms 2.26% AbstractCellBasedWriter::WriteDouble (inline) 7ms 0.27% 50.08% 58ms 2.26% std::vector::_M_realloc_insert 14ms 0.55% 50.62% 57ms 2.22% AbstractCellProperty::IsSame 0 0% 50.62% 56ms 2.18% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 12ms 0.47% 51.09% 55ms 2.15% std::num_put::_M_insert_int 1ms 0.039% 51.13% 54ms 2.11% boost::numeric::ublas::vector_assign (inline) 28ms 1.09% 52.22% 53ms 2.07% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.039% 52.26% 53ms 2.07% std::_Rb_tree::_M_insert_unique 0 0% 52.26% 53ms 2.07% std::set::insert (inline) 0 0% 52.26% 51ms 1.99% std::_Destroy (inline) 0 0% 52.26% 51ms 1.99% std::_Destroy_aux::__destroy (inline) 0 0% 52.26% 51ms 1.99% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 48ms 1.87% 54.13% 48ms 1.87% std::from_chars 3ms 0.12% 54.25% 47ms 1.83% VertexMesh::Clear 47ms 1.83% 56.08% 47ms 1.83% unlink_chunk 6ms 0.23% 56.32% 46ms 1.79% VertexMeshWriter::GetNextNode 5ms 0.2% 56.51% 45ms 1.76% std::_Rb_tree::_M_insert_ (inline) 16ms 0.62% 57.14% 43ms 1.68% std::type_info::operator== (inline) 27ms 1.05% 58.19% 42ms 1.64% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 58.19% 42ms 1.64% DistributedBoxCollection::IsOwned 0 0% 58.19% 42ms 1.64% DistributedBoxCollection::~DistributedBoxCollection 0 0% 58.19% 42ms 1.64% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 58.19% 41ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 58.19% 41ms 1.60% std::map::lower_bound (inline) 39ms 1.52% 59.71% 39ms 1.52% __memcpy_avx_unaligned_erms 1ms 0.039% 59.75% 39ms 1.52% std::less::operator() (inline) 0 0% 59.75% 38ms 1.48% DistributedBoxCollection::SetupLocalBoxesHalfOnly 38ms 1.48% 61.23% 38ms 1.48% std::operator< (inline) 0 0% 61.23% 37ms 1.44% VertexMeshWriter::MakeVtkMesh 0 0% 61.23% 37ms 1.44% _dl_init 12ms 0.47% 61.70% 37ms 1.44% boost::numeric::ublas::indexing_vector_assign 0 0% 61.70% 37ms 1.44% call_init (inline) 2ms 0.078% 61.78% 37ms 1.44% std::_Vector_base::_M_allocate (inline) 0 0% 61.78% 36ms 1.40% _dl_start_user 1ms 0.039% 61.82% 35ms 1.37% 0 0% 61.82% 35ms 1.37% CxxTest::RealWorldDescription::setUp 0 0% 61.82% 35ms 1.37% PMPI_Init_thread 0 0% 61.82% 35ms 1.37% PetscInitialize 0 0% 61.82% 35ms 1.37% PetscSetup::setUpWorld 0 0% 61.82% 35ms 1.37% PetscSetupUtils::CommonSetup 0 0% 61.82% 35ms 1.37% PetscSetupUtils::InitialisePetsc 0 0% 61.82% 35ms 1.37% ompi_mpi_init 0 0% 61.82% 32ms 1.25% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.039% 61.86% 32ms 1.25% std::unique_ptr::~unique_ptr (inline) 0 0% 61.86% 31ms 1.21% std::default_delete::operator() (inline) 23ms 0.9% 62.75% 31ms 1.21% std::num_put::do_put 3ms 0.12% 62.87% 30ms 1.17% Node::ConstructNodeAttributes (inline) 0 0% 62.87% 30ms 1.17% Node::SetRadius 0 0% 62.87% 30ms 1.17% VtkMeshWriter::MakeVtkMesh 0 0% 62.87% 30ms 1.17% std::make_unique (inline) 2ms 0.078% 62.95% 30ms 1.17% std::ostream::write 3ms 0.12% 63.07% 30ms 1.17% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 63.07% 29ms 1.13% PottsMesh::GetVonNeumannNeighbouringNodeIndices 10ms 0.39% 63.46% 29ms 1.13% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 63.46% 29ms 1.13% vtkXMLWriter::WritePointsAppendedData 1ms 0.039% 63.49% 28ms 1.09% Cell::GetCellId 0 0% 63.49% 28ms 1.09% Cell::GetMutationState 2ms 0.078% 63.57% 28ms 1.09% Node::GetPoint 4ms 0.16% 63.73% 28ms 1.09% __find_specmb (inline) 0 0% 63.73% 28ms 1.09% std::_Rb_tree::find (inline) 7ms 0.27% 64.00% 28ms 1.09% std::__new_allocator::construct (inline) 0 0% 64.00% 28ms 1.09% std::allocator_traits::construct (inline) 0 0% 64.00% 28ms 1.09% std::basic_filebuf::open 0 0% 64.00% 28ms 1.09% std::map::find (inline) 0 0% 64.00% 27ms 1.05% CellIdWriter::GetCellDataForVtkOutput 0 0% 64.00% 27ms 1.05% std::map::~map (inline) 3ms 0.12% 64.12% 27ms 1.05% vtkAOSDataArrayTemplate::InsertTuple 1ms 0.039% 64.16% 27ms 1.05% vtkXMLWriter::WriteBinaryData 1ms 0.039% 64.20% 26ms 1.01% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.039% 64.24% 25ms 0.98% _IO_new_fopen 25ms 0.98% 65.21% 25ms 0.98% __GI___writev 3ms 0.12% 65.33% 25ms 0.98% boost::serialization::singleton::get_instance 0 0% 65.33% 25ms 0.98% std::__basic_file::open 0 0% 65.33% 25ms 0.98% vtkDataArray::ComputeRange 17ms 0.66% 65.99% 24ms 0.94% AbstractMesh::GetNode 0 0% 65.99% 24ms 0.94% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 65.99% 24ms 0.94% Edge::Edge 0 0% 65.99% 24ms 0.94% _IO_new_file_fopen 0 0% 65.99% 24ms 0.94% __GI__IO_file_open 0 0% 65.99% 24ms 0.94% __fopen_internal (inline) 24ms 0.94% 66.93% 24ms 0.94% __libc_open64 24ms 0.94% 67.86% 24ms 0.94% __mpn_mul_1 24ms 0.94% 68.80% 24ms 0.94% __strchrnul_avx2 0 0% 68.80% 24ms 0.94% orte_init 0 0% 68.80% 24ms 0.94% std::__basic_file::xsputn_2 0 0% 68.80% 23ms 0.9% Edge::SetNodes (inline) 0 0% 68.80% 22ms 0.86% OutputFileHandler::OpenOutputFile 21ms 0.82% 69.62% 22ms 0.86% __GI___libc_write 22ms 0.86% 70.48% 22ms 0.86% std::_Rb_tree_increment 0 0% 70.48% 22ms 0.86% std::__basic_file::xsputn 0 0% 70.48% 22ms 0.86% std::basic_filebuf::_M_convert_to_external 0 0% 70.48% 22ms 0.86% std::basic_filebuf::overflow 3ms 0.12% 70.59% 22ms 0.86% std::vector::emplace_back (inline) 0 0% 70.59% 22ms 0.86% tcache_get (inline) 22ms 0.86% 71.45% 22ms 0.86% tcache_get_n (inline) 0 0% 71.45% 22ms 0.86% vtkOutputStream::WriteStream 0 0% 71.45% 22ms 0.86% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 71.45% 22ms 0.86% vtkXMLWriter::WriteBinaryDataBlock 0 0% 71.45% 22ms 0.86% vtkXMLWriter::WritePointDataAppendedData 0 0% 71.45% 21ms 0.82% boost::numeric::ublas::c_vector::assign (inline) 0 0% 71.45% 21ms 0.82% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 6ms 0.23% 71.68% 21ms 0.82% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.82% 72.50% 21ms 0.82% std::ostream::sentry::sentry 0 0% 72.50% 21ms 0.82% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 72.50% 20ms 0.78% Edge::~Edge (inline) 1ms 0.039% 72.54% 20ms 0.78% MutableElement::MutableElement 20ms 0.78% 73.32% 20ms 0.78% [libchaste_cell_based.so] 20ms 0.78% 74.10% 20ms 0.78% boost::numeric::ublas::c_vector::operator() 0 0% 74.10% 20ms 0.78% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 20ms 0.78% 74.88% 20ms 0.78% std::_Rb_tree_header::_M_reset (inline) 0 0% 74.88% 20ms 0.78% std::_Rb_tree_header::_Rb_tree_header (inline) 20ms 0.78% 75.66% 20ms 0.78% std::codecvt::do_always_noconv 3ms 0.12% 75.78% 20ms 0.78% tbb::detail::r1::cancel_group_execution 3ms 0.12% 75.90% 19ms 0.74% NodeAttributes::NodeAttributes 0 0% 75.90% 19ms 0.74% VertexElement::VertexElement 19ms 0.74% 76.64% 19ms 0.74% __strlen_avx2 0 0% 76.64% 19ms 0.74% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 76.64% 19ms 0.74% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 3ms 0.12% 76.76% 18ms 0.7% AbstractTetrahedralMeshWriter::GetNextNode 1ms 0.039% 76.79% 18ms 0.7% Node::AddElement 3ms 0.12% 76.91% 18ms 0.7% __cxa_finalize 0 0% 76.91% 18ms 0.7% _dl_call_fini 18ms 0.7% 77.61% 18ms 0.7% boost::numeric::ublas::same_impl_ex 0 0% 77.61% 18ms 0.7% std::basic_filebuf::close 0 0% 77.61% 18ms 0.7% std::basic_ofstream::close (inline) 0 0% 77.61% 18ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPiece 0 0% 77.61% 17ms 0.66% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.61% 17ms 0.66% NodesOnlyMesh::Clear (inline) 17ms 0.66% 78.28% 17ms 0.66% [libchaste_mesh.so] 0 0% 78.28% 17ms 0.66% __GI__dl_catch_exception 0 0% 78.28% 17ms 0.66% _dl_catch_error 0 0% 78.28% 17ms 0.66% _dlerror_run 0 0% 78.28% 16ms 0.62% BoundaryNodeWriter::VisitAnyPopulation 16ms 0.62% 78.90% 16ms 0.62% __GI___uselocale 0 0% 78.90% 16ms 0.62% __GI_exit 16ms 0.62% 79.52% 16ms 0.62% __printf_buffer_write 0 0% 79.52% 16ms 0.62% __run_exit_handlers 0 0% 79.52% 16ms 0.62% _dl_fini 16ms 0.62% 80.15% 16ms 0.62% std::_Rb_tree_insert_and_rebalance 0 0% 80.15% 16ms 0.62% std::basic_ofstream::basic_ofstream (inline) 0 0% 80.15% 16ms 0.62% std::basic_ofstream::open (inline) 0 0% 80.15% 15ms 0.59% PottsBasedCellPopulation::AcceptCellWriter 1ms 0.039% 80.19% 15ms 0.59% VertexElement::~VertexElement 0 0% 80.19% 15ms 0.59% _GLOBAL__sub_I_VoronoiDataWriter.cpp 4ms 0.16% 80.34% 15ms 0.59% boost::detail::shared_count::~shared_count (inline) 3ms 0.12% 80.46% 15ms 0.59% boost::serialization::detail::singleton_wrapper::~singleton_wrapper 0 0% 80.46% 15ms 0.59% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.46% 15ms 0.59% opal_stackframe_output 0 0% 80.46% 15ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 80.46% 15ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 1ms 0.039% 80.50% 15ms 0.59% std::_Rb_tree::_M_insert_node (inline) 0 0% 80.50% 15ms 0.59% std::vector::vector (inline) 3ms 0.12% 80.62% 14ms 0.55% CellPropertyCollection::AddProperty 1ms 0.039% 80.66% 14ms 0.55% Edge::AddElement 0 0% 80.66% 14ms 0.55% MutableElement::RegisterWithNodes (inline) 6ms 0.23% 80.89% 14ms 0.55% boost::serialization::typeid_system::extended_type_info_typeid_0::is_equal 0 0% 80.89% 14ms 0.55% hwloc_topology_load 0 0% 80.89% 13ms 0.51% CellPopulationElementWriter::Visit 13ms 0.51% 81.40% 13ms 0.51% Node::GetIndex 1ms 0.039% 81.44% 13ms 0.51% OutputFileHandler::OutputFileHandler 0 0% 81.44% 13ms 0.51% VertexMeshWriter::GetNextElement 13ms 0.51% 81.94% 13ms 0.51% __mpn_divrem 0 0% 81.94% 13ms 0.51% mca_base_framework_open 13ms 0.51% 82.45% 13ms 0.51% operator delete 8ms 0.31% 82.76% 13ms 0.51% std::locale::facet::_S_get_c_locale 0 0% 82.76% 13ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 82.76% 13ms 0.51% vtkXMLWriter::WriteArrayAppended