File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4248ms, 82.23% of 5166ms total Dropped 758 nodes (cum <= 25.83ms) flat flat% sum% cum cum% 0 0% 0% 5020ms 97.17% __libc_start_call_main 0 0% 0% 5020ms 97.17% __libc_start_main_impl 0 0% 0% 5020ms 97.17% _start 0 0% 0% 5005ms 96.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5005ms 96.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5005ms 96.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5005ms 96.88% main 0 0% 0% 4971ms 96.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4971ms 96.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4971ms 96.23% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4961ms 96.03% AbstractCellBasedSimulation::Solve 0 0% 0% 4585ms 88.75% AbstractCellPopulation::WriteResultsToFiles 12ms 0.23% 0.23% 4357ms 84.34% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.23% 2255ms 43.65% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.097% 0.33% 2014ms 38.99% VertexMeshWriter::MakeVtkMesh 3ms 0.058% 0.39% 1462ms 28.30% vtkPolygon::New 8ms 0.15% 0.54% 1456ms 28.18% vtkPolygon::vtkPolygon 4ms 0.077% 0.62% 1068ms 20.67% vtkCell::vtkCell 1ms 0.019% 0.64% 869ms 16.82% vtkPoints::New 7ms 0.14% 0.77% 835ms 16.16% vtkPoints::vtkPoints 3ms 0.058% 0.83% 751ms 14.54% VertexMeshWriter::WriteFiles 34ms 0.66% 1.49% 736ms 14.25% operator new 3ms 0.058% 1.55% 707ms 13.69% std::ostream::operator<< (inline) 58ms 1.12% 2.67% 700ms 13.55% std::ostream::_M_insert 1ms 0.019% 2.69% 692ms 13.40% vtkQuad::New 294ms 5.69% 8.38% 691ms 13.38% __GI___libc_malloc 8ms 0.15% 8.54% 688ms 13.32% vtkQuad::vtkQuad 4ms 0.077% 8.61% 654ms 12.66% vtkLine::New 3ms 0.058% 8.67% 637ms 12.33% vtkLine::vtkLine 1ms 0.019% 8.69% 628ms 12.16% vtkTriangle::New 131ms 2.54% 11.23% 621ms 12.02% __GI___libc_free 7ms 0.14% 11.36% 617ms 11.94% vtkTriangle::vtkTriangle 42ms 0.81% 12.18% 580ms 11.23% std::num_put::_M_insert_float 28ms 0.54% 12.72% 523ms 10.12% vtkPoints::SetDataType 1ms 0.019% 12.74% 494ms 9.56% vtkPolygon::~vtkPolygon 1ms 0.019% 12.76% 494ms 9.56% vtkStreamingDemandDrivenPipeline::Update 0 0% 12.76% 494ms 9.56% vtkXMLWriterBase::Write 0 0% 12.76% 485ms 9.39% vtkDemandDrivenPipeline::ProcessRequest 0 0% 12.76% 485ms 9.39% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.76% 483ms 9.35% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.76% 482ms 9.33% vtkCompositeDataPipeline::ExecuteData 0 0% 12.76% 482ms 9.33% vtkExecutive::CallAlgorithm 0 0% 12.76% 482ms 9.33% vtkXMLUnstructuredDataWriter::ProcessRequest 332ms 6.43% 19.18% 479ms 9.27% _int_free 10ms 0.19% 19.38% 475ms 9.19% std::__cxx11::collate::do_transform 8ms 0.15% 19.53% 447ms 8.65% ___vsnprintf 0 0% 19.53% 440ms 8.52% __vsnprintf_internal (inline) 49ms 0.95% 20.48% 436ms 8.44% __printf_buffer 0 0% 20.48% 426ms 8.25% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 20.48% 426ms 8.25% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 3ms 0.058% 20.54% 393ms 7.61% vtkCell::~vtkCell 0 0% 20.54% 393ms 7.61% vtkXMLWriter::WriteBinaryData 0 0% 20.54% 391ms 7.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 20.54% 391ms 7.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 20.54% 368ms 7.12% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.077% 20.62% 368ms 7.12% PottsBasedCellPopulation::UpdateCellLocations 0 0% 20.62% 361ms 6.99% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 14ms 0.27% 20.89% 359ms 6.95% __printf_fp_l_buffer 0 0% 20.89% 359ms 6.95% __printf_fp_spec (inline) 53ms 1.03% 21.91% 358ms 6.93% std::__new_allocator::allocate (inline) 0 0% 21.91% 356ms 6.89% std::allocator_traits::allocate (inline) 50ms 0.97% 22.88% 351ms 6.79% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 219ms 4.24% 27.12% 327ms 6.33% _int_malloc 143ms 2.77% 29.89% 319ms 6.17% __printf_fp_buffer_1 0 0% 29.89% 301ms 5.83% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 29.89% 297ms 5.75% VtkMeshWriter::WriteFiles 5ms 0.097% 29.98% 297ms 5.75% std::__new_allocator::deallocate (inline) 0 0% 29.98% 294ms 5.69% std::allocator_traits::deallocate (inline) 0 0% 29.98% 275ms 5.32% vtkXMLWriter::WritePointsAppendedData 21ms 0.41% 30.39% 267ms 5.17% vtkObject::vtkObject 3ms 0.058% 30.45% 265ms 5.13% vtkPoints::~vtkPoints 1ms 0.019% 30.47% 259ms 5.01% std::set::set (inline) 16ms 0.31% 30.78% 257ms 4.97% std::_Rb_tree::_Rb_tree 6ms 0.12% 30.89% 246ms 4.76% vtkQuad::~vtkQuad 45ms 0.87% 31.77% 238ms 4.61% vtkObject::Modified 0 0% 31.77% 221ms 4.28% std::_Rb_tree::_M_create_node (inline) 2ms 0.039% 31.80% 209ms 4.05% vtkTriangle::~vtkTriangle 0 0% 31.80% 208ms 4.03% std::_Rb_tree::_M_get_node (inline) 2ms 0.039% 31.84% 207ms 4.01% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.019% 31.86% 206ms 3.99% VertexMesh::~VertexMesh 0 0% 31.86% 204ms 3.95% vtkLine::GetParametricCenter 0 0% 31.86% 203ms 3.93% vtkXMLWriter::WriteCompressionBlock 14ms 0.27% 32.13% 199ms 3.85% std::_Rb_tree::_M_copy (inline) 0 0% 32.13% 197ms 3.81% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.019% 32.15% 195ms 3.77% vtkDataCompressor::Compress 0 0% 32.15% 194ms 3.76% compress2 0 0% 32.15% 194ms 3.76% vtkZLibDataCompressor::CompressBuffer 50ms 0.97% 33.12% 191ms 3.70% crc32 0 0% 33.12% 191ms 3.70% deflate 5ms 0.097% 33.22% 190ms 3.68% vtkBase64OutputStream::Write 2ms 0.039% 33.26% 188ms 3.64% vtkFloatArray::New 42ms 0.81% 34.07% 187ms 3.62% std::_Rb_tree::_M_erase 187ms 3.62% 37.69% 187ms 3.62% vtkTimeStamp::Modified 7ms 0.14% 37.82% 186ms 3.60% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.058% 37.88% 185ms 3.58% vtkDataArray::CreateDataArray 15ms 0.29% 38.17% 184ms 3.56% vtkBase64OutputStream::EncodeTriplet 0 0% 38.17% 182ms 3.52% VertexMesh::VertexMesh 23ms 0.45% 38.62% 182ms 3.52% std::_Rb_tree::_M_clone_node (inline) 0 0% 38.62% 182ms 3.52% vtkDoubleArray::vtkDoubleArray 1ms 0.019% 38.64% 180ms 3.48% std::vector::~vector (inline) 2ms 0.039% 38.68% 178ms 3.45% NodesOnlyMesh::ConstructNodesWithoutMesh 8ms 0.15% 38.83% 177ms 3.43% vtkIdList::AllocateInternal 2ms 0.039% 38.87% 176ms 3.41% vtkTypeFloat64Array::New 133ms 2.57% 41.44% 174ms 3.37% malloc_consolidate 1ms 0.019% 41.46% 171ms 3.31% vtkFloatArray::vtkFloatArray 9ms 0.17% 41.64% 170ms 3.29% MutableElement::BuildEdges 0 0% 41.64% 170ms 3.29% VertexMesh::GenerateEdgesFromElements (inline) 148ms 2.86% 44.50% 168ms 3.25% vtkObjectBase::UnRegisterInternal 3ms 0.058% 44.56% 167ms 3.23% std::_Vector_base::_M_deallocate (inline) 18ms 0.35% 44.91% 159ms 3.08% std::vector::_M_default_append 3ms 0.058% 44.97% 156ms 3.02% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 2ms 0.039% 45.01% 154ms 2.98% NodeLocationWriter::VisitAnyPopulation 1ms 0.019% 45.03% 154ms 2.98% vtkTypeFloat64Array::vtkTypeFloat64Array 4ms 0.077% 45.10% 153ms 2.96% EdgeHelper::GetEdgeFromNodes 0 0% 45.10% 148ms 2.86% std::_Vector_base::_M_allocate (inline) 62ms 1.20% 46.30% 146ms 2.83% std::ostream::write 0 0% 46.30% 146ms 2.83% std::set::~set (inline) 0 0% 46.30% 145ms 2.81% std::_Rb_tree::_M_drop_node (inline) 0 0% 46.30% 139ms 2.69% std::_Vector_base::~_Vector_base (inline) 0 0% 46.30% 137ms 2.65% EdgeHelper::~EdgeHelper (inline) 131ms 2.54% 48.84% 134ms 2.59% [libz.so.1.3] 0 0% 48.84% 130ms 2.52% std::_Rb_tree::_M_put_node (inline) 2ms 0.039% 48.88% 122ms 2.36% tbb::detail::r1::parallel_pipeline 0 0% 48.88% 116ms 2.25% clone3 0 0% 48.88% 116ms 2.25% start_thread 5ms 0.097% 48.97% 112ms 2.17% std::map::operator[] (partial-inline) 5ms 0.097% 49.07% 111ms 2.15% vtkFloatArray::~vtkFloatArray 0 0% 49.07% 110ms 2.13% vtkIdList::Allocate 1ms 0.019% 49.09% 109ms 2.11% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 49.09% 108ms 2.09% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.039% 49.13% 104ms 2.01% tbb::detail::r1::reset 42ms 0.81% 49.94% 103ms 1.99% hack_digit 102ms 1.97% 51.92% 102ms 1.97% [libvtkCommonCore-9.3.so.9.3] 8ms 0.15% 52.07% 102ms 1.97% _int_free_maybe_consolidate 101ms 1.96% 54.03% 101ms 1.96% __strcmp_evex 0 0% 54.03% 97ms 1.88% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 31ms 0.6% 54.63% 97ms 1.88% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 54.63% 96ms 1.86% AbstractCellProperty::IsSubType (inline) 30ms 0.58% 55.21% 95ms 1.84% __dynamic_cast 54ms 1.05% 56.25% 93ms 1.80% tbb::detail::r1::wait_bounded_queue_monitor 44ms 0.85% 57.10% 93ms 1.80% vtkTypeFloat64Array::PrintSelf 47ms 0.91% 58.01% 92ms 1.78% std::basic_filebuf::xsputn 4ms 0.077% 58.09% 92ms 1.78% vtkDoubleArray::~vtkDoubleArray 2ms 0.039% 58.13% 89ms 1.72% std::operator<< (inline) 25ms 0.48% 58.61% 87ms 1.68% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.019% 58.63% 86ms 1.66% vtkXMLWriter::WritePointDataAppendedData 37ms 0.72% 59.35% 85ms 1.65% std::__ostream_insert 4ms 0.077% 59.43% 85ms 1.65% vtkIdList::New 85ms 1.65% 61.07% 85ms 1.65% vtkObjectBase::vtkObjectBase 7ms 0.14% 61.21% 84ms 1.63% AbstractCellProperty::IsType (inline) 3ms 0.058% 61.27% 84ms 1.63% CellPropertyCollection::HasProperty 0 0% 61.27% 83ms 1.61% Cell::HasCellProperty (inline) 3ms 0.058% 61.32% 83ms 1.61% vtkDataArray::vtkDataArray 2ms 0.039% 61.36% 79ms 1.53% std::vector::push_back (inline) 3ms 0.058% 61.42% 78ms 1.51% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.058% 61.48% 78ms 1.51% vtkAbstractArray::vtkAbstractArray 1ms 0.019% 61.50% 70ms 1.36% NodesOnlyMesh::SetUpBoxCollection 43ms 0.83% 62.33% 70ms 1.36% std::basic_streambuf::xsputn 69ms 1.34% 63.67% 69ms 1.34% [libstdc++.so.6.0.33] 0 0% 63.67% 69ms 1.34% std::_Rb_tree::lower_bound (inline) 0 0% 63.67% 69ms 1.34% std::map::lower_bound (inline) 0 0% 63.67% 68ms 1.32% VertexMesh::Clear 0 0% 63.67% 66ms 1.28% NodesOnlyMesh::~NodesOnlyMesh 6ms 0.12% 63.78% 65ms 1.26% vtkDataArray::~vtkDataArray 0 0% 63.78% 64ms 1.24% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.039% 63.82% 63ms 1.22% std::_Rb_tree::_M_insert_unique 0 0% 63.82% 63ms 1.22% std::set::insert (inline) 13ms 0.25% 64.07% 62ms 1.20% VertexMeshWriter::GetNextNode 12ms 0.23% 64.31% 61ms 1.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.019% 64.32% 59ms 1.14% Cell::GetCellProliferativeType 2ms 0.039% 64.36% 57ms 1.10% std::vector::_M_realloc_insert 55ms 1.06% 65.43% 55ms 1.06% [libchaste_cell_based.so] 55ms 1.06% 66.49% 55ms 1.06% unlink_chunk 7ms 0.14% 66.63% 54ms 1.05% AbstractCellProperty::IsSame 6ms 0.12% 66.74% 53ms 1.03% std::_Rb_tree::_M_insert_ (inline) 5ms 0.097% 66.84% 53ms 1.03% vtkIdList::~vtkIdList 0 0% 66.84% 52ms 1.01% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.019% 66.86% 52ms 1.01% boost::numeric::ublas::vector_assign (inline) 0 0% 66.86% 50ms 0.97% std::make_unique (inline) 0 0% 66.86% 47ms 0.91% std::_Destroy (inline) 0 0% 66.86% 47ms 0.91% std::_Destroy_aux::__destroy (inline) 11ms 0.21% 67.07% 47ms 0.91% std::type_info::operator== (inline) 46ms 0.89% 67.96% 46ms 0.89% __mpn_divrem 0 0% 67.96% 46ms 0.89% tcache_get (inline) 46ms 0.89% 68.85% 46ms 0.89% tcache_get_n (inline) 0 0% 68.85% 46ms 0.89% vtkDoubleArray::New 19ms 0.37% 69.22% 43ms 0.83% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.52% 69.74% 43ms 0.83% std::_Hashtable::clear 42ms 0.81% 70.56% 42ms 0.81% __memcpy_evex_unaligned_erms 0 0% 70.56% 40ms 0.77% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.56% 40ms 0.77% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 70.56% 40ms 0.77% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 70.56% 40ms 0.77% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 70.56% 40ms 0.77% std::map::~map (inline) 7ms 0.14% 70.69% 40ms 0.77% std::num_put::_M_insert_int 39ms 0.75% 71.45% 40ms 0.77% vtkObjectBase::RegisterInternal 2ms 0.039% 71.49% 39ms 0.75% boost::detail::shared_count::~shared_count (inline) 0 0% 71.49% 39ms 0.75% boost::shared_ptr::~shared_ptr (inline) 39ms 0.75% 72.24% 39ms 0.75% std::_Rb_tree_header::_M_reset (inline) 1ms 0.019% 72.26% 38ms 0.74% DistributedBoxCollection::SetupLocalBoxesHalfOnly 38ms 0.74% 73.00% 38ms 0.74% __GI_sched_yield 3ms 0.058% 73.05% 38ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 36ms 0.7% 73.75% 37ms 0.72% boost::detail::sp_counted_base::release 4ms 0.077% 73.83% 37ms 0.72% vtkIdList::vtkIdList 36ms 0.7% 74.53% 37ms 0.72% vtkObjectBase::Delete 20ms 0.39% 74.91% 36ms 0.7% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 74.91% 36ms 0.7% DistributedBoxCollection::IsOwned 1ms 0.019% 74.93% 35ms 0.68% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 74.93% 34ms 0.66% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 74.93% 34ms 0.66% _dl_init 0 0% 74.93% 34ms 0.66% call_init (inline) 13ms 0.25% 75.18% 34ms 0.66% std::__new_allocator::construct (inline) 0 0% 75.18% 34ms 0.66% std::allocator_traits::construct (inline) 0 0% 75.18% 33ms 0.64% Cell::GetMutationState 0 0% 75.18% 33ms 0.64% Edge::Edge 0 0% 75.18% 33ms 0.64% std::less::operator() (inline) 33ms 0.64% 75.82% 33ms 0.64% std::operator< (inline) 1ms 0.019% 75.84% 32ms 0.62% Cell::GetCellId 11ms 0.21% 76.05% 32ms 0.62% boost::numeric::ublas::indexing_vector_assign 32ms 0.62% 76.67% 32ms 0.62% std::_Rb_tree_increment 5ms 0.097% 76.77% 32ms 0.62% vtkDataArrayPrivate::DoComputeVectorRange 3ms 0.058% 76.83% 32ms 0.62% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 76.83% 31ms 0.6% std::basic_filebuf::open 0 0% 76.83% 31ms 0.6% std::unique_ptr::~unique_ptr (inline) 0 0% 76.83% 30ms 0.58% CellIdWriter::GetCellDataForVtkOutput 0 0% 76.83% 30ms 0.58% CxxTest::RealWorldDescription::setUp 0 0% 76.83% 30ms 0.58% Edge::SetNodes (inline) 0 0% 76.83% 30ms 0.58% PetscInitialize 0 0% 76.83% 30ms 0.58% PetscSetup::setUpWorld 0 0% 76.83% 30ms 0.58% PetscSetupUtils::CommonSetup 0 0% 76.83% 30ms 0.58% PetscSetupUtils::InitialisePetsc 0 0% 76.83% 30ms 0.58% VertexElement::~VertexElement 0 0% 76.83% 30ms 0.58% _dl_start_user 0 0% 76.83% 30ms 0.58% std::default_delete::operator() (inline) 0 0% 76.83% 30ms 0.58% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 76.83% 30ms 0.58% vtkDataArray::ComputeRange 30ms 0.58% 77.41% 30ms 0.58% vtkObject::~vtkObject 0 0% 77.41% 29ms 0.56% PMPI_Init_thread 4ms 0.077% 77.49% 29ms 0.56% VertexMeshWriter::GetNextElement 29ms 0.56% 78.05% 29ms 0.56% [libchaste_mesh.so] 0 0% 78.05% 29ms 0.56% _IO_new_fopen 0 0% 78.05% 29ms 0.56% __fopen_internal (inline) 16ms 0.31% 78.36% 29ms 0.56% __printf_buffer_write 0 0% 78.36% 29ms 0.56% ompi_mpi_init 2ms 0.039% 78.40% 28ms 0.54% 2ms 0.039% 78.44% 28ms 0.54% AbstractMesh::NodeIterator::IsAllowedNode (inline) 0 0% 78.44% 28ms 0.54% AbstractMesh::NodeIterator::operator++ (inline) 0 0% 78.44% 28ms 0.54% VtkMeshWriter::MakeVtkMesh 0 0% 78.44% 28ms 0.54% _IO_new_file_fopen 0 0% 78.44% 28ms 0.54% std::__basic_file::open 5ms 0.097% 78.53% 28ms 0.54% tbb::detail::r1::cancel_group_execution 6ms 0.12% 78.65% 28ms 0.54% vtkAOSDataArrayTemplate::InsertTuple 2ms 0.039% 78.69% 27ms 0.52% MutableElement::~MutableElement 1ms 0.019% 78.71% 27ms 0.52% Node::AddElement 0 0% 78.71% 27ms 0.52% __GI__IO_file_open 27ms 0.52% 79.23% 27ms 0.52% std::_Rb_tree::_S_right (inline) 24ms 0.46% 79.69% 27ms 0.52% std::num_put::do_put 27ms 0.52% 80.22% 27ms 0.52% tcache_put (inline) 26ms 0.5% 80.72% 26ms 0.5% Node::IsDeleted 0 0% 80.72% 26ms 0.5% NodesOnlyMesh::Clear (inline) 26ms 0.5% 81.22% 26ms 0.5% __libc_open64 26ms 0.5% 81.73% 26ms 0.5% __strlen_evex 0 0% 81.73% 26ms 0.5% boost::numeric::ublas::c_vector::assign (inline) 26ms 0.5% 82.23% 26ms 0.5% boost::numeric::ublas::c_vector::operator()