File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3853ms, 77.01% of 5003ms total Dropped 773 nodes (cum <= 25.02ms) flat flat% sum% cum cum% 0 0% 0% 4739ms 94.72% __libc_start_call_main 0 0% 0% 4739ms 94.72% __libc_start_main_impl 0 0% 0% 4739ms 94.72% _start 0 0% 0% 4723ms 94.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4723ms 94.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4723ms 94.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4723ms 94.40% main 0 0% 0% 4683ms 93.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4683ms 93.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4683ms 93.60% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4672ms 93.38% AbstractCellBasedSimulation::Solve 0 0% 0% 4334ms 86.63% AbstractCellPopulation::WriteResultsToFiles 12ms 0.24% 0.24% 4097ms 81.89% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.24% 1962ms 39.22% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.04% 0.28% 1699ms 33.96% VertexMeshWriter::MakeVtkMesh 0 0% 0.28% 1243ms 24.85% vtkPolygon::New 3ms 0.06% 0.34% 1241ms 24.81% vtkPolygon::vtkPolygon 8ms 0.16% 0.5% 906ms 18.11% vtkCell::vtkCell 0 0% 0.5% 803ms 16.05% VertexMeshWriter::WriteFiles 3ms 0.06% 0.56% 772ms 15.43% vtkPoints::New 0 0% 0.56% 771ms 15.41% std::ostream::operator<< (inline) 56ms 1.12% 1.68% 770ms 15.39% std::ostream::_M_insert 9ms 0.18% 1.86% 732ms 14.63% vtkPoints::vtkPoints 37ms 0.74% 2.60% 685ms 13.69% operator new 203ms 4.06% 6.66% 649ms 12.97% __GI___libc_malloc 33ms 0.66% 7.32% 628ms 12.55% std::num_put::_M_insert_float 1ms 0.02% 7.34% 582ms 11.63% vtkLine::New 1ms 0.02% 7.36% 582ms 11.63% vtkQuad::New 3ms 0.06% 7.42% 581ms 11.61% vtkQuad::vtkQuad 0 0% 7.42% 578ms 11.55% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.42% 578ms 11.55% vtkXMLWriterBase::Write 0 0% 7.42% 577ms 11.53% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.42% 575ms 11.49% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.42% 574ms 11.47% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.42% 573ms 11.45% vtkCompositeDataPipeline::ExecuteData 0 0% 7.42% 573ms 11.45% vtkExecutive::CallAlgorithm 0 0% 7.42% 571ms 11.41% vtkXMLUnstructuredDataWriter::ProcessRequest 10ms 0.2% 7.62% 567ms 11.33% vtkLine::vtkLine 1ms 0.02% 7.64% 548ms 10.95% vtkTriangle::New 7ms 0.14% 7.78% 538ms 10.75% vtkTriangle::vtkTriangle 158ms 3.16% 10.93% 512ms 10.23% __GI___libc_free 0 0% 10.93% 500ms 9.99% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.93% 500ms 9.99% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 9ms 0.18% 11.11% 477ms 9.53% std::__cxx11::collate::do_transform 32ms 0.64% 11.75% 458ms 9.15% vtkPoints::SetDataType 4ms 0.08% 11.83% 448ms 8.95% ___vsnprintf 1ms 0.02% 11.85% 445ms 8.89% __vsnprintf_internal (inline) 0 0% 11.85% 438ms 8.75% vtkXMLWriter::WriteBinaryData 46ms 0.92% 12.77% 436ms 8.71% __printf_buffer 0 0% 12.77% 428ms 8.55% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 12.77% 427ms 8.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.77% 425ms 8.49% vtkXMLWriter::WriteBinaryDataBlock 1ms 0.02% 12.79% 402ms 8.04% vtkPolygon::~vtkPolygon 252ms 5.04% 17.83% 375ms 7.50% _int_malloc 1ms 0.02% 17.85% 366ms 7.32% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.85% 362ms 7.24% VtkMeshWriter::WriteFiles 3ms 0.06% 17.91% 358ms 7.16% __printf_fp_spec (inline) 16ms 0.32% 18.23% 355ms 7.10% __printf_fp_l_buffer 213ms 4.26% 22.49% 352ms 7.04% _int_free 0 0% 22.49% 325ms 6.50% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.1% 22.59% 325ms 6.50% PottsBasedCellPopulation::UpdateCellLocations 0 0% 22.59% 322ms 6.44% vtkXMLWriter::WritePointsAppendedData 5ms 0.1% 22.69% 319ms 6.38% vtkCell::~vtkCell 157ms 3.14% 25.82% 317ms 6.34% __printf_fp_buffer_1 41ms 0.82% 26.64% 311ms 6.22% std::__new_allocator::allocate (inline) 0 0% 26.64% 310ms 6.20% std::allocator_traits::allocate (inline) 46ms 0.92% 27.56% 306ms 6.12% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 2ms 0.04% 27.60% 263ms 5.26% std::__new_allocator::deallocate (inline) 0 0% 27.60% 257ms 5.14% std::allocator_traits::deallocate (inline) 0 0% 27.60% 242ms 4.84% tbb::detail::r1::parallel_pipeline 0 0% 27.60% 232ms 4.64% vtkXMLWriter::WriteCompressionBlock 0 0% 27.60% 230ms 4.60% clone3 0 0% 27.60% 230ms 4.60% start_thread 0 0% 27.60% 230ms 4.60% tbb::detail::r1::reset 98ms 1.96% 29.56% 230ms 4.60% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 29.56% 226ms 4.52% vtkDataCompressor::Compress 0 0% 29.56% 224ms 4.48% compress2 0 0% 29.56% 224ms 4.48% vtkZLibDataCompressor::CompressBuffer 65ms 1.30% 30.86% 219ms 4.38% crc32 0 0% 30.86% 219ms 4.38% deflate 18ms 0.36% 31.22% 205ms 4.10% std::_Rb_tree::_Rb_tree 0 0% 31.22% 205ms 4.10% std::set::set (inline) 2ms 0.04% 31.26% 199ms 3.98% vtkPoints::~vtkPoints 5ms 0.1% 31.36% 195ms 3.90% vtkBase64OutputStream::Write 0 0% 31.36% 191ms 3.82% std::_Rb_tree::_M_create_node (inline) 20ms 0.4% 31.76% 190ms 3.80% vtkBase64OutputStream::EncodeTriplet 0 0% 31.76% 188ms 3.76% VertexMesh::~VertexMesh 4ms 0.08% 31.84% 184ms 3.68% vtkFloatArray::New 0 0% 31.84% 183ms 3.66% std::_Rb_tree::_M_get_node (inline) 10ms 0.2% 32.04% 177ms 3.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 32.04% 176ms 3.52% vtkQuad::~vtkQuad 0 0% 32.04% 175ms 3.50% std::_Rb_tree::_Alloc_node::operator() (inline) 60ms 1.20% 33.24% 172ms 3.44% std::_Rb_tree::_M_erase 2ms 0.04% 33.28% 170ms 3.40% NodesOnlyMesh::ConstructNodesWithoutMesh 103ms 2.06% 35.34% 169ms 3.38% malloc_consolidate 0 0% 35.34% 165ms 3.30% NodeLocationWriter::VisitAnyPopulation 0 0% 35.34% 164ms 3.28% vtkTriangle::~vtkTriangle 3ms 0.06% 35.40% 163ms 3.26% vtkFloatArray::vtkFloatArray 0 0% 35.40% 161ms 3.22% std::vector::~vector (inline) 4ms 0.08% 35.48% 161ms 3.22% vtkIdList::AllocateInternal 9ms 0.18% 35.66% 160ms 3.20% std::_Vector_base::_M_deallocate (inline) 46ms 0.92% 36.58% 159ms 3.18% std::ostream::write 3ms 0.06% 36.64% 159ms 3.18% vtkLine::GetParametricCenter 16ms 0.32% 36.96% 158ms 3.16% std::vector::_M_default_append 0 0% 36.96% 154ms 3.08% VertexMesh::VertexMesh 13ms 0.26% 37.22% 154ms 3.08% std::_Rb_tree::_M_copy (inline) 0 0% 37.22% 153ms 3.06% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 5ms 0.1% 37.32% 148ms 2.96% vtkDataArray::CreateDataArray 142ms 2.84% 40.16% 147ms 2.94% [libz.so.1.3] 60ms 1.20% 41.36% 146ms 2.92% std::basic_filebuf::xsputn 1ms 0.02% 41.38% 146ms 2.92% vtkDoubleArray::vtkDoubleArray 0 0% 41.38% 142ms 2.84% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.12% 41.50% 140ms 2.80% MutableElement::BuildEdges 4ms 0.08% 41.58% 140ms 2.80% vtkTypeFloat64Array::~vtkTypeFloat64Array 9ms 0.18% 41.75% 138ms 2.76% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.75% 137ms 2.74% EdgeHelper::~EdgeHelper (inline) 4ms 0.08% 41.83% 136ms 2.72% vtkTypeFloat64Array::New 133ms 2.66% 44.49% 133ms 2.66% __GI_sched_yield 1ms 0.02% 44.51% 131ms 2.62% std::_Vector_base::~_Vector_base (inline) 0 0% 44.51% 127ms 2.54% std::_Vector_base::_M_allocate (inline) 3ms 0.06% 44.57% 126ms 2.52% vtkFloatArray::~vtkFloatArray 2ms 0.04% 44.61% 120ms 2.40% vtkTypeFloat64Array::vtkTypeFloat64Array 2ms 0.04% 44.65% 118ms 2.36% EdgeHelper::GetEdgeFromNodes 0 0% 44.65% 118ms 2.36% std::set::~set (inline) 0 0% 44.65% 108ms 2.16% std::_Rb_tree::_M_drop_node (inline) 2ms 0.04% 44.69% 106ms 2.12% CellPropertyCollection::GetPropertiesType (inline) 0 0% 44.69% 105ms 2.10% std::_Rb_tree::_M_put_node (inline) 27ms 0.54% 45.23% 105ms 2.10% vtkObject::vtkObject 0 0% 45.23% 105ms 2.10% vtkXMLWriter::WritePointDataAppendedData 0 0% 45.23% 104ms 2.08% vtkIdList::Allocate 102ms 2.04% 47.27% 102ms 2.04% __strcmp_avx2 45ms 0.9% 48.17% 102ms 2.04% std::__ostream_insert 1ms 0.02% 48.19% 99ms 1.98% std::operator<< (inline) 53ms 1.06% 49.25% 95ms 1.90% hack_digit 68ms 1.36% 50.61% 94ms 1.88% std::basic_streambuf::xsputn 2ms 0.04% 50.65% 93ms 1.86% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 57ms 1.14% 51.79% 93ms 1.86% vtkObjectBase::UnRegisterInternal 5ms 0.1% 51.89% 91ms 1.82% CellPropertyCollection::HasProperty 0 0% 51.89% 89ms 1.78% Cell::HasCellProperty (inline) 0 0% 51.89% 86ms 1.72% AbstractCellProperty::IsSubType (inline) 26ms 0.52% 52.41% 86ms 1.72% __dynamic_cast 3ms 0.06% 52.47% 86ms 1.72% _int_free_maybe_consolidate 2ms 0.04% 52.51% 86ms 1.72% std::map::operator[] (partial-inline) 86ms 1.72% 54.23% 86ms 1.72% unlink_chunk 4ms 0.08% 54.31% 85ms 1.70% AbstractCellProperty::IsType (inline) 11ms 0.22% 54.53% 81ms 1.62% vtkAOSDataArrayTemplate::DataElementChanged 4ms 0.08% 54.61% 80ms 1.60% vtkIdList::New 3ms 0.06% 54.67% 77ms 1.54% std::vector::push_back (inline) 3ms 0.06% 54.73% 74ms 1.48% AbstractCellPopulation::GetCellUsingLocationIndex 36ms 0.72% 55.45% 73ms 1.46% vtkTypeFloat64Array::PrintSelf 0 0% 55.45% 71ms 1.42% std::set::insert (inline) 2ms 0.04% 55.49% 71ms 1.42% vtkDoubleArray::~vtkDoubleArray 2ms 0.04% 55.53% 70ms 1.40% std::_Rb_tree::_M_insert_unique 22ms 0.44% 55.97% 69ms 1.38% vtkObject::Modified 0 0% 55.97% 67ms 1.34% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 9ms 0.18% 56.15% 66ms 1.32% vtkDataArray::vtkDataArray 0 0% 56.15% 65ms 1.30% NodesOnlyMesh::SetUpBoxCollection 11ms 0.22% 56.37% 64ms 1.28% AbstractCellProperty::IsSame 5ms 0.1% 56.47% 64ms 1.28% boost::numeric::ublas::c_vector::c_vector (inline) 62ms 1.24% 57.71% 62ms 1.24% __GI___writev 0 0% 57.71% 62ms 1.24% std::__basic_file::xsputn_2 0 0% 57.71% 61ms 1.22% PottsMesh::GetMooreNeighbouringNodeIndices 35ms 0.7% 58.40% 61ms 1.22% std::_Hashtable::clear 60ms 1.20% 59.60% 60ms 1.20% __memcpy_avx_unaligned_erms 0 0% 59.60% 59ms 1.18% NodesOnlyMesh::~NodesOnlyMesh 0 0% 59.60% 59ms 1.18% std::map::~map (inline) 0 0% 59.60% 59ms 1.18% tcache_get (inline) 59ms 1.18% 60.78% 59ms 1.18% tcache_get_n (inline) 0 0% 60.78% 58ms 1.16% boost::numeric::ublas::vector_assign (inline) 9ms 0.18% 60.96% 57ms 1.14% std::num_put::_M_insert_int 0 0% 60.96% 56ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 3ms 0.06% 61.02% 55ms 1.10% std::_Rb_tree::_M_insert_ (inline) 0 0% 61.02% 54ms 1.08% Cell::GetCellProliferativeType 12ms 0.24% 61.26% 53ms 1.06% VertexMeshWriter::GetNextNode 14ms 0.28% 61.54% 53ms 1.06% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.3% 61.84% 53ms 1.06% std::type_info::operator== (inline) 3ms 0.06% 61.90% 53ms 1.06% std::vector::_M_realloc_insert 17ms 0.34% 62.24% 53ms 1.06% vtkAbstractArray::vtkAbstractArray 9ms 0.18% 62.42% 52ms 1.04% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 62.42% 51ms 1.02% VertexMesh::Clear 49ms 0.98% 63.40% 50ms 1% vtkObject::~vtkObject 0 0% 63.40% 47ms 0.94% std::_Rb_tree::lower_bound (inline) 0 0% 63.40% 47ms 0.94% std::map::lower_bound (inline) 45ms 0.9% 64.30% 45ms 0.9% vtkTimeStamp::Modified 44ms 0.88% 65.18% 44ms 0.88% [libvtkCommonCore-9.3.so.9.3] 0 0% 65.18% 44ms 0.88% std::basic_filebuf::open 0 0% 65.18% 44ms 0.88% vtkDataArray::ComputeRange 0 0% 65.18% 43ms 0.86% std::__basic_file::xsputn 0 0% 65.18% 43ms 0.86% std::basic_filebuf::_M_convert_to_external 0 0% 65.18% 43ms 0.86% std::basic_filebuf::overflow 42ms 0.84% 66.02% 42ms 0.84% __GI___libc_write 42ms 0.84% 66.86% 42ms 0.84% std::ostream::sentry::sentry 19ms 0.38% 67.24% 41ms 0.82% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.08% 67.32% 41ms 0.82% vtkAOSDataArrayTemplate::InsertTuple 39ms 0.78% 68.10% 41ms 0.82% vtkObjectBase::Delete 18ms 0.36% 68.46% 40ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.46% 40ms 0.8% DistributedBoxCollection::IsOwned 0 0% 68.46% 40ms 0.8% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 68.46% 39ms 0.78% _IO_new_file_fopen 0 0% 68.46% 39ms 0.78% _IO_new_fopen 0 0% 68.46% 39ms 0.78% __GI__IO_file_open 0 0% 68.46% 39ms 0.78% __fopen_internal (inline) 39ms 0.78% 69.24% 39ms 0.78% __libc_open64 0 0% 69.24% 39ms 0.78% std::__basic_file::open 4ms 0.08% 69.32% 38ms 0.76% tbb::detail::r1::cancel_group_execution 0 0% 69.32% 38ms 0.76% vtkDoubleArray::New 4ms 0.08% 69.40% 37ms 0.74% DistributedBoxCollection::SetupLocalBoxesHalfOnly 16ms 0.32% 69.72% 37ms 0.74% _int_free_merge_chunk 9ms 0.18% 69.90% 37ms 0.74% boost::numeric::ublas::indexing_vector_assign 2ms 0.04% 69.94% 37ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.12% 70.06% 37ms 0.74% vtkDataArray::~vtkDataArray 0 0% 70.06% 36ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 70.06% 36ms 0.72% PetscInitialize 0 0% 70.06% 36ms 0.72% PetscSetup::setUpWorld 0 0% 70.06% 36ms 0.72% PetscSetupUtils::CommonSetup 0 0% 70.06% 36ms 0.72% PetscSetupUtils::InitialisePetsc 5ms 0.1% 70.16% 36ms 0.72% vtkDataArrayPrivate::DoComputeVectorRange 36ms 0.72% 70.88% 36ms 0.72% vtkObjectBase::vtkObjectBase 36ms 0.72% 71.60% 36ms 0.72% vtkObjectBase::~vtkObjectBase 0 0% 71.60% 35ms 0.7% PMPI_Init_thread 0 0% 71.60% 35ms 0.7% ompi_mpi_init 0 0% 71.60% 35ms 0.7% std::make_unique (inline) 6ms 0.12% 71.72% 35ms 0.7% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 71.72% 34ms 0.68% OutputFileHandler::OpenOutputFile 0 0% 71.72% 34ms 0.68% _dl_init 0 0% 71.72% 34ms 0.68% _dl_start_user 0 0% 71.72% 34ms 0.68% call_init (inline) 4ms 0.08% 71.80% 34ms 0.68% vtkIdList::~vtkIdList 0 0% 71.80% 33ms 0.66% DistributedBoxCollection::~DistributedBoxCollection 0 0% 71.80% 33ms 0.66% NodesOnlyMesh::ClearBoxCollection (inline) 33ms 0.66% 72.46% 33ms 0.66% __memset_avx2_unaligned_erms 0 0% 72.46% 33ms 0.66% std::_Destroy (inline) 1ms 0.02% 72.48% 33ms 0.66% std::_Destroy_aux::__destroy (inline) 0 0% 72.48% 33ms 0.66% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 72.48% 33ms 0.66% std::_Rb_tree_header::_Rb_tree_header (inline) 27ms 0.54% 73.02% 33ms 0.66% std::num_put::do_put 32ms 0.64% 73.66% 32ms 0.64% std::_Rb_tree_header::_M_reset (inline) 26ms 0.52% 74.18% 32ms 0.64% vtkObject::ObjectFinalize 2ms 0.04% 74.22% 31ms 0.62% Cell::GetCellId 1ms 0.02% 74.24% 31ms 0.62% Cell::GetMutationState 31ms 0.62% 74.86% 31ms 0.62% [libstdc++.so.6.0.33] 0 0% 74.86% 30ms 0.6% CellIdWriter::GetCellDataForVtkOutput 2ms 0.04% 74.90% 30ms 0.6% Node::ConstructNodeAttributes (inline) 0 0% 74.90% 30ms 0.6% Node::SetRadius 1ms 0.02% 74.92% 30ms 0.6% PottsMesh::GetVonNeumannNeighbouringNodeIndices 1ms 0.02% 74.94% 29ms 0.58% 29ms 0.58% 75.51% 29ms 0.58% boost::numeric::ublas::c_vector::operator() 0 0% 75.51% 28ms 0.56% std::basic_ofstream::basic_ofstream (inline) 0 0% 75.51% 28ms 0.56% std::basic_ofstream::open (inline) 3ms 0.06% 75.57% 27ms 0.54% Edge::Edge 1ms 0.02% 75.59% 27ms 0.54% VertexElement::VertexElement 27ms 0.54% 76.13% 27ms 0.54% __strlen_avx2 7ms 0.14% 76.27% 27ms 0.54% std::__new_allocator::construct (inline) 0 0% 76.27% 27ms 0.54% std::allocator_traits::construct (inline) 1ms 0.02% 76.29% 26ms 0.52% Node::AddElement 0 0% 76.29% 26ms 0.52% NodesOnlyMesh::Clear (inline) 5ms 0.1% 76.39% 26ms 0.52% __find_specmb (inline) 26ms 0.52% 76.91% 26ms 0.52% std::_Rb_tree_increment 0 0% 76.91% 26ms 0.52% vtkDataArrayPrivate::DoComputeScalarRange 5ms 0.1% 77.01% 26ms 0.52% vtkIdList::vtkIdList