File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2272ms, 81.14% of 2800ms total Dropped 584 nodes (cum <= 14ms) flat flat% sum% cum cum% 0 0% 0% 2653ms 94.75% __libc_start_call_main 0 0% 0% 2653ms 94.75% __libc_start_main_impl 0 0% 0% 2653ms 94.75% _start 0 0% 0% 2641ms 94.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 2641ms 94.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 2641ms 94.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 2641ms 94.32% main 0 0% 0% 2613ms 93.32% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 2613ms 93.32% CxxTest::TestRunner::runTest (inline) 0 0% 0% 2613ms 93.32% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 2605ms 93.04% AbstractCellBasedSimulation::Solve 0 0% 0% 2445ms 87.32% AbstractCellPopulation::WriteResultsToFiles 5ms 0.18% 0.18% 2327ms 83.11% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.18% 1238ms 44.21% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.18% 1079ms 38.54% VertexMeshWriter::MakeVtkMesh 0 0% 0.18% 779ms 27.82% vtkPolygon::New 0 0% 0.18% 779ms 27.82% vtkPolygon::vtkPolygon 1ms 0.036% 0.21% 583ms 20.82% vtkCell::vtkCell 2ms 0.071% 0.29% 449ms 16.04% vtkPoints::New 5ms 0.18% 0.46% 426ms 15.21% vtkPoints::vtkPoints 16ms 0.57% 1.04% 392ms 14.00% operator new 1ms 0.036% 1.07% 383ms 13.68% vtkLine::New 1ms 0.036% 1.11% 379ms 13.54% VertexMeshWriter::WriteFiles 190ms 6.79% 7.89% 378ms 13.50% __GI___libc_malloc 4ms 0.14% 8.04% 370ms 13.21% vtkLine::vtkLine 19ms 0.68% 8.71% 355ms 12.68% std::ostream::_M_insert 2ms 0.071% 8.79% 354ms 12.64% std::ostream::operator<< (inline) 1ms 0.036% 8.82% 353ms 12.61% vtkTriangle::New 0 0% 8.82% 345ms 12.32% vtkQuad::New 0 0% 8.82% 345ms 12.32% vtkQuad::vtkQuad 2ms 0.071% 8.89% 344ms 12.29% vtkTriangle::vtkTriangle 0 0% 8.89% 300ms 10.71% vtkExecutive::CallAlgorithm 0 0% 8.89% 300ms 10.71% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.89% 300ms 10.71% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.89% 300ms 10.71% vtkXMLWriterBase::Write 0 0% 8.89% 299ms 10.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.89% 299ms 10.68% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.89% 298ms 10.64% vtkCompositeDataPipeline::ExecuteData 0 0% 8.89% 298ms 10.64% vtkXMLUnstructuredDataWriter::ProcessRequest 23ms 0.82% 9.71% 292ms 10.43% std::num_put::_M_insert_float 0 0% 9.71% 288ms 10.29% vtkPolygon::~vtkPolygon 35ms 1.25% 10.96% 286ms 10.21% __GI___libc_free 7ms 0.25% 11.21% 265ms 9.46% vtkPoints::SetDataType 0 0% 11.21% 258ms 9.21% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.21% 258ms 9.21% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 189ms 6.75% 17.96% 245ms 8.75% _int_free 0 0% 17.96% 235ms 8.39% vtkXMLWriter::WriteBinaryData 1ms 0.036% 18.00% 233ms 8.32% vtkCell::~vtkCell 1ms 0.036% 18.04% 229ms 8.18% vtkXMLWriter::WriteBinaryDataBlock 0 0% 18.04% 229ms 8.18% vtkXMLWriter::WriteBinaryDataInternal 8ms 0.29% 18.32% 215ms 7.68% std::__cxx11::collate::do_transform 0 0% 18.32% 210ms 7.50% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.071% 18.39% 202ms 7.21% ___vsnprintf 0 0% 18.39% 200ms 7.14% __vsnprintf_internal (inline) 26ms 0.93% 19.32% 196ms 7.00% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 28ms 1.00% 20.32% 195ms 6.96% __printf_buffer 12ms 0.43% 20.75% 178ms 6.36% vtkObject::vtkObject 12ms 0.43% 21.18% 174ms 6.21% std::__new_allocator::allocate (inline) 0 0% 21.18% 174ms 6.21% std::allocator_traits::allocate (inline) 0 0% 21.18% 174ms 6.21% vtkXMLWriter::WritePointsAppendedData 93ms 3.32% 24.50% 168ms 6.00% _int_malloc 11ms 0.39% 24.89% 167ms 5.96% vtkObject::Modified 0 0% 24.89% 164ms 5.86% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.89% 163ms 5.82% VtkMeshWriter::WriteFiles 8ms 0.29% 25.18% 158ms 5.64% __printf_fp_l_buffer 0 0% 25.18% 158ms 5.64% __printf_fp_spec (inline) 0 0% 25.18% 156ms 5.57% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.14% 25.32% 156ms 5.57% PottsBasedCellPopulation::UpdateCellLocations 154ms 5.50% 30.82% 154ms 5.50% vtkTimeStamp::Modified 3ms 0.11% 30.93% 152ms 5.43% std::__new_allocator::deallocate (inline) 0 0% 30.93% 150ms 5.36% std::allocator_traits::deallocate (inline) 127ms 4.54% 35.46% 145ms 5.18% vtkObjectBase::UnRegisterInternal 1ms 0.036% 35.50% 143ms 5.11% vtkPoints::~vtkPoints 57ms 2.04% 37.54% 141ms 5.04% __printf_fp_buffer_1 0 0% 37.54% 141ms 5.04% vtkQuad::~vtkQuad 0 0% 37.54% 126ms 4.50% tbb::detail::r1::parallel_pipeline 1ms 0.036% 37.57% 125ms 4.46% vtkTriangle::~vtkTriangle 0 0% 37.57% 123ms 4.39% clone3 0 0% 37.57% 123ms 4.39% start_thread 2ms 0.071% 37.64% 121ms 4.32% vtkBase64OutputStream::Write 0 0% 37.64% 120ms 4.29% tbb::detail::r1::reset 65ms 2.32% 39.96% 118ms 4.21% tbb::detail::r1::wait_bounded_queue_monitor 8ms 0.29% 40.25% 117ms 4.18% vtkBase64OutputStream::EncodeTriplet 0 0% 40.25% 116ms 4.14% std::_Rb_tree::_M_create_node (inline) 0 0% 40.25% 113ms 4.04% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 40.25% 112ms 4.00% std::_Rb_tree::_M_get_node (inline) 0 0% 40.25% 111ms 3.96% vtkFloatArray::New 0 0% 40.25% 108ms 3.86% vtkXMLWriter::WriteCompressionBlock 1ms 0.036% 40.29% 106ms 3.79% vtkLine::GetParametricCenter 11ms 0.39% 40.68% 104ms 3.71% std::_Rb_tree::_M_erase 0 0% 40.68% 102ms 3.64% vtkDataCompressor::Compress 0 0% 40.68% 102ms 3.64% vtkFloatArray::vtkFloatArray 0 0% 40.68% 101ms 3.61% compress2 17ms 0.61% 41.29% 101ms 3.61% crc32 0 0% 41.29% 101ms 3.61% deflate 1ms 0.036% 41.32% 101ms 3.61% std::_Rb_tree::_Rb_tree 33ms 1.18% 42.50% 101ms 3.61% std::ostream::write 0 0% 42.50% 101ms 3.61% std::set::set (inline) 0 0% 42.50% 101ms 3.61% vtkZLibDataCompressor::CompressBuffer 64ms 2.29% 44.79% 100ms 3.57% malloc_consolidate 0 0% 44.79% 97ms 3.46% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.071% 44.86% 96ms 3.43% vtkDataArray::CreateDataArray 1ms 0.036% 44.89% 95ms 3.39% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 3ms 0.11% 45.00% 94ms 3.36% std::_Rb_tree::~_Rb_tree (inline) 0 0% 45.00% 94ms 3.36% vtkDoubleArray::vtkDoubleArray 1ms 0.036% 45.04% 93ms 3.32% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 45.04% 93ms 3.32% VertexMesh::VertexMesh 0 0% 45.04% 91ms 3.25% std::_Rb_tree::_M_drop_node (inline) 1ms 0.036% 45.07% 90ms 3.21% MutableElement::BuildEdges 0 0% 45.07% 90ms 3.21% VertexMesh::GenerateEdgesFromElements (inline) 3ms 0.11% 45.18% 90ms 3.21% vtkIdList::AllocateInternal 8ms 0.29% 45.46% 89ms 3.18% std::_Rb_tree::_M_copy (inline) 0 0% 45.46% 88ms 3.14% vtkTypeFloat64Array::New 0 0% 45.46% 86ms 3.07% VertexMesh::~VertexMesh 0 0% 45.46% 84ms 3.00% std::set::~set (inline) 82ms 2.93% 48.39% 82ms 2.93% [libz.so.1.3] 2ms 0.071% 48.46% 82ms 2.93% vtkTypeFloat64Array::vtkTypeFloat64Array 11ms 0.39% 48.86% 81ms 2.89% std::_Rb_tree::_M_clone_node (inline) 28ms 1.00% 49.86% 80ms 2.86% std::basic_filebuf::xsputn 0 0% 49.86% 78ms 2.79% std::_Rb_tree::_M_put_node (inline) 1ms 0.036% 49.89% 77ms 2.75% EdgeHelper::GetEdgeFromNodes 0 0% 49.89% 75ms 2.68% std::vector::~vector (inline) 15ms 0.54% 50.43% 74ms 2.64% std::vector::_M_default_append 0 0% 50.43% 73ms 2.61% NodeLocationWriter::VisitAnyPopulation 0 0% 50.43% 72ms 2.57% std::_Vector_base::_M_deallocate (inline) 71ms 2.54% 52.96% 71ms 2.54% vtkObjectBase::vtkObjectBase 1ms 0.036% 53.00% 68ms 2.43% vtkIdList::Allocate 0 0% 53.00% 62ms 2.21% std::_Vector_base::_M_allocate (inline) 2ms 0.071% 53.07% 62ms 2.21% vtkDataArray::vtkDataArray 20ms 0.71% 53.79% 61ms 2.18% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.071% 53.86% 60ms 2.14% vtkAbstractArray::vtkAbstractArray 4ms 0.14% 54.00% 59ms 2.11% CellPropertyCollection::HasProperty 0 0% 54.00% 58ms 2.07% Cell::HasCellProperty (inline) 58ms 2.07% 56.07% 58ms 2.07% __strcmp_evex 0 0% 56.07% 58ms 2.07% vtkFloatArray::~vtkFloatArray 1ms 0.036% 56.11% 57ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 0 0% 56.11% 55ms 1.96% AbstractCellProperty::IsType (inline) 0 0% 56.11% 55ms 1.96% std::_Vector_base::~_Vector_base (inline) 0 0% 56.11% 54ms 1.93% EdgeHelper::~EdgeHelper (inline) 0 0% 56.11% 53ms 1.89% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 53ms 1.89% 58.00% 53ms 1.89% __GI_sched_yield 1ms 0.036% 58.04% 52ms 1.86% std::vector::push_back (inline) 0 0% 58.04% 51ms 1.82% vtkIdList::New 2ms 0.071% 58.11% 50ms 1.79% AbstractCellPopulation::GetCellUsingLocationIndex 18ms 0.64% 58.75% 50ms 1.79% vtkTypeFloat64Array::PrintSelf 9ms 0.32% 59.07% 49ms 1.75% std::__ostream_insert 2ms 0.071% 59.14% 49ms 1.75% std::map::operator[] (partial-inline) 23ms 0.82% 59.96% 48ms 1.71% hack_digit 1ms 0.036% 60.00% 47ms 1.68% std::operator<< (inline) 0 0% 60.00% 46ms 1.64% AbstractCellProperty::IsSubType (inline) 3ms 0.11% 60.11% 46ms 1.64% __dynamic_cast 37ms 1.32% 61.43% 46ms 1.64% std::basic_streambuf::xsputn 0 0% 61.43% 46ms 1.64% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 10ms 0.36% 61.79% 45ms 1.61% AbstractCellProperty::IsSame 0 0% 61.79% 44ms 1.57% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 44ms 1.57% 63.36% 44ms 1.57% unlink_chunk 1ms 0.036% 63.39% 44ms 1.57% vtkDoubleArray::~vtkDoubleArray 2ms 0.071% 63.46% 43ms 1.54% _int_free_maybe_consolidate 42ms 1.50% 64.96% 42ms 1.50% __GI___writev 0 0% 64.96% 42ms 1.50% std::__basic_file::xsputn_2 0 0% 64.96% 41ms 1.46% std::_Rb_tree::_M_insert_unique 0 0% 64.96% 41ms 1.46% std::set::insert (inline) 0 0% 64.96% 38ms 1.36% NodesOnlyMesh::~NodesOnlyMesh 19ms 0.68% 65.64% 36ms 1.29% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.11% 65.75% 36ms 1.29% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.25% 66.00% 36ms 1.29% std::_Rb_tree::_M_insert_ (inline) 4ms 0.14% 66.14% 36ms 1.29% vtkDataArray::~vtkDataArray 0 0% 66.14% 35ms 1.25% NodesOnlyMesh::SetUpBoxCollection 3ms 0.11% 66.25% 35ms 1.25% std::type_info::operator== (inline) 1ms 0.036% 66.29% 34ms 1.21% std::vector::_M_realloc_insert 0 0% 66.29% 34ms 1.21% vtkXMLWriter::WritePointDataAppendedData 2ms 0.071% 66.36% 33ms 1.18% Cell::GetCellProliferativeType 0 0% 66.36% 32ms 1.14% VertexMesh::Clear 2ms 0.071% 66.43% 32ms 1.14% boost::detail::shared_count::~shared_count (inline) 1ms 0.036% 66.46% 32ms 1.14% boost::numeric::ublas::vector_assign (inline) 0 0% 66.46% 32ms 1.14% boost::shared_ptr::~shared_ptr (inline) 6ms 0.21% 66.68% 31ms 1.11% std::num_put::_M_insert_int 30ms 1.07% 67.75% 30ms 1.07% [libvtkCommonCore-9.3.so.9.3] 29ms 1.04% 68.79% 30ms 1.07% boost::detail::sp_counted_base::release 0 0% 68.79% 29ms 1.04% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.036% 68.82% 29ms 1.04% std::basic_filebuf::_M_convert_to_external 0 0% 68.82% 29ms 1.04% std::basic_filebuf::overflow 4ms 0.14% 68.96% 29ms 1.04% vtkIdList::~vtkIdList 10ms 0.36% 69.32% 28ms 1.00% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.036% 69.36% 28ms 1.00% std::__basic_file::xsputn 3ms 0.11% 69.46% 27ms 0.96% VertexMeshWriter::GetNextNode 27ms 0.96% 70.43% 27ms 0.96% __GI___libc_write 0 0% 70.43% 27ms 0.96% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.036% 70.46% 27ms 0.96% std::make_unique (inline) 27ms 0.96% 71.43% 27ms 0.96% vtkObjectBase::RegisterInternal 0 0% 71.43% 26ms 0.93% CxxTest::RealWorldDescription::setUp 0 0% 71.43% 26ms 0.93% PMPI_Init_thread 0 0% 71.43% 26ms 0.93% PetscInitialize 0 0% 71.43% 26ms 0.93% PetscSetup::setUpWorld 0 0% 71.43% 26ms 0.93% PetscSetupUtils::CommonSetup 0 0% 71.43% 26ms 0.93% PetscSetupUtils::InitialisePetsc 26ms 0.93% 72.36% 26ms 0.93% __memcpy_avx512_unaligned_erms 0 0% 72.36% 26ms 0.93% ompi_mpi_init 1ms 0.036% 72.39% 26ms 0.93% vtkIdList::vtkIdList 1ms 0.036% 72.43% 25ms 0.89% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 72.43% 25ms 0.89% _dl_init 0 0% 72.43% 25ms 0.89% call_init (inline) 0 0% 72.43% 24ms 0.86% _dl_start_user 16ms 0.57% 73.00% 24ms 0.86% std::_Hashtable::clear 5ms 0.18% 73.18% 24ms 0.86% std::__new_allocator::construct (inline) 0 0% 73.18% 24ms 0.86% std::allocator_traits::construct (inline) 0 0% 73.18% 23ms 0.82% Cell::GetMutationState 0 0% 73.18% 23ms 0.82% std::_Destroy (inline) 0 0% 73.18% 23ms 0.82% std::_Destroy_aux::__destroy (inline) 0 0% 73.18% 23ms 0.82% std::basic_filebuf::open 0 0% 73.18% 22ms 0.79% 1ms 0.036% 73.21% 22ms 0.79% DistributedBoxCollection::IsOwned 11ms 0.39% 73.61% 22ms 0.79% boost::numeric::ublas::indexing_vector_assign 9ms 0.32% 73.93% 21ms 0.75% DistributedBoxCollection::CalculateContainingBox (inline) 21ms 0.75% 74.68% 21ms 0.75% boost::numeric::ublas::c_vector::operator() 0 0% 74.68% 21ms 0.75% vtkDoubleArray::New 0 0% 74.68% 20ms 0.71% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 74.68% 20ms 0.71% NodesOnlyMesh::Clear (inline) 0 0% 74.68% 20ms 0.71% _IO_new_file_fopen 0 0% 74.68% 20ms 0.71% _IO_new_fopen 0 0% 74.68% 20ms 0.71% __GI__IO_file_open 0 0% 74.68% 20ms 0.71% __fopen_internal (inline) 20ms 0.71% 75.39% 20ms 0.71% __libc_open64 0 0% 75.39% 20ms 0.71% std::_Rb_tree::lower_bound (inline) 0 0% 75.39% 20ms 0.71% std::__basic_file::open 0 0% 75.39% 20ms 0.71% std::map::lower_bound (inline) 20ms 0.71% 76.11% 20ms 0.71% std::ostream::sentry::sentry 6ms 0.21% 76.32% 19ms 0.68% boost::serialization::singleton::get_instance 0 0% 76.32% 19ms 0.68% orte_init 0 0% 76.32% 19ms 0.68% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.32% 18ms 0.64% DistributedBoxCollection::~DistributedBoxCollection 0 0% 76.32% 18ms 0.64% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 76.32% 18ms 0.64% OutputFileHandler::OpenOutputFile 18ms 0.64% 76.96% 18ms 0.64% vtkObject::~vtkObject 1ms 0.036% 77.00% 17ms 0.61% Node::AddElement 1ms 0.036% 77.04% 17ms 0.61% Node::GetPoint 1ms 0.036% 77.07% 17ms 0.61% Node::SetRadius 17ms 0.61% 77.68% 17ms 0.61% __mpn_divrem 0 0% 77.68% 17ms 0.61% std::basic_filebuf::sync 0 0% 77.68% 17ms 0.61% std::default_delete::operator() (inline) 0 0% 77.68% 17ms 0.61% std::ostream::flush 0 0% 77.68% 17ms 0.61% std::unique_ptr::~unique_ptr (inline) 0 0% 77.68% 16ms 0.57% Node::ConstructNodeAttributes (inline) 0 0% 77.68% 16ms 0.57% VtkMeshWriter::MakeVtkMesh 16ms 0.57% 78.25% 16ms 0.57% [libstdc++.so.6.0.33] 0 0% 78.25% 16ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.25% 16ms 0.57% std::basic_ofstream::basic_ofstream (inline) 0 0% 78.25% 16ms 0.57% std::basic_ofstream::open (inline) 15ms 0.54% 78.79% 16ms 0.57% std::num_put::do_put 14ms 0.5% 79.29% 16ms 0.57% vtkObject::ObjectFinalize 0 0% 79.29% 15ms 0.54% Edge::AddElement 0 0% 79.29% 15ms 0.54% Edge::Edge 0 0% 79.29% 15ms 0.54% tcache_get (inline) 15ms 0.54% 79.82% 15ms 0.54% tcache_get_n (inline) 1ms 0.036% 79.86% 15ms 0.54% vtkPoints::Modified 0 0% 79.86% 15ms 0.54% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 79.86% 14ms 0.5% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.036% 79.89% 14ms 0.5% Cell::GetCellId 0 0% 79.89% 14ms 0.5% CellIdWriter::GetCellDataForVtkOutput 0 0% 79.89% 14ms 0.5% Edge::SetNodes (inline) 0 0% 79.89% 14ms 0.5% MutableElement::MutableElement 1ms 0.036% 79.93% 14ms 0.5% MutableElement::RegisterWithNodes (inline) 14ms 0.5% 80.43% 14ms 0.5% __memchr_evex 3ms 0.11% 80.54% 14ms 0.5% _dl_runtime_resolve_xsavec 0 0% 80.54% 14ms 0.5% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.071% 80.61% 14ms 0.5% std::basic_filebuf::_M_terminate_output 0 0% 80.61% 14ms 0.5% std::basic_filebuf::close 1ms 0.036% 80.64% 14ms 0.5% std::less::operator() (inline) 0 0% 80.64% 14ms 0.5% vtkDataArray::ComputeRange 0 0% 80.64% 14ms 0.5% vtkDataArrayPrivate::DoComputeVectorRange 14ms 0.5% 81.14% 14ms 0.5% vtkObjectBase::Delete