File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4230ms, 81.46% of 5193ms total Dropped 763 nodes (cum <= 25.96ms) flat flat% sum% cum cum% 0 0% 0% 5036ms 96.98% __libc_start_call_main 0 0% 0% 5036ms 96.98% __libc_start_main_impl 0 0% 0% 5036ms 96.98% _start 0 0% 0% 5018ms 96.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5018ms 96.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5018ms 96.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5018ms 96.63% main 0 0% 0% 4987ms 96.03% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4987ms 96.03% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4987ms 96.03% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4977ms 95.84% AbstractCellBasedSimulation::Solve 0 0% 0% 4602ms 88.62% AbstractCellPopulation::WriteResultsToFiles 11ms 0.21% 0.21% 4367ms 84.09% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.21% 2240ms 43.13% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.12% 0.33% 1993ms 38.38% VertexMeshWriter::MakeVtkMesh 0 0% 0.33% 1422ms 27.38% vtkPolygon::New 7ms 0.13% 0.46% 1419ms 27.33% vtkPolygon::vtkPolygon 2ms 0.039% 0.5% 1028ms 19.80% vtkCell::vtkCell 2ms 0.039% 0.54% 836ms 16.10% vtkPoints::New 7ms 0.13% 0.67% 805ms 15.50% vtkPoints::vtkPoints 30ms 0.58% 1.25% 768ms 14.79% operator new 3ms 0.058% 1.31% 762ms 14.67% VertexMeshWriter::WriteFiles 303ms 5.83% 7.14% 730ms 14.06% __GI___libc_malloc 2ms 0.039% 7.18% 722ms 13.90% std::ostream::operator<< (inline) 55ms 1.06% 8.24% 720ms 13.86% std::ostream::_M_insert 8ms 0.15% 8.40% 670ms 12.90% vtkQuad::New 2ms 0.039% 8.43% 657ms 12.65% vtkLine::New 6ms 0.12% 8.55% 657ms 12.65% vtkQuad::vtkQuad 11ms 0.21% 8.76% 634ms 12.21% vtkLine::vtkLine 124ms 2.39% 11.15% 630ms 12.13% __GI___libc_free 2ms 0.039% 11.19% 618ms 11.90% vtkTriangle::New 1ms 0.019% 11.21% 602ms 11.59% vtkTriangle::vtkTriangle 40ms 0.77% 11.98% 590ms 11.36% std::num_put::_M_insert_float 0 0% 11.98% 495ms 9.53% vtkStreamingDemandDrivenPipeline::Update 0 0% 11.98% 495ms 9.53% vtkXMLWriterBase::Write 0 0% 11.98% 494ms 9.51% vtkDemandDrivenPipeline::ProcessRequest 3ms 0.058% 12.04% 492ms 9.47% vtkPolygon::~vtkPolygon 0 0% 12.04% 491ms 9.46% vtkExecutive::CallAlgorithm 0 0% 12.04% 491ms 9.46% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.04% 491ms 9.46% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 12.04% 490ms 9.44% vtkDemandDrivenPipeline::ExecuteData 332ms 6.39% 18.43% 489ms 9.42% _int_free 0 0% 18.43% 489ms 9.42% vtkCompositeDataPipeline::ExecuteData 11ms 0.21% 18.64% 484ms 9.32% std::__cxx11::collate::do_transform 24ms 0.46% 19.10% 484ms 9.32% vtkPoints::SetDataType 4ms 0.077% 19.18% 439ms 8.45% ___vsnprintf 1ms 0.019% 19.20% 435ms 8.38% __vsnprintf_internal (inline) 45ms 0.87% 20.07% 432ms 8.32% __printf_buffer 0 0% 20.07% 430ms 8.28% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 20.07% 430ms 8.28% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 20.07% 394ms 7.59% vtkXMLWriter::WriteBinaryData 9ms 0.17% 20.24% 392ms 7.55% vtkCell::~vtkCell 1ms 0.019% 20.26% 388ms 7.47% vtkXMLWriter::WriteBinaryDataInternal 0 0% 20.26% 387ms 7.45% vtkXMLWriter::WriteBinaryDataBlock 56ms 1.08% 21.34% 378ms 7.28% std::__new_allocator::allocate (inline) 0 0% 21.34% 377ms 7.26% std::allocator_traits::allocate (inline) 0 0% 21.34% 366ms 7.05% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 21.34% 362ms 6.97% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.019% 21.36% 362ms 6.97% PottsBasedCellPopulation::UpdateCellLocations 1ms 0.019% 21.37% 360ms 6.93% __printf_fp_spec (inline) 21ms 0.4% 21.78% 359ms 6.91% __printf_fp_l_buffer 33ms 0.64% 22.41% 356ms 6.86% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 204ms 3.93% 26.34% 333ms 6.41% _int_malloc 167ms 3.22% 29.56% 322ms 6.20% __printf_fp_buffer_1 3ms 0.058% 29.62% 322ms 6.20% std::__new_allocator::deallocate (inline) 0 0% 29.62% 320ms 6.16% std::allocator_traits::deallocate (inline) 1ms 0.019% 29.64% 309ms 5.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 29.64% 303ms 5.83% VtkMeshWriter::WriteFiles 0 0% 29.64% 277ms 5.33% vtkXMLWriter::WritePointsAppendedData 0 0% 29.64% 273ms 5.26% std::_Rb_tree::_M_create_node (inline) 24ms 0.46% 30.10% 269ms 5.18% vtkObject::vtkObject 0 0% 30.10% 266ms 5.12% std::set::set (inline) 15ms 0.29% 30.39% 262ms 5.05% std::_Rb_tree::_Rb_tree 0 0% 30.39% 254ms 4.89% std::_Rb_tree::_M_get_node (inline) 2ms 0.039% 30.43% 249ms 4.79% vtkPoints::~vtkPoints 0 0% 30.43% 232ms 4.47% std::_Rb_tree::_Alloc_node::operator() (inline) 36ms 0.69% 31.12% 226ms 4.35% vtkObject::Modified 1ms 0.019% 31.14% 224ms 4.31% vtkTriangle::~vtkTriangle 0 0% 31.14% 218ms 4.20% vtkLine::GetParametricCenter 11ms 0.21% 31.35% 217ms 4.18% std::_Rb_tree::_M_copy (inline) 0 0% 31.35% 216ms 4.16% VertexMesh::~VertexMesh 1ms 0.019% 31.37% 215ms 4.14% vtkFloatArray::New 4ms 0.077% 31.45% 210ms 4.04% vtkQuad::~vtkQuad 23ms 0.44% 31.89% 203ms 3.91% std::_Rb_tree::_M_clone_node (inline) 13ms 0.25% 32.14% 202ms 3.89% std::_Rb_tree::~_Rb_tree (inline) 0 0% 32.14% 201ms 3.87% vtkXMLWriter::WriteCompressionBlock 39ms 0.75% 32.89% 200ms 3.85% std::_Rb_tree::_M_erase 1ms 0.019% 32.91% 197ms 3.79% vtkFloatArray::vtkFloatArray 0 0% 32.91% 192ms 3.70% compress2 3ms 0.058% 32.97% 192ms 3.70% vtkBase64OutputStream::Write 0 0% 32.97% 192ms 3.70% vtkDataCompressor::Compress 0 0% 32.97% 192ms 3.70% vtkZLibDataCompressor::CompressBuffer 46ms 0.89% 33.85% 189ms 3.64% crc32 0 0% 33.85% 189ms 3.64% deflate 2ms 0.039% 33.89% 189ms 3.64% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 33.89% 185ms 3.56% VertexMesh::VertexMesh 19ms 0.37% 34.26% 184ms 3.54% vtkBase64OutputStream::EncodeTriplet 181ms 3.49% 37.74% 181ms 3.49% vtkTimeStamp::Modified 128ms 2.46% 40.21% 180ms 3.47% malloc_consolidate 0 0% 40.21% 177ms 3.41% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.039% 40.25% 176ms 3.39% std::_Vector_base::_M_deallocate (inline) 0 0% 40.25% 176ms 3.39% std::vector::~vector (inline) 5ms 0.096% 40.34% 174ms 3.35% MutableElement::BuildEdges 0 0% 40.34% 174ms 3.35% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 40.34% 173ms 3.33% vtkDataArray::CreateDataArray 1ms 0.019% 40.36% 168ms 3.24% vtkTypeFloat64Array::New 1ms 0.019% 40.38% 163ms 3.14% vtkDoubleArray::vtkDoubleArray 0 0% 40.38% 159ms 3.06% std::_Rb_tree::_M_drop_node (inline) 6ms 0.12% 40.50% 158ms 3.04% vtkIdList::AllocateInternal 0 0% 40.50% 157ms 3.02% std::set::~set (inline) 0 0% 40.50% 156ms 3.00% NodeLocationWriter::VisitAnyPopulation 3ms 0.058% 40.55% 148ms 2.85% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 3ms 0.058% 40.61% 148ms 2.85% EdgeHelper::GetEdgeFromNodes 0 0% 40.61% 146ms 2.81% EdgeHelper::~EdgeHelper (inline) 0 0% 40.61% 146ms 2.81% std::_Rb_tree::_M_put_node (inline) 58ms 1.12% 41.73% 144ms 2.77% std::ostream::write 120ms 2.31% 44.04% 144ms 2.77% vtkObjectBase::UnRegisterInternal 0 0% 44.04% 142ms 2.73% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 44.04% 137ms 2.64% std::_Vector_base::~_Vector_base (inline) 135ms 2.60% 46.64% 136ms 2.62% [libz.so.1.3] 10ms 0.19% 46.83% 135ms 2.60% std::vector::_M_default_append 0 0% 46.83% 133ms 2.56% tbb::detail::r1::parallel_pipeline 0 0% 46.83% 132ms 2.54% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 46.83% 126ms 2.43% clone3 0 0% 46.83% 126ms 2.43% start_thread 0 0% 46.83% 123ms 2.37% std::_Vector_base::_M_allocate (inline) 4ms 0.077% 46.91% 117ms 2.25% tbb::detail::r1::reset 115ms 2.21% 49.12% 115ms 2.21% [libvtkCommonCore-9.3.so.9.3] 4ms 0.077% 49.20% 114ms 2.20% vtkFloatArray::~vtkFloatArray 5ms 0.096% 49.30% 112ms 2.16% std::map::operator[] (partial-inline) 0 0% 49.30% 112ms 2.16% vtkIdList::Allocate 2ms 0.039% 49.34% 110ms 2.12% CellPropertyCollection::GetPropertiesType (inline) 49ms 0.94% 50.28% 105ms 2.02% vtkTypeFloat64Array::PrintSelf 1ms 0.019% 50.30% 103ms 1.98% vtkIdList::New 53ms 1.02% 51.32% 99ms 1.91% hack_digit 99ms 1.91% 53.23% 99ms 1.91% vtkObjectBase::vtkObjectBase 53ms 1.02% 54.25% 98ms 1.89% std::basic_filebuf::xsputn 66ms 1.27% 55.52% 98ms 1.89% tbb::detail::r1::wait_bounded_queue_monitor 33ms 0.64% 56.15% 97ms 1.87% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 56.15% 96ms 1.85% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 7ms 0.13% 56.29% 96ms 1.85% _int_free_maybe_consolidate 52ms 1.00% 57.29% 95ms 1.83% std::__ostream_insert 0 0% 57.29% 94ms 1.81% std::operator<< (inline) 0 0% 57.29% 92ms 1.77% vtkDataArray::vtkDataArray 1ms 0.019% 57.31% 91ms 1.75% AbstractCellProperty::IsSubType (inline) 1ms 0.019% 57.33% 91ms 1.75% vtkDoubleArray::~vtkDoubleArray 7ms 0.13% 57.46% 90ms 1.73% vtkAbstractArray::vtkAbstractArray 32ms 0.62% 58.08% 89ms 1.71% __dynamic_cast 0 0% 58.08% 89ms 1.71% vtkXMLWriter::WritePointDataAppendedData 0 0% 58.08% 78ms 1.50% std::vector::push_back (inline) 0 0% 58.08% 77ms 1.48% tcache_get (inline) 77ms 1.48% 59.56% 77ms 1.48% tcache_get_n (inline) 0 0% 59.56% 75ms 1.44% Cell::HasCellProperty (inline) 3ms 0.058% 59.62% 75ms 1.44% CellPropertyCollection::HasProperty 3ms 0.058% 59.68% 74ms 1.42% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.019% 59.70% 72ms 1.39% Cell::GetCellProliferativeType 3ms 0.058% 59.75% 70ms 1.35% AbstractCellProperty::IsType (inline) 1ms 0.019% 59.77% 70ms 1.35% VertexMesh::Clear 9ms 0.17% 59.95% 70ms 1.35% VertexMeshWriter::GetNextNode 69ms 1.33% 61.27% 69ms 1.33% __strcmp_evex 68ms 1.31% 62.58% 68ms 1.31% [libstdc++.so.6.0.33] 1ms 0.019% 62.60% 68ms 1.31% std::_Rb_tree::_M_insert_unique 0 0% 62.60% 68ms 1.31% std::set::insert (inline) 16ms 0.31% 62.91% 67ms 1.29% std::_Rb_tree::_M_lower_bound (inline) 66ms 1.27% 64.18% 66ms 1.27% unlink_chunk 0 0% 64.18% 65ms 1.25% NodesOnlyMesh::SetUpBoxCollection 17ms 0.33% 64.51% 65ms 1.25% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 64.51% 63ms 1.21% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 62ms 1.19% 65.70% 62ms 1.19% [libchaste_cell_based.so] 0 0% 65.70% 61ms 1.17% NodesOnlyMesh::~NodesOnlyMesh 41ms 0.79% 66.49% 61ms 1.17% std::basic_streambuf::xsputn 9ms 0.17% 66.67% 61ms 1.17% vtkDataArray::~vtkDataArray 6ms 0.12% 66.78% 59ms 1.14% std::_Rb_tree::_M_insert_ (inline) 2ms 0.039% 66.82% 56ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.019% 66.84% 55ms 1.06% std::vector::_M_realloc_insert 53ms 1.02% 67.86% 53ms 1.02% tcache_put (inline) 15ms 0.29% 68.15% 52ms 1.00% std::num_put::_M_insert_int 0 0% 68.15% 51ms 0.98% std::_Rb_tree::lower_bound (inline) 0 0% 68.15% 51ms 0.98% std::map::lower_bound (inline) 11ms 0.21% 68.36% 49ms 0.94% AbstractCellProperty::IsSame 0 0% 68.36% 49ms 0.94% boost::numeric::ublas::vector_assign (inline) 0 0% 68.36% 47ms 0.91% std::_Destroy (inline) 0 0% 68.36% 47ms 0.91% std::_Destroy_aux::__destroy (inline) 13ms 0.25% 68.61% 45ms 0.87% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.61% 45ms 0.87% DistributedBoxCollection::IsOwned 0 0% 68.61% 45ms 0.87% std::map::~map (inline) 4ms 0.077% 68.69% 45ms 0.87% vtkIdList::~vtkIdList 0 0% 68.69% 44ms 0.85% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 4ms 0.077% 68.77% 44ms 0.85% vtkIdList::vtkIdList 25ms 0.48% 69.25% 41ms 0.79% std::_Hashtable::clear 0 0% 69.25% 41ms 0.79% std::_Rb_tree::_Auto_node::_Auto_node (inline) 19ms 0.37% 69.61% 41ms 0.79% std::__new_allocator::construct (inline) 0 0% 69.61% 41ms 0.79% std::allocator_traits::construct (inline) 41ms 0.79% 70.40% 41ms 0.79% vtkObjectBase::RegisterInternal 7ms 0.13% 70.54% 41ms 0.79% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 70.54% 40ms 0.77% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 70.54% 40ms 0.77% PottsMesh::GetVonNeumannNeighbouringNodeIndices 20ms 0.39% 70.92% 40ms 0.77% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 70.92% 40ms 0.77% std::make_unique (inline) 39ms 0.75% 71.67% 39ms 0.75% __memcpy_evex_unaligned_erms 10ms 0.19% 71.87% 38ms 0.73% std::type_info::operator== (inline) 3ms 0.058% 71.92% 38ms 0.73% tbb::detail::r1::cancel_group_execution 0 0% 71.92% 38ms 0.73% vtk::detail::smp::vtkSMPToolsImplForTBB 4ms 0.077% 72.00% 38ms 0.73% vtkAOSDataArrayTemplate::InsertTuple 35ms 0.67% 72.67% 38ms 0.73% vtkObject::~vtkObject 10ms 0.19% 72.87% 37ms 0.71% boost::numeric::ublas::indexing_vector_assign 4ms 0.077% 72.94% 37ms 0.71% vtkDataArrayPrivate::DoComputeVectorRange 36ms 0.69% 73.64% 36ms 0.69% boost::numeric::ublas::c_vector::operator() 0 0% 73.64% 34ms 0.65% boost::detail::shared_count::~shared_count (inline) 0 0% 73.64% 34ms 0.65% boost::shared_ptr::~shared_ptr (inline) 0 0% 73.64% 33ms 0.64% _dl_init 32ms 0.62% 74.25% 33ms 0.64% boost::detail::sp_counted_base::release 0 0% 74.25% 33ms 0.64% call_init (inline) 0 0% 74.25% 33ms 0.64% std::less::operator() (inline) 33ms 0.64% 74.89% 33ms 0.64% std::operator< (inline) 2ms 0.039% 74.93% 32ms 0.62% AbstractMesh::NodeIterator::IsAllowedNode (inline) 0 0% 74.93% 32ms 0.62% AbstractMesh::NodeIterator::operator++ (inline) 0 0% 74.93% 32ms 0.62% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 74.93% 32ms 0.62% DistributedBoxCollection::~DistributedBoxCollection 32ms 0.62% 75.54% 32ms 0.62% Node::GetIndex 0 0% 75.54% 32ms 0.62% NodesOnlyMesh::ClearBoxCollection (inline) 1ms 0.019% 75.56% 32ms 0.62% VertexElement::VertexElement 0 0% 75.56% 32ms 0.62% VertexElement::~VertexElement 0 0% 75.56% 31ms 0.6% Cell::GetCellId 0 0% 75.56% 31ms 0.6% MutableElement::MutableElement 1ms 0.019% 75.58% 31ms 0.6% Node::AddElement 31ms 0.6% 76.18% 31ms 0.6% [libchaste_mesh.so] 31ms 0.6% 76.78% 31ms 0.6% __mpn_divrem 0 0% 76.78% 31ms 0.6% _dl_start_user 0 0% 76.78% 31ms 0.6% std::__basic_file::xsputn_2 7ms 0.13% 76.91% 31ms 0.6% vtk::detail::smp::vtkSMPToolsImpl::For 7ms 0.13% 77.05% 31ms 0.6% vtkAOSDataArrayTemplate::AllocateTuples 2ms 0.039% 77.08% 30ms 0.58% Node::GetPoint 0 0% 77.08% 30ms 0.58% VtkMeshWriter::MakeVtkMesh 30ms 0.58% 77.66% 30ms 0.58% __GI___writev 0 0% 77.66% 30ms 0.58% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.019% 77.68% 30ms 0.58% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 77.68% 30ms 0.58% vtkDataArray::ComputeRange 0 0% 77.68% 30ms 0.58% vtkDoubleArray::New 28ms 0.54% 78.22% 30ms 0.58% vtkObjectBase::Delete 30ms 0.58% 78.80% 30ms 0.58% vtkObjectBase::~vtkObjectBase 0 0% 78.80% 29ms 0.56% CellIdWriter::GetCellDataForVtkOutput 0 0% 78.80% 29ms 0.56% NodesOnlyMesh::Clear (inline) 29ms 0.56% 79.36% 29ms 0.56% __GI___uselocale 29ms 0.56% 79.92% 29ms 0.56% __GI_sched_yield 28ms 0.54% 80.45% 28ms 0.54% std::_Rb_tree_header::_M_reset (inline) 0 0% 80.45% 28ms 0.54% std::default_delete::operator() (inline) 24ms 0.46% 80.92% 28ms 0.54% std::num_put::do_put 0 0% 80.92% 28ms 0.54% std::unique_ptr::~unique_ptr (inline) 0 0% 80.92% 27ms 0.52% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 80.92% 27ms 0.52% CxxTest::RealWorldDescription::setUp 0 0% 80.92% 27ms 0.52% PMPI_Init_thread 0 0% 80.92% 27ms 0.52% PetscInitialize 0 0% 80.92% 27ms 0.52% PetscSetup::setUpWorld 0 0% 80.92% 27ms 0.52% PetscSetupUtils::CommonSetup 0 0% 80.92% 27ms 0.52% PetscSetupUtils::InitialisePetsc 0 0% 80.92% 27ms 0.52% ompi_mpi_init 2ms 0.039% 80.96% 27ms 0.52% vtkDataSet::GetCellTypes 0 0% 80.96% 26ms 0.5% MutableElement::RegisterWithNodes (inline) 26ms 0.5% 81.46% 26ms 0.5% Node::IsDeleted 0 0% 81.46% 26ms 0.5% PottsBasedCellPopulation::AcceptCellWriter