File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4192ms, 81.21% of 5162ms total Dropped 751 nodes (cum <= 25.81ms) flat flat% sum% cum cum% 0 0% 0% 5030ms 97.44% __libc_start_call_main 0 0% 0% 5030ms 97.44% __libc_start_main_impl 0 0% 0% 5030ms 97.44% _start 0 0% 0% 5015ms 97.15% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5015ms 97.15% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5015ms 97.15% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5015ms 97.15% main 0 0% 0% 4980ms 96.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4980ms 96.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4980ms 96.47% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4969ms 96.26% AbstractCellBasedSimulation::Solve 0 0% 0% 4582ms 88.76% AbstractCellPopulation::WriteResultsToFiles 8ms 0.15% 0.15% 4359ms 84.44% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.15% 2239ms 43.37% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.077% 0.23% 1998ms 38.71% VertexMeshWriter::MakeVtkMesh 1ms 0.019% 0.25% 1421ms 27.53% vtkPolygon::New 3ms 0.058% 0.31% 1415ms 27.41% vtkPolygon::vtkPolygon 7ms 0.14% 0.45% 1017ms 19.70% vtkCell::vtkCell 3ms 0.058% 0.5% 818ms 15.85% vtkPoints::New 10ms 0.19% 0.7% 783ms 15.17% vtkPoints::vtkPoints 44ms 0.85% 1.55% 781ms 15.13% operator new 0 0% 1.55% 759ms 14.70% VertexMeshWriter::WriteFiles 1ms 0.019% 1.57% 733ms 14.20% std::ostream::operator<< (inline) 306ms 5.93% 7.50% 732ms 14.18% __GI___libc_malloc 77ms 1.49% 8.99% 729ms 14.12% std::ostream::_M_insert 4ms 0.077% 9.07% 692ms 13.41% vtkQuad::New 5ms 0.097% 9.16% 684ms 13.25% vtkQuad::vtkQuad 0 0% 9.16% 634ms 12.28% vtkLine::New 7ms 0.14% 9.30% 616ms 11.93% vtkLine::vtkLine 4ms 0.077% 9.38% 599ms 11.60% vtkTriangle::New 119ms 2.31% 11.68% 584ms 11.31% __GI___libc_free 37ms 0.72% 12.40% 583ms 11.29% std::num_put::_M_insert_float 3ms 0.058% 12.46% 583ms 11.29% vtkTriangle::vtkTriangle 4ms 0.077% 12.53% 518ms 10.03% vtkPolygon::~vtkPolygon 0 0% 12.53% 498ms 9.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 12.53% 498ms 9.65% vtkXMLWriterBase::Write 0 0% 12.53% 496ms 9.61% vtkDemandDrivenPipeline::ProcessRequest 0 0% 12.53% 494ms 9.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.53% 494ms 9.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.53% 493ms 9.55% vtkCompositeDataPipeline::ExecuteData 0 0% 12.53% 491ms 9.51% vtkExecutive::CallAlgorithm 1ms 0.019% 12.55% 490ms 9.49% vtkXMLUnstructuredDataWriter::ProcessRequest 10ms 0.19% 12.75% 481ms 9.32% std::__cxx11::collate::do_transform 18ms 0.35% 13.10% 477ms 9.24% vtkPoints::SetDataType 312ms 6.04% 19.14% 450ms 8.72% _int_free 5ms 0.097% 19.24% 444ms 8.60% ___vsnprintf 2ms 0.039% 19.28% 441ms 8.54% __vsnprintf_internal (inline) 43ms 0.83% 20.11% 429ms 8.31% __printf_buffer 0 0% 20.11% 427ms 8.27% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 20.11% 427ms 8.27% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 7ms 0.14% 20.24% 412ms 7.98% vtkCell::~vtkCell 62ms 1.20% 21.45% 399ms 7.73% std::__new_allocator::allocate (inline) 0 0% 21.45% 396ms 7.67% std::allocator_traits::allocate (inline) 0 0% 21.45% 390ms 7.56% vtkXMLWriter::WriteBinaryData 0 0% 21.45% 387ms 7.50% vtkXMLWriter::WriteBinaryDataInternal 2ms 0.039% 21.48% 386ms 7.48% vtkXMLWriter::WriteBinaryDataBlock 0 0% 21.48% 377ms 7.30% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.058% 21.54% 377ms 7.30% PottsBasedCellPopulation::UpdateCellLocations 0 0% 21.54% 372ms 7.21% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 222ms 4.30% 25.84% 358ms 6.94% _int_malloc 1ms 0.019% 25.86% 357ms 6.92% __printf_fp_spec (inline) 18ms 0.35% 26.21% 356ms 6.90% __printf_fp_l_buffer 32ms 0.62% 26.83% 356ms 6.90% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 157ms 3.04% 29.87% 326ms 6.32% __printf_fp_buffer_1 6ms 0.12% 29.99% 307ms 5.95% std::__new_allocator::deallocate (inline) 1ms 0.019% 30.01% 306ms 5.93% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 30.01% 301ms 5.83% VtkMeshWriter::WriteFiles 0 0% 30.01% 299ms 5.79% std::allocator_traits::deallocate (inline) 0 0% 30.01% 291ms 5.64% vtkXMLWriter::WritePointsAppendedData 7ms 0.14% 30.14% 272ms 5.27% vtkPoints::~vtkPoints 0 0% 30.14% 270ms 5.23% std::set::set (inline) 9ms 0.17% 30.32% 269ms 5.21% std::_Rb_tree::_Rb_tree 0 0% 30.32% 263ms 5.09% std::_Rb_tree::_M_create_node (inline) 20ms 0.39% 30.71% 263ms 5.09% vtkObject::vtkObject 0 0% 30.71% 251ms 4.86% std::_Rb_tree::_M_get_node (inline) 9ms 0.17% 30.88% 246ms 4.77% vtkQuad::~vtkQuad 2ms 0.039% 30.92% 236ms 4.57% vtkTriangle::~vtkTriangle 0 0% 30.92% 234ms 4.53% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.23% 31.15% 224ms 4.34% std::_Rb_tree::_M_copy (inline) 0 0% 31.15% 223ms 4.32% vtkLine::GetParametricCenter 23ms 0.45% 31.60% 219ms 4.24% vtkObject::Modified 29ms 0.56% 32.16% 211ms 4.09% std::_Rb_tree::_M_clone_node (inline) 0 0% 32.16% 209ms 4.05% VertexMesh::~VertexMesh 0 0% 32.16% 207ms 4.01% vtkXMLWriter::WriteCompressionBlock 2ms 0.039% 32.20% 205ms 3.97% vtkFloatArray::New 9ms 0.17% 32.37% 200ms 3.87% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.097% 32.47% 200ms 3.87% vtkTypeFloat64Array::~vtkTypeFloat64Array 52ms 1.01% 33.48% 199ms 3.86% std::_Rb_tree::_M_erase 0 0% 33.48% 198ms 3.84% vtkDataCompressor::Compress 0 0% 33.48% 196ms 3.80% compress2 0 0% 33.48% 196ms 3.80% vtkZLibDataCompressor::CompressBuffer 47ms 0.91% 34.39% 195ms 3.78% crc32 0 0% 34.39% 195ms 3.78% deflate 4ms 0.077% 34.46% 193ms 3.74% vtkFloatArray::vtkFloatArray 129ms 2.50% 36.96% 189ms 3.66% malloc_consolidate 188ms 3.64% 40.60% 188ms 3.64% vtkTimeStamp::Modified 1ms 0.019% 40.62% 186ms 3.60% VertexMesh::VertexMesh 0 0% 40.62% 184ms 3.56% NodesOnlyMesh::ConstructNodesWithoutMesh 3ms 0.058% 40.68% 183ms 3.55% vtkBase64OutputStream::Write 1ms 0.019% 40.70% 182ms 3.53% std::vector::~vector (inline) 4ms 0.077% 40.78% 179ms 3.47% vtkIdList::AllocateInternal 7ms 0.14% 40.91% 177ms 3.43% std::_Vector_base::_M_deallocate (inline) 15ms 0.29% 41.20% 176ms 3.41% vtkBase64OutputStream::EncodeTriplet 1ms 0.019% 41.22% 170ms 3.29% VertexMesh::GenerateEdgesFromElements (inline) 10ms 0.19% 41.42% 169ms 3.27% MutableElement::BuildEdges 1ms 0.019% 41.44% 167ms 3.24% vtkDoubleArray::vtkDoubleArray 3ms 0.058% 41.50% 164ms 3.18% vtkDataArray::CreateDataArray 1ms 0.019% 41.51% 161ms 3.12% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 131ms 2.54% 44.05% 160ms 3.10% vtkObjectBase::UnRegisterInternal 8ms 0.15% 44.21% 158ms 3.06% std::vector::_M_default_append 2ms 0.039% 44.25% 156ms 3.02% vtkTypeFloat64Array::New 0 0% 44.25% 154ms 2.98% std::set::~set (inline) 0 0% 44.25% 152ms 2.94% NodeLocationWriter::VisitAnyPopulation 0 0% 44.25% 146ms 2.83% std::_Rb_tree::_M_drop_node (inline) 0 0% 44.25% 145ms 2.81% std::_Vector_base::_M_allocate (inline) 4ms 0.077% 44.32% 143ms 2.77% EdgeHelper::GetEdgeFromNodes 138ms 2.67% 47.00% 142ms 2.75% [libz.so.1.3] 1ms 0.019% 47.02% 142ms 2.75% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 47.02% 141ms 2.73% EdgeHelper::~EdgeHelper (inline) 0 0% 47.02% 138ms 2.67% std::_Vector_base::~_Vector_base (inline) 0 0% 47.02% 129ms 2.50% vtkIdList::Allocate 128ms 2.48% 49.50% 128ms 2.48% [libvtkCommonCore-9.3.so.9.3] 0 0% 49.50% 128ms 2.48% std::_Rb_tree::_M_put_node (inline) 39ms 0.76% 50.25% 123ms 2.38% std::ostream::write 0 0% 50.25% 122ms 2.36% PottsMesh::GetMooreNeighbouringNodeIndices 41ms 0.79% 51.05% 112ms 2.17% vtkTypeFloat64Array::PrintSelf 54ms 1.05% 52.09% 108ms 2.09% hack_digit 4ms 0.077% 52.17% 106ms 2.05% std::map::operator[] (partial-inline) 0 0% 52.17% 106ms 2.05% tbb::detail::r1::parallel_pipeline 5ms 0.097% 52.27% 104ms 2.01% vtkFloatArray::~vtkFloatArray 0 0% 52.27% 103ms 2.00% clone3 0 0% 52.27% 103ms 2.00% start_thread 34ms 0.66% 52.93% 102ms 1.98% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.019% 52.94% 98ms 1.90% Cell::HasCellProperty (inline) 98ms 1.90% 54.84% 98ms 1.90% vtkObjectBase::vtkObjectBase 1ms 0.019% 54.86% 97ms 1.88% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.039% 54.90% 97ms 1.88% CellPropertyCollection::HasProperty 1ms 0.019% 54.92% 97ms 1.88% tbb::detail::r1::reset 1ms 0.019% 54.94% 96ms 1.86% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 62ms 1.20% 56.14% 90ms 1.74% tbb::detail::r1::wait_bounded_queue_monitor 4ms 0.077% 56.22% 89ms 1.72% AbstractCellProperty::IsType (inline) 4ms 0.077% 56.30% 89ms 1.72% _int_free_maybe_consolidate 1ms 0.019% 56.32% 86ms 1.67% vtkDataArray::vtkDataArray 36ms 0.7% 57.01% 85ms 1.65% std::__ostream_insert 2ms 0.039% 57.05% 85ms 1.65% std::vector::push_back (inline) 84ms 1.63% 58.68% 84ms 1.63% __strcmp_evex 0 0% 58.68% 83ms 1.61% AbstractCellProperty::IsSubType (inline) 3ms 0.058% 58.74% 83ms 1.61% vtkAbstractArray::vtkAbstractArray 82ms 1.59% 60.33% 82ms 1.59% unlink_chunk 1ms 0.019% 60.34% 81ms 1.57% std::operator<< (inline) 2ms 0.039% 60.38% 81ms 1.57% vtkIdList::New 43ms 0.83% 61.22% 80ms 1.55% std::basic_filebuf::xsputn 0 0% 61.22% 80ms 1.55% std::set::insert (inline) 0 0% 61.22% 80ms 1.55% vtkXMLWriter::WritePointDataAppendedData 21ms 0.41% 61.62% 79ms 1.53% __dynamic_cast 53ms 1.03% 62.65% 79ms 1.53% std::basic_streambuf::xsputn 1ms 0.019% 62.67% 78ms 1.51% std::_Rb_tree::_M_insert_unique 20ms 0.39% 63.06% 77ms 1.49% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.039% 63.10% 76ms 1.47% vtkDoubleArray::~vtkDoubleArray 8ms 0.15% 63.25% 73ms 1.41% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 63.25% 71ms 1.38% NodesOnlyMesh::SetUpBoxCollection 3ms 0.058% 63.31% 70ms 1.36% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 63.31% 68ms 1.32% VertexMesh::Clear 10ms 0.19% 63.50% 68ms 1.32% std::_Rb_tree::_M_insert_ (inline) 0 0% 63.50% 66ms 1.28% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 66ms 1.28% 64.78% 66ms 1.28% [libchaste_cell_based.so] 0 0% 64.78% 65ms 1.26% NodesOnlyMesh::~NodesOnlyMesh 0 0% 64.78% 65ms 1.26% boost::numeric::ublas::vector_assign (inline) 0 0% 64.78% 65ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 64.78% 65ms 1.26% std::map::lower_bound (inline) 6ms 0.12% 64.90% 64ms 1.24% vtkDataArray::~vtkDataArray 4ms 0.077% 64.97% 62ms 1.20% std::vector::_M_realloc_insert 1ms 0.019% 64.99% 61ms 1.18% Cell::GetCellProliferativeType 8ms 0.15% 65.15% 61ms 1.18% VertexMeshWriter::GetNextNode 0 0% 65.15% 61ms 1.18% tcache_get (inline) 61ms 1.18% 66.33% 61ms 1.18% tcache_get_n (inline) 6ms 0.12% 66.45% 60ms 1.16% AbstractCellProperty::IsSame 55ms 1.07% 67.51% 55ms 1.07% [libstdc++.so.6.0.33] 35ms 0.68% 68.19% 55ms 1.07% std::_Hashtable::clear 15ms 0.29% 68.48% 54ms 1.05% std::type_info::operator== (inline) 0 0% 68.48% 54ms 1.05% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 52ms 1.01% 69.49% 52ms 1.01% vtkObjectBase::RegisterInternal 0 0% 69.49% 50ms 0.97% std::_Destroy (inline) 0 0% 69.49% 50ms 0.97% std::_Destroy_aux::__destroy (inline) 22ms 0.43% 69.91% 47ms 0.91% boost::numeric::ublas::indexing_vector_assign 46ms 0.89% 70.81% 46ms 0.89% __memcpy_evex_unaligned_erms 0 0% 70.81% 46ms 0.89% std::map::~map (inline) 1ms 0.019% 70.83% 45ms 0.87% vtkDoubleArray::New 13ms 0.25% 71.08% 44ms 0.85% std::num_put::_M_insert_int 1ms 0.019% 71.10% 43ms 0.83% DistributedBoxCollection::SetupLocalBoxesHalfOnly 2ms 0.039% 71.14% 42ms 0.81% std::make_unique (inline) 5ms 0.097% 71.23% 40ms 0.77% vtkIdList::~vtkIdList 0 0% 71.23% 39ms 0.76% PottsMesh::GetVonNeumannNeighbouringNodeIndices 18ms 0.35% 71.58% 38ms 0.74% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 71.58% 37ms 0.72% DistributedBoxCollection::~DistributedBoxCollection 0 0% 71.58% 37ms 0.72% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 71.58% 37ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.58% 36ms 0.7% Cell::GetMutationState 17ms 0.33% 71.91% 36ms 0.7% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.91% 36ms 0.7% DistributedBoxCollection::IsOwned 1ms 0.019% 71.93% 36ms 0.7% VertexElement::~VertexElement 0 0% 71.93% 36ms 0.7% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 71.93% 36ms 0.7% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 71.93% 35ms 0.68% CellProliferativeTypesWriter::GetCellDataForVtkOutput 35ms 0.68% 72.61% 35ms 0.68% __mpn_divrem 0 0% 72.61% 35ms 0.68% boost::detail::shared_count::~shared_count (inline) 32ms 0.62% 73.23% 35ms 0.68% boost::detail::sp_counted_base::release 0 0% 73.23% 35ms 0.68% boost::shared_ptr::~shared_ptr (inline) 4ms 0.077% 73.30% 35ms 0.68% vtkIdList::vtkIdList 6ms 0.12% 73.42% 35ms 0.68% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.019% 73.44% 33ms 0.64% Cell::GetCellId 33ms 0.64% 74.08% 33ms 0.64% std::_Rb_tree_header::_M_reset (inline) 33ms 0.64% 74.72% 33ms 0.64% vtkBase64Utilities::EncodeTriplet 33ms 0.64% 75.36% 33ms 0.64% vtkObject::~vtkObject 33ms 0.64% 76.00% 33ms 0.64% vtkObjectBase::~vtkObjectBase 0 0% 76.00% 32ms 0.62% CxxTest::RealWorldDescription::setUp 0 0% 76.00% 32ms 0.62% PMPI_Init_thread 0 0% 76.00% 32ms 0.62% PetscInitialize 0 0% 76.00% 32ms 0.62% PetscSetup::setUpWorld 0 0% 76.00% 32ms 0.62% PetscSetupUtils::CommonSetup 0 0% 76.00% 32ms 0.62% PetscSetupUtils::InitialisePetsc 0 0% 76.00% 32ms 0.62% _dl_init 0 0% 76.00% 32ms 0.62% call_init (inline) 0 0% 76.00% 32ms 0.62% ompi_mpi_init 32ms 0.62% 76.62% 32ms 0.62% std::_Rb_tree::_S_right (inline) 32ms 0.62% 77.24% 32ms 0.62% std::_Rb_tree_increment 12ms 0.23% 77.47% 32ms 0.62% std::__new_allocator::construct (inline) 0 0% 77.47% 32ms 0.62% std::allocator_traits::construct (inline) 29ms 0.56% 78.03% 32ms 0.62% vtkObjectBase::Delete 4ms 0.077% 78.11% 31ms 0.6% VertexMeshWriter::GetNextElement 31ms 0.6% 78.71% 31ms 0.6% tcache_put (inline) 0 0% 78.71% 30ms 0.58% CellIdWriter::GetCellDataForVtkOutput 0 0% 78.71% 30ms 0.58% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.019% 78.73% 30ms 0.58% std::default_delete::operator() (inline) 25ms 0.48% 79.21% 30ms 0.58% std::num_put::do_put 0 0% 79.21% 30ms 0.58% std::unique_ptr::~unique_ptr (inline) 1ms 0.019% 79.23% 29ms 0.56% Node::GetPoint 0 0% 79.23% 29ms 0.56% _dl_start_user 0 0% 79.23% 29ms 0.56% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.039% 79.27% 29ms 0.56% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 79.27% 29ms 0.56% std::basic_filebuf::open 0 0% 79.27% 28ms 0.54% 1ms 0.019% 79.29% 28ms 0.54% Node::SetRadius 0 0% 79.29% 28ms 0.54% NodesOnlyMesh::Clear (inline) 1ms 0.019% 79.31% 28ms 0.54% std::__basic_file::open 0 0% 79.31% 27ms 0.52% Edge::AddElement 0 0% 79.31% 27ms 0.52% MutableElement::~MutableElement 0 0% 79.31% 27ms 0.52% Node::ConstructNodeAttributes (inline) 1ms 0.019% 79.33% 27ms 0.52% VtkMeshWriter::MakeVtkMesh 14ms 0.27% 79.60% 27ms 0.52% __printf_buffer_write 1ms 0.019% 79.62% 27ms 0.52% std::less::operator() (inline) 0 0% 79.62% 27ms 0.52% vtkDataArray::ComputeRange 0 0% 79.62% 26ms 0.5% _IO_new_fopen 26ms 0.5% 80.12% 26ms 0.5% __GI___uselocale 26ms 0.5% 80.63% 26ms 0.5% __GI___writev 0 0% 80.63% 26ms 0.5% __fopen_internal (inline) 0 0% 80.63% 26ms 0.5% std::__basic_file::xsputn_2 26ms 0.5% 81.13% 26ms 0.5% std::operator< (inline) 4ms 0.077% 81.21% 26ms 0.5% vtkAOSDataArrayTemplate::InsertTuple