File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4153ms, 78.67% of 5279ms total Dropped 735 nodes (cum <= 26.39ms) flat flat% sum% cum cum% 0 0% 0% 5131ms 97.20% __libc_start_call_main 0 0% 0% 5131ms 97.20% __libc_start_main_impl 0 0% 0% 5131ms 97.20% _start 0 0% 0% 5115ms 96.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5115ms 96.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5115ms 96.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5115ms 96.89% main 0 0% 0% 5083ms 96.29% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5083ms 96.29% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5083ms 96.29% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 5073ms 96.10% AbstractCellBasedSimulation::Solve 0 0% 0% 4683ms 88.71% AbstractCellPopulation::WriteResultsToFiles 14ms 0.27% 0.27% 4439ms 84.09% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.27% 2253ms 42.68% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.095% 0.36% 2011ms 38.09% VertexMeshWriter::MakeVtkMesh 2ms 0.038% 0.4% 1436ms 27.20% vtkPolygon::New 7ms 0.13% 0.53% 1432ms 27.13% vtkPolygon::vtkPolygon 5ms 0.095% 0.63% 1055ms 19.98% vtkCell::vtkCell 4ms 0.076% 0.7% 888ms 16.82% vtkPoints::New 3ms 0.057% 0.76% 853ms 16.16% vtkPoints::vtkPoints 29ms 0.55% 1.31% 791ms 14.98% operator new 2ms 0.038% 1.34% 787ms 14.91% VertexMeshWriter::WriteFiles 337ms 6.38% 7.73% 753ms 14.26% __GI___libc_malloc 0 0% 7.73% 722ms 13.68% std::ostream::operator<< (inline) 48ms 0.91% 8.64% 721ms 13.66% std::ostream::_M_insert 3ms 0.057% 8.69% 676ms 12.81% vtkQuad::New 5ms 0.095% 8.79% 671ms 12.71% vtkQuad::vtkQuad 0 0% 8.79% 642ms 12.16% vtkLine::New 5ms 0.095% 8.88% 627ms 11.88% vtkLine::vtkLine 48ms 0.91% 9.79% 605ms 11.46% std::num_put::_M_insert_float 3ms 0.057% 9.85% 600ms 11.37% vtkTriangle::New 132ms 2.50% 12.35% 597ms 11.31% __GI___libc_free 5ms 0.095% 12.45% 583ms 11.04% vtkTriangle::vtkTriangle 15ms 0.28% 12.73% 509ms 9.64% vtkPoints::SetDataType 0 0% 12.73% 496ms 9.40% vtkDemandDrivenPipeline::ProcessRequest 0 0% 12.73% 496ms 9.40% vtkStreamingDemandDrivenPipeline::Update 0 0% 12.73% 496ms 9.40% vtkXMLWriterBase::Write 0 0% 12.73% 495ms 9.38% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.73% 494ms 9.36% vtkCompositeDataPipeline::ExecuteData 0 0% 12.73% 494ms 9.36% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.73% 494ms 9.36% vtkExecutive::CallAlgorithm 1ms 0.019% 12.75% 492ms 9.32% vtkPolygon::~vtkPolygon 0 0% 12.75% 492ms 9.32% vtkXMLUnstructuredDataWriter::ProcessRequest 13ms 0.25% 12.99% 491ms 9.30% std::__cxx11::collate::do_transform 2ms 0.038% 13.03% 454ms 8.60% ___vsnprintf 1ms 0.019% 13.05% 452ms 8.56% __vsnprintf_internal (inline) 297ms 5.63% 18.68% 450ms 8.52% _int_free 31ms 0.59% 19.27% 449ms 8.51% __printf_buffer 0 0% 19.27% 435ms 8.24% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 19.27% 435ms 8.24% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 72ms 1.36% 20.63% 411ms 7.79% std::__new_allocator::allocate (inline) 0 0% 20.63% 411ms 7.79% std::allocator_traits::allocate (inline) 2ms 0.038% 20.67% 388ms 7.35% vtkCell::~vtkCell 0 0% 20.67% 386ms 7.31% vtkXMLWriter::WriteBinaryData 1ms 0.019% 20.69% 383ms 7.26% vtkXMLWriter::WriteBinaryDataInternal 0 0% 20.69% 382ms 7.24% vtkXMLWriter::WriteBinaryDataBlock 2ms 0.038% 20.72% 377ms 7.14% __printf_fp_spec (inline) 0 0% 20.72% 375ms 7.10% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.057% 20.78% 375ms 7.10% PottsBasedCellPopulation::UpdateCellLocations 15ms 0.28% 21.06% 375ms 7.10% __printf_fp_l_buffer 1ms 0.019% 21.08% 375ms 7.10% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 39ms 0.74% 21.82% 353ms 6.69% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 217ms 4.11% 25.93% 339ms 6.42% _int_malloc 153ms 2.90% 28.83% 330ms 6.25% __printf_fp_buffer_1 0 0% 28.83% 318ms 6.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 28.83% 315ms 5.97% VtkMeshWriter::WriteFiles 3ms 0.057% 28.89% 304ms 5.76% std::__new_allocator::deallocate (inline) 0 0% 28.89% 301ms 5.70% std::allocator_traits::deallocate (inline) 1ms 0.019% 28.91% 283ms 5.36% std::set::set (inline) 14ms 0.27% 29.17% 281ms 5.32% std::_Rb_tree::_Rb_tree 0 0% 29.17% 281ms 5.32% vtkXMLWriter::WritePointsAppendedData 0 0% 29.17% 269ms 5.10% std::_Rb_tree::_M_create_node (inline) 19ms 0.36% 29.53% 260ms 4.93% vtkObject::vtkObject 4ms 0.076% 29.61% 257ms 4.87% vtkPoints::~vtkPoints 0 0% 29.61% 253ms 4.79% std::_Rb_tree::_M_get_node (inline) 0 0% 29.61% 246ms 4.66% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.13% 29.74% 233ms 4.41% std::_Rb_tree::_M_copy (inline) 2ms 0.038% 29.78% 233ms 4.41% vtkQuad::~vtkQuad 30ms 0.57% 30.35% 230ms 4.36% vtkObject::Modified 1ms 0.019% 30.37% 227ms 4.30% vtkFloatArray::New 0 0% 30.37% 223ms 4.22% VertexMesh::~VertexMesh 27ms 0.51% 30.88% 221ms 4.19% std::_Rb_tree::_M_clone_node (inline) 0 0% 30.88% 221ms 4.19% vtkTriangle::~vtkTriangle 2ms 0.038% 30.91% 214ms 4.05% vtkFloatArray::vtkFloatArray 0 0% 30.91% 209ms 3.96% vtkLine::GetParametricCenter 0 0% 30.91% 205ms 3.88% vtkXMLWriter::WriteCompressionBlock 8ms 0.15% 31.07% 200ms 3.79% std::_Rb_tree::~_Rb_tree (inline) 0 0% 31.07% 198ms 3.75% compress2 52ms 0.99% 32.05% 198ms 3.75% std::_Rb_tree::_M_erase 0 0% 32.05% 198ms 3.75% vtkDataCompressor::Compress 0 0% 32.05% 198ms 3.75% vtkZLibDataCompressor::CompressBuffer 53ms 1.00% 33.06% 195ms 3.69% crc32 0 0% 33.06% 195ms 3.69% deflate 193ms 3.66% 36.71% 193ms 3.66% vtkTimeStamp::Modified 130ms 2.46% 39.17% 191ms 3.62% malloc_consolidate 2ms 0.038% 39.21% 190ms 3.60% VertexMesh::VertexMesh 1ms 0.019% 39.23% 190ms 3.60% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.038% 39.27% 181ms 3.43% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 39.27% 181ms 3.43% std::vector::~vector (inline) 4ms 0.076% 39.34% 181ms 3.43% vtkBase64OutputStream::Write 9ms 0.17% 39.52% 180ms 3.41% std::_Vector_base::_M_deallocate (inline) 25ms 0.47% 39.99% 176ms 3.33% vtkBase64OutputStream::EncodeTriplet 146ms 2.77% 42.75% 174ms 3.30% vtkObjectBase::UnRegisterInternal 4ms 0.076% 42.83% 173ms 3.28% vtkIdList::AllocateInternal 7ms 0.13% 42.96% 172ms 3.26% MutableElement::BuildEdges 0 0% 42.96% 172ms 3.26% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.019% 42.98% 164ms 3.11% vtkDataArray::CreateDataArray 0 0% 42.98% 158ms 2.99% std::_Vector_base::_M_allocate (inline) 11ms 0.21% 43.19% 158ms 2.99% std::vector::_M_default_append 0 0% 43.19% 156ms 2.96% std::set::~set (inline) 3ms 0.057% 43.25% 155ms 2.94% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 1ms 0.019% 43.27% 155ms 2.94% NodeLocationWriter::VisitAnyPopulation 5ms 0.095% 43.36% 152ms 2.88% vtkTypeFloat64Array::New 1ms 0.019% 43.38% 151ms 2.86% EdgeHelper::GetEdgeFromNodes 0 0% 43.38% 148ms 2.80% EdgeHelper::~EdgeHelper (inline) 0 0% 43.38% 145ms 2.75% std::_Rb_tree::_M_drop_node (inline) 1ms 0.019% 43.40% 145ms 2.75% std::_Vector_base::~_Vector_base (inline) 0 0% 43.40% 143ms 2.71% vtkDoubleArray::vtkDoubleArray 137ms 2.60% 45.99% 138ms 2.61% [libz.so.1.3] 35ms 0.66% 46.66% 131ms 2.48% std::ostream::write 0 0% 46.66% 130ms 2.46% std::_Rb_tree::_M_put_node (inline) 2ms 0.038% 46.69% 128ms 2.42% PottsMesh::GetMooreNeighbouringNodeIndices 3ms 0.057% 46.75% 128ms 2.42% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.019% 46.77% 127ms 2.41% tbb::detail::r1::parallel_pipeline 2ms 0.038% 46.81% 119ms 2.25% vtkFloatArray::~vtkFloatArray 0 0% 46.81% 116ms 2.20% vtkIdList::Allocate 0 0% 46.81% 115ms 2.18% clone3 0 0% 46.81% 115ms 2.18% start_thread 112ms 2.12% 48.93% 112ms 2.12% [libvtkCommonCore-9.3.so.9.3] 0 0% 48.93% 111ms 2.10% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.019% 48.95% 107ms 2.03% tbb::detail::r1::reset 61ms 1.16% 50.10% 106ms 2.01% std::basic_filebuf::xsputn 9ms 0.17% 50.27% 103ms 1.95% _int_free_maybe_consolidate 1ms 0.019% 50.29% 101ms 1.91% std::vector::push_back (inline) 2ms 0.038% 50.33% 99ms 1.88% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 99ms 1.88% 52.21% 99ms 1.88% __strcmp_evex 55ms 1.04% 53.25% 99ms 1.88% hack_digit 99ms 1.88% 55.12% 99ms 1.88% vtkObjectBase::vtkObjectBase 4ms 0.076% 55.20% 97ms 1.84% vtkDoubleArray::~vtkDoubleArray 36ms 0.68% 55.88% 95ms 1.80% vtkTypeFloat64Array::PrintSelf 48ms 0.91% 56.79% 94ms 1.78% tbb::detail::r1::wait_bounded_queue_monitor 45ms 0.85% 57.64% 93ms 1.76% std::__ostream_insert 2ms 0.038% 57.68% 91ms 1.72% vtkDataArray::vtkDataArray 1ms 0.019% 57.70% 91ms 1.72% vtkXMLWriter::WritePointDataAppendedData 3ms 0.057% 57.76% 90ms 1.70% AbstractCellProperty::IsSubType (inline) 0 0% 57.76% 90ms 1.70% std::operator<< (inline) 3ms 0.057% 57.81% 89ms 1.69% std::map::operator[] (partial-inline) 2ms 0.038% 57.85% 89ms 1.69% vtkAbstractArray::vtkAbstractArray 13ms 0.25% 58.10% 87ms 1.65% __dynamic_cast 1ms 0.019% 58.12% 86ms 1.63% std::set::insert (inline) 16ms 0.3% 58.42% 85ms 1.61% VertexMeshWriter::GetNextNode 0 0% 58.42% 85ms 1.61% std::_Rb_tree::_M_insert_unique 3ms 0.057% 58.48% 83ms 1.57% AbstractCellPopulation::GetCellUsingLocationIndex 30ms 0.57% 59.05% 83ms 1.57% vtkAOSDataArrayTemplate::DataElementChanged 18ms 0.34% 59.39% 81ms 1.53% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.19% 59.58% 76ms 1.44% AbstractCellProperty::IsType (inline) 1ms 0.019% 59.59% 76ms 1.44% Cell::HasCellProperty (inline) 3ms 0.057% 59.65% 76ms 1.44% CellPropertyCollection::HasProperty 2ms 0.038% 59.69% 75ms 1.42% VertexMesh::Clear 5ms 0.095% 59.78% 75ms 1.42% vtkIdList::New 74ms 1.40% 61.19% 74ms 1.40% unlink_chunk 0 0% 61.19% 73ms 1.38% NodesOnlyMesh::SetUpBoxCollection 4ms 0.076% 61.26% 71ms 1.34% std::vector::_M_realloc_insert 7ms 0.13% 61.39% 68ms 1.29% std::_Rb_tree::_M_insert_ (inline) 66ms 1.25% 62.64% 66ms 1.25% [libstdc++.so.6.0.33] 1ms 0.019% 62.66% 64ms 1.21% boost::numeric::ublas::vector_assign (inline) 40ms 0.76% 63.42% 64ms 1.21% std::basic_streambuf::xsputn 1ms 0.019% 63.44% 63ms 1.19% Cell::GetCellProliferativeType 9ms 0.17% 63.61% 62ms 1.17% vtkDataArray::~vtkDataArray 18ms 0.34% 63.95% 61ms 1.16% std::_Rb_tree::_M_lower_bound (inline) 0 0% 63.95% 59ms 1.12% NodesOnlyMesh::~NodesOnlyMesh 0 0% 63.95% 58ms 1.10% std::make_unique (inline) 0 0% 63.95% 58ms 1.10% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 25ms 0.47% 64.43% 57ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.43% 54ms 1.02% tcache_get (inline) 54ms 1.02% 65.45% 54ms 1.02% tcache_get_n (inline) 23ms 0.44% 65.88% 53ms 1.00% std::_Hashtable::clear 3ms 0.057% 65.94% 52ms 0.99% DistributedBoxCollection::SetupLocalBoxesHalfOnly 9ms 0.17% 66.11% 49ms 0.93% AbstractCellProperty::IsSame 49ms 0.93% 67.04% 49ms 0.93% [libchaste_cell_based.so] 49ms 0.93% 67.97% 49ms 0.93% __GI_sched_yield 15ms 0.28% 68.25% 49ms 0.93% boost::numeric::ublas::indexing_vector_assign 0 0% 68.25% 48ms 0.91% std::_Rb_tree::lower_bound (inline) 0 0% 68.25% 48ms 0.91% std::map::lower_bound (inline) 15ms 0.28% 68.54% 47ms 0.89% std::__new_allocator::construct (inline) 0 0% 68.54% 47ms 0.89% std::allocator_traits::construct (inline) 11ms 0.21% 68.74% 47ms 0.89% std::num_put::_M_insert_int 47ms 0.89% 69.63% 47ms 0.89% vtkObject::~vtkObject 0 0% 69.63% 46ms 0.87% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 6ms 0.11% 69.75% 46ms 0.87% vtkIdList::~vtkIdList 0 0% 69.75% 44ms 0.83% std::_Destroy (inline) 0 0% 69.75% 44ms 0.83% std::_Destroy_aux::__destroy (inline) 0 0% 69.75% 44ms 0.83% std::map::~map (inline) 41ms 0.78% 70.52% 41ms 0.78% __memcpy_evex_unaligned_erms 8ms 0.15% 70.68% 40ms 0.76% std::type_info::operator== (inline) 2ms 0.038% 70.71% 40ms 0.76% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.019% 70.73% 39ms 0.74% Node::AddElement 3ms 0.057% 70.79% 39ms 0.74% Node::GetPoint 0 0% 70.79% 39ms 0.74% VertexElement::~VertexElement 2ms 0.038% 70.83% 38ms 0.72% DistributedBoxCollection::IsOwned 38ms 0.72% 71.55% 38ms 0.72% [libchaste_mesh.so] 5ms 0.095% 71.64% 38ms 0.72% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.019% 71.66% 37ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.66% 36ms 0.68% Cell::GetMutationState 16ms 0.3% 71.96% 36ms 0.68% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.96% 36ms 0.68% _dl_init 0 0% 71.96% 36ms 0.68% call_init (inline) 35ms 0.66% 72.63% 36ms 0.68% vtkObjectBase::Delete 35ms 0.66% 73.29% 36ms 0.68% vtkObjectBase::RegisterInternal 0 0% 73.29% 35ms 0.66% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 73.29% 35ms 0.66% vtkDataArray::ComputeRange 2ms 0.038% 73.33% 35ms 0.66% vtkDoubleArray::New 0 0% 73.33% 34ms 0.64% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.19% 73.52% 34ms 0.64% __find_specmb (inline) 1ms 0.019% 73.54% 34ms 0.64% boost::detail::shared_count::~shared_count (inline) 0 0% 73.54% 34ms 0.64% boost::shared_ptr::~shared_ptr (inline) 1ms 0.019% 73.56% 33ms 0.63% AbstractMesh::NodeIterator::operator++ (inline) 1ms 0.019% 73.57% 33ms 0.63% Edge::Edge 1ms 0.019% 73.59% 33ms 0.63% PottsBasedCellPopulation::AcceptCellWriter 0 0% 73.59% 33ms 0.63% _dl_start_user 0 0% 73.59% 33ms 0.63% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.038% 73.63% 33ms 0.63% std::_Rb_tree_header::_Rb_tree_header (inline) 2ms 0.038% 73.67% 32ms 0.61% AbstractMesh::NodeIterator::IsAllowedNode (inline) 0 0% 73.67% 32ms 0.61% OutputFileHandler::OpenOutputFile 18ms 0.34% 74.01% 32ms 0.61% __printf_buffer_write 31ms 0.59% 74.60% 32ms 0.61% boost::detail::sp_counted_base::release 0 0% 74.60% 32ms 0.61% boost::numeric::ublas::c_vector::assign (inline) 0 0% 74.60% 32ms 0.61% std::basic_filebuf::open 0 0% 74.60% 31ms 0.59% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.60% 31ms 0.59% Edge::SetNodes (inline) 0 0% 74.60% 31ms 0.59% MutableElement::MutableElement 0 0% 74.60% 31ms 0.59% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 74.60% 31ms 0.59% VertexElement::VertexElement 1ms 0.019% 74.62% 31ms 0.59% VertexMeshWriter::GetNextElement 2ms 0.038% 74.65% 31ms 0.59% VtkMeshWriter::MakeVtkMesh 0 0% 74.65% 31ms 0.59% std::unique_ptr::~unique_ptr (inline) 31ms 0.59% 75.24% 31ms 0.59% tcache_put (inline) 0 0% 75.24% 31ms 0.59% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 75.24% 30ms 0.57% Cell::GetCellId 0 0% 75.24% 30ms 0.57% CellProliferativeTypesWriter::GetCellDataForVtkOutput 30ms 0.57% 75.81% 30ms 0.57% Node::GetIndex 30ms 0.57% 76.38% 30ms 0.57% Node::IsDeleted 30ms 0.57% 76.95% 30ms 0.57% __mpn_divrem 0 0% 76.95% 30ms 0.57% std::default_delete::operator() (inline) 24ms 0.45% 77.40% 30ms 0.57% std::num_put::do_put 1ms 0.019% 77.42% 30ms 0.57% tbb::detail::r1::cancel_group_execution 3ms 0.057% 77.48% 30ms 0.57% vtkAOSDataArrayTemplate::InsertTuple 0 0% 77.48% 29ms 0.55% CxxTest::RealWorldDescription::setUp 0 0% 77.48% 29ms 0.55% PMPI_Init_thread 0 0% 77.48% 29ms 0.55% PetscInitialize 0 0% 77.48% 29ms 0.55% PetscSetup::setUpWorld 0 0% 77.48% 29ms 0.55% PetscSetupUtils::CommonSetup 0 0% 77.48% 29ms 0.55% PetscSetupUtils::InitialisePetsc 0 0% 77.48% 29ms 0.55% ompi_mpi_init 29ms 0.55% 78.03% 29ms 0.55% std::_Rb_tree_header::_M_reset (inline) 1ms 0.019% 78.05% 29ms 0.55% vtkIdList::vtkIdList 2ms 0.038% 78.08% 28ms 0.53% Node::~Node 0 0% 78.08% 28ms 0.53% NodesOnlyMesh::Clear (inline) 3ms 0.057% 78.14% 28ms 0.53% boost::serialization::singleton::get_instance 28ms 0.53% 78.67% 28ms 0.53% vtkObjectBase::~vtkObjectBase 0 0% 78.67% 27ms 0.51% MutableElement::RegisterWithNodes (inline) 0 0% 78.67% 27ms 0.51% Node::ConstructNodeAttributes (inline) 0 0% 78.67% 27ms 0.51% Node::SetRadius 0 0% 78.67% 27ms 0.51% _IO_new_file_fopen 0 0% 78.67% 27ms 0.51% _IO_new_fopen 0 0% 78.67% 27ms 0.51% __GI__IO_file_open 0 0% 78.67% 27ms 0.51% __fopen_internal (inline)