File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3144ms, 79.09% of 3975ms total Dropped 735 nodes (cum <= 19.88ms) flat flat% sum% cum cum% 0 0% 0% 3793ms 95.42% __libc_start_call_main 0 0% 0% 3793ms 95.42% __libc_start_main_impl 0 0% 0% 3793ms 95.42% _start 0 0% 0% 3777ms 95.02% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3777ms 95.02% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3777ms 95.02% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3777ms 95.02% main 0 0% 0% 3738ms 94.04% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3738ms 94.04% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3738ms 94.04% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3729ms 93.81% AbstractCellBasedSimulation::Solve 0 0% 0% 3430ms 86.29% AbstractCellPopulation::WriteResultsToFiles 14ms 0.35% 0.35% 3261ms 82.04% PottsBasedCellPopulation::WriteVtkResultsToFile 1ms 0.025% 0.38% 1632ms 41.06% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.025% 0.4% 1396ms 35.12% VertexMeshWriter::MakeVtkMesh 0 0% 0.4% 1040ms 26.16% vtkPolygon::New 3ms 0.075% 0.48% 1038ms 26.11% vtkPolygon::vtkPolygon 6ms 0.15% 0.63% 737ms 18.54% vtkCell::vtkCell 7ms 0.18% 0.81% 635ms 15.97% vtkPoints::New 7ms 0.18% 0.98% 587ms 14.77% vtkPoints::vtkPoints 2ms 0.05% 1.03% 560ms 14.09% VertexMeshWriter::WriteFiles 30ms 0.75% 1.79% 516ms 12.98% operator new 151ms 3.80% 5.58% 502ms 12.63% __GI___libc_malloc 44ms 1.11% 6.69% 497ms 12.50% std::ostream::_M_insert 0 0% 6.69% 496ms 12.48% std::ostream::operator<< (inline) 0 0% 6.69% 480ms 12.08% vtkQuad::New 2ms 0.05% 6.74% 479ms 12.05% vtkQuad::vtkQuad 0 0% 6.74% 475ms 11.95% vtkLine::New 1ms 0.025% 6.77% 472ms 11.87% vtkXMLWriterBase::Write 0 0% 6.77% 470ms 11.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.77% 469ms 11.80% vtkDemandDrivenPipeline::ProcessRequest 6ms 0.15% 6.92% 467ms 11.75% vtkLine::vtkLine 0 0% 6.92% 464ms 11.67% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.92% 463ms 11.65% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.92% 463ms 11.65% vtkExecutive::CallAlgorithm 0 0% 6.92% 462ms 11.62% vtkCompositeDataPipeline::ExecuteData 0 0% 6.92% 460ms 11.57% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 6.92% 443ms 11.14% vtkTriangle::New 2ms 0.05% 6.97% 441ms 11.09% vtkTriangle::vtkTriangle 0 0% 6.97% 405ms 10.19% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 6.97% 405ms 10.19% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 22ms 0.55% 7.52% 386ms 9.71% vtkPoints::SetDataType 33ms 0.83% 8.35% 383ms 9.64% std::num_put::_M_insert_float 84ms 2.11% 10.47% 377ms 9.48% __GI___libc_free 0 0% 10.47% 366ms 9.21% vtkXMLWriter::WriteBinaryData 0 0% 10.47% 360ms 9.06% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.47% 359ms 9.03% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.47% 341ms 8.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 10.47% 314ms 7.90% vtkPolygon::~vtkPolygon 8ms 0.2% 10.67% 308ms 7.75% std::__cxx11::collate::do_transform 181ms 4.55% 15.22% 290ms 7.30% _int_malloc 168ms 4.23% 19.45% 289ms 7.27% _int_free 2ms 0.05% 19.50% 284ms 7.14% ___vsnprintf 0 0% 19.50% 283ms 7.12% OnLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.2% 19.70% 283ms 7.12% PottsBasedCellPopulation::UpdateCellLocations 0 0% 19.70% 282ms 7.09% __vsnprintf_internal (inline) 1ms 0.025% 19.72% 279ms 7.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 19.72% 276ms 6.94% VtkMeshWriter::WriteFiles 41ms 1.03% 20.75% 276ms 6.94% __printf_buffer 0 0% 20.75% 262ms 6.59% vtkXMLWriter::WritePointsAppendedData 3ms 0.075% 20.83% 252ms 6.34% vtkCell::~vtkCell 43ms 1.08% 21.91% 232ms 5.84% std::__new_allocator::allocate (inline) 0 0% 21.91% 230ms 5.79% std::allocator_traits::allocate (inline) 53ms 1.33% 23.25% 224ms 5.64% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 9ms 0.23% 23.47% 214ms 5.38% __printf_fp_l_buffer 0 0% 23.47% 214ms 5.38% __printf_fp_spec (inline) 2ms 0.05% 23.52% 206ms 5.18% std::__new_allocator::deallocate (inline) 0 0% 23.52% 205ms 5.16% std::allocator_traits::deallocate (inline) 89ms 2.24% 25.76% 197ms 4.96% __printf_fp_buffer_1 0 0% 25.76% 185ms 4.65% std::set::set (inline) 10ms 0.25% 26.01% 185ms 4.65% vtkBase64OutputStream::Write 16ms 0.4% 26.42% 184ms 4.63% std::_Rb_tree::_Rb_tree 0 0% 26.42% 178ms 4.48% vtkXMLWriter::WriteCompressionBlock 12ms 0.3% 26.72% 172ms 4.33% vtkBase64OutputStream::EncodeTriplet 0 0% 26.72% 171ms 4.30% VertexMesh::~VertexMesh 0 0% 26.72% 169ms 4.25% compress2 0 0% 26.72% 169ms 4.25% vtkDataCompressor::Compress 0 0% 26.72% 169ms 4.25% vtkZLibDataCompressor::CompressBuffer 39ms 0.98% 27.70% 168ms 4.23% crc32 0 0% 27.70% 168ms 4.23% deflate 2ms 0.05% 27.75% 166ms 4.18% vtkPoints::~vtkPoints 1ms 0.025% 27.77% 155ms 3.90% tbb::detail::r1::parallel_pipeline 90ms 2.26% 30.04% 153ms 3.85% malloc_consolidate 0 0% 30.04% 151ms 3.80% clone3 0 0% 30.04% 151ms 3.80% start_thread 0 0% 30.04% 151ms 3.80% std::_Rb_tree::_M_create_node (inline) 56ms 1.41% 31.45% 151ms 3.80% std::_Rb_tree::_M_erase 3ms 0.075% 31.52% 150ms 3.77% std::_Rb_tree::~_Rb_tree (inline) 0 0% 31.52% 142ms 3.57% std::_Rb_tree::_M_get_node (inline) 38ms 0.96% 32.48% 142ms 3.57% std::ostream::write 3ms 0.075% 32.55% 142ms 3.57% tbb::detail::r1::reset 0 0% 32.55% 140ms 3.52% std::vector::~vector (inline) 4ms 0.1% 32.65% 139ms 3.50% vtkFloatArray::New 0 0% 32.65% 136ms 3.42% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.3% 32.96% 136ms 3.42% std::_Rb_tree::_M_copy (inline) 3ms 0.075% 33.03% 134ms 3.37% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.025% 33.06% 134ms 3.37% vtkIdList::AllocateInternal 2ms 0.05% 33.11% 134ms 3.37% vtkLine::GetParametricCenter 11ms 0.28% 33.38% 133ms 3.35% std::_Vector_base::_M_deallocate (inline) 46ms 1.16% 34.54% 131ms 3.30% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 34.54% 129ms 3.25% vtkQuad::~vtkQuad 5ms 0.13% 34.67% 127ms 3.19% vtkDataArray::CreateDataArray 4ms 0.1% 34.77% 125ms 3.14% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 13ms 0.33% 35.09% 124ms 3.12% std::_Rb_tree::_M_clone_node (inline) 64ms 1.61% 36.70% 124ms 3.12% std::basic_filebuf::xsputn 0 0% 36.70% 124ms 3.12% vtkTriangle::~vtkTriangle 121ms 3.04% 39.75% 123ms 3.09% [libz.so.1.3] 0 0% 39.75% 121ms 3.04% EdgeHelper::~EdgeHelper (inline) 1ms 0.025% 39.77% 120ms 3.02% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 39.77% 118ms 2.97% std::_Vector_base::~_Vector_base (inline) 10ms 0.25% 40.03% 118ms 2.97% vtkTypeFloat64Array::New 0 0% 40.03% 117ms 2.94% vtkFloatArray::vtkFloatArray 2ms 0.05% 40.08% 117ms 2.94% vtkFloatArray::~vtkFloatArray 0 0% 40.08% 114ms 2.87% VertexMesh::VertexMesh 6ms 0.15% 40.23% 113ms 2.84% vtkDoubleArray::vtkDoubleArray 0 0% 40.23% 108ms 2.72% VertexMesh::GenerateEdgesFromElements (inline) 4ms 0.1% 40.33% 107ms 2.69% MutableElement::BuildEdges 1ms 0.025% 40.35% 105ms 2.64% NodeLocationWriter::VisitAnyPopulation 13ms 0.33% 40.68% 104ms 2.62% std::vector::_M_default_append 0 0% 40.68% 100ms 2.52% std::set::~set (inline) 0 0% 40.68% 97ms 2.44% vtkIdList::Allocate 37ms 0.93% 41.61% 97ms 2.44% vtkTypeFloat64Array::PrintSelf 1ms 0.025% 41.64% 95ms 2.39% EdgeHelper::GetEdgeFromNodes 5ms 0.13% 41.76% 94ms 2.36% vtkTypeFloat64Array::vtkTypeFloat64Array 18ms 0.45% 42.21% 93ms 2.34% vtkObject::vtkObject 0 0% 42.21% 91ms 2.29% std::_Rb_tree::_M_drop_node (inline) 37ms 0.93% 43.14% 90ms 2.26% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.025% 43.17% 89ms 2.24% std::_Vector_base::_M_allocate (inline) 24ms 0.6% 43.77% 88ms 2.21% vtkObject::Modified 86ms 2.16% 45.94% 86ms 2.16% __GI_sched_yield 0 0% 45.94% 83ms 2.09% std::_Rb_tree::_M_put_node (inline) 82ms 2.06% 48.00% 82ms 2.06% __strcmp_evex 0 0% 48.00% 81ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 81ms 2.04% 50.04% 81ms 2.04% unlink_chunk 57ms 1.43% 51.47% 81ms 2.04% vtkObjectBase::UnRegisterInternal 0 0% 51.47% 79ms 1.99% vtkXMLWriter::WritePointDataAppendedData 0 0% 51.47% 77ms 1.94% AbstractCellProperty::IsSubType (inline) 3ms 0.075% 51.55% 77ms 1.94% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 24ms 0.6% 52.15% 77ms 1.94% __dynamic_cast 5ms 0.13% 52.28% 77ms 1.94% _int_free_maybe_consolidate 5ms 0.13% 52.40% 77ms 1.94% std::map::operator[] (partial-inline) 26ms 0.65% 53.06% 75ms 1.89% std::__ostream_insert 0 0% 53.06% 72ms 1.81% Cell::HasCellProperty (inline) 4ms 0.1% 53.16% 72ms 1.81% CellPropertyCollection::HasProperty 1ms 0.025% 53.18% 72ms 1.81% std::operator<< (inline) 1ms 0.025% 53.21% 70ms 1.76% AbstractCellProperty::IsType (inline) 31ms 0.78% 53.99% 67ms 1.69% hack_digit 4ms 0.1% 54.09% 65ms 1.64% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 54.09% 64ms 1.61% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 63ms 1.58% 55.67% 63ms 1.58% vtkTimeStamp::Modified 0 0% 55.67% 62ms 1.56% PottsMesh::GetMooreNeighbouringNodeIndices 40ms 1.01% 56.68% 60ms 1.51% std::_Hashtable::clear 21ms 0.53% 57.21% 60ms 1.51% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.075% 57.28% 60ms 1.51% std::vector::push_back (inline) 2ms 0.05% 57.33% 58ms 1.46% vtkIdList::New 9ms 0.23% 57.56% 57ms 1.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 57.56% 55ms 1.38% tcache_get (inline) 55ms 1.38% 58.94% 55ms 1.38% tcache_get_n (inline) 9ms 0.23% 59.17% 54ms 1.36% AbstractCellProperty::IsSame 0 0% 59.17% 54ms 1.36% NodesOnlyMesh::SetUpBoxCollection 6ms 0.15% 59.32% 52ms 1.31% vtkDoubleArray::~vtkDoubleArray 0 0% 59.32% 50ms 1.26% VertexMesh::Clear 3ms 0.075% 59.40% 50ms 1.26% VertexMeshWriter::GetNextNode 33ms 0.83% 60.23% 50ms 1.26% std::basic_streambuf::xsputn 0 0% 60.23% 50ms 1.26% std::map::~map (inline) 1ms 0.025% 60.25% 47ms 1.18% boost::numeric::ublas::vector_assign (inline) 0 0% 60.25% 45ms 1.13% NodesOnlyMesh::~NodesOnlyMesh 11ms 0.28% 60.53% 45ms 1.13% std::type_info::operator== (inline) 44ms 1.11% 61.64% 44ms 1.11% vtkObject::~vtkObject 8ms 0.2% 61.84% 43ms 1.08% std::vector::_M_realloc_insert 9ms 0.23% 62.06% 42ms 1.06% std::num_put::_M_insert_int 5ms 0.13% 62.19% 42ms 1.06% vtkDataArray::vtkDataArray 1ms 0.025% 62.21% 41ms 1.03% Cell::GetCellProliferativeType 41ms 1.03% 63.25% 41ms 1.03% __GI___writev 0 0% 63.25% 41ms 1.03% std::_Rb_tree::lower_bound (inline) 0 0% 63.25% 41ms 1.03% std::__basic_file::xsputn_2 0 0% 63.25% 41ms 1.03% std::map::lower_bound (inline) 3ms 0.075% 63.32% 38ms 0.96% std::_Rb_tree::_M_insert_unique 0 0% 63.32% 38ms 0.96% std::set::insert (inline) 11ms 0.28% 63.60% 37ms 0.93% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.025% 63.62% 36ms 0.91% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 36ms 0.91% 64.53% 36ms 0.91% std::ostream::sentry::sentry 8ms 0.2% 64.73% 36ms 0.91% vtkAbstractArray::vtkAbstractArray 0 0% 64.73% 35ms 0.88% CxxTest::RealWorldDescription::setUp 0 0% 64.73% 35ms 0.88% PMPI_Init_thread 0 0% 64.73% 35ms 0.88% PetscInitialize 0 0% 64.73% 35ms 0.88% PetscSetup::setUpWorld 0 0% 64.73% 35ms 0.88% PetscSetupUtils::CommonSetup 0 0% 64.73% 35ms 0.88% PetscSetupUtils::InitialisePetsc 0 0% 64.73% 35ms 0.88% _dl_init 0 0% 64.73% 35ms 0.88% call_init (inline) 0 0% 64.73% 35ms 0.88% ompi_mpi_init 2ms 0.05% 64.78% 34ms 0.86% 1ms 0.025% 64.81% 34ms 0.86% DistributedBoxCollection::SetupLocalBoxesHalfOnly 26ms 0.65% 65.46% 34ms 0.86% __cxxabiv1::__si_class_type_info::__do_dyncast 17ms 0.43% 65.89% 34ms 0.86% _int_free_merge_chunk 10ms 0.25% 66.14% 34ms 0.86% boost::numeric::ublas::indexing_vector_assign 18ms 0.45% 66.59% 33ms 0.83% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 66.59% 33ms 0.83% DistributedBoxCollection::IsOwned 0 0% 66.59% 33ms 0.83% vtkDoubleArray::New 1ms 0.025% 66.62% 32ms 0.81% PottsMesh::GetVonNeumannNeighbouringNodeIndices 32ms 0.81% 67.42% 32ms 0.81% __memset_avx512_unaligned_erms 31ms 0.78% 68.20% 31ms 0.78% Node::GetIndex 31ms 0.78% 68.98% 31ms 0.78% __memcpy_avx512_unaligned_erms 0 0% 68.98% 31ms 0.78% _dl_start_user 0 0% 68.98% 31ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 0 0% 68.98% 31ms 0.78% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 68.98% 31ms 0.78% std::_Rb_tree_header::_Rb_tree_header (inline) 2ms 0.05% 69.03% 30ms 0.75% std::_Rb_tree::_M_insert_ (inline) 30ms 0.75% 69.79% 30ms 0.75% std::_Rb_tree_header::_M_reset (inline) 1ms 0.025% 69.81% 30ms 0.75% std::make_unique (inline) 0 0% 69.81% 29ms 0.73% VertexMeshWriter::GetNextElement 29ms 0.73% 70.54% 29ms 0.73% __GI___libc_write 0 0% 70.54% 29ms 0.73% std::__basic_file::xsputn 0 0% 70.54% 29ms 0.73% std::basic_filebuf::_M_convert_to_external 0 0% 70.54% 29ms 0.73% std::basic_filebuf::overflow 29ms 0.73% 71.27% 29ms 0.73% vtkObjectBase::~vtkObjectBase 0 0% 71.27% 28ms 0.7% Cell::GetCellId 1ms 0.025% 71.30% 28ms 0.7% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 71.30% 27ms 0.68% std::_Destroy (inline) 0 0% 71.30% 27ms 0.68% std::_Destroy_aux::__destroy (inline) 1ms 0.025% 71.32% 27ms 0.68% std::basic_filebuf::open 5ms 0.13% 71.45% 27ms 0.68% vtkIdList::~vtkIdList 5ms 0.13% 71.57% 27ms 0.68% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 26ms 0.65% 72.23% 26ms 0.65% [libstdc++.so.6.0.33] 1ms 0.025% 72.25% 26ms 0.65% std::less::operator() (inline) 0 0% 72.25% 26ms 0.65% vtkDataArray::ComputeRange 4ms 0.1% 72.35% 26ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 72.35% 25ms 0.63% CellIdWriter::GetCellDataForVtkOutput 0 0% 72.35% 25ms 0.63% DistributedBoxCollection::~DistributedBoxCollection 0 0% 72.35% 25ms 0.63% NodesOnlyMesh::ClearBoxCollection (inline) 25ms 0.63% 72.98% 25ms 0.63% [libvtkCommonCore-9.3.so.9.3] 0 0% 72.98% 25ms 0.63% _IO_new_fopen 0 0% 72.98% 25ms 0.63% __fopen_internal (inline) 25ms 0.63% 73.61% 25ms 0.63% boost::numeric::ublas::c_vector::operator() 25ms 0.63% 74.24% 25ms 0.63% std::operator< (inline) 1ms 0.025% 74.26% 24ms 0.6% AbstractMesh::NodeIterator::operator++ (inline) 0 0% 74.26% 24ms 0.6% VertexElement::~VertexElement 1ms 0.025% 74.29% 24ms 0.6% VtkMeshWriter::MakeVtkMesh 0 0% 74.29% 24ms 0.6% _IO_new_file_fopen 0 0% 74.29% 24ms 0.6% __GI__IO_file_open 1ms 0.025% 74.31% 24ms 0.6% boost::serialization::singleton::get_instance 0 0% 74.31% 24ms 0.6% std::__basic_file::open 1ms 0.025% 74.34% 24ms 0.6% vtk::detail::smp::vtkSMPToolsImpl::For 20ms 0.5% 74.84% 24ms 0.6% vtkObject::ObjectFinalize 4ms 0.1% 74.94% 23ms 0.58% AbstractMesh::NodeIterator::IsAllowedNode (inline) 23ms 0.58% 75.52% 23ms 0.58% __libc_open64 23ms 0.58% 76.10% 23ms 0.58% __mpn_divrem 0 0% 76.10% 23ms 0.58% orte_init 23ms 0.58% 76.68% 23ms 0.58% vtkObjectBase::UnRegister 3ms 0.075% 76.75% 22ms 0.55% Node::~Node 1ms 0.025% 76.78% 22ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 76.78% 22ms 0.55% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 76.78% 21ms 0.53% Cell::GetMutationState 9ms 0.23% 77.01% 21ms 0.53% std::__new_allocator::construct (inline) 0 0% 77.01% 21ms 0.53% std::allocator_traits::construct (inline) 19ms 0.48% 77.48% 21ms 0.53% std::num_put::do_put 2ms 0.05% 77.53% 21ms 0.53% vtkAOSDataArrayTemplate::InsertTuple 21ms 0.53% 78.06% 21ms 0.53% vtkObjectBase::vtkObjectBase 0 0% 78.06% 20ms 0.5% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.025% 78.09% 20ms 0.5% Node::GetPoint 20ms 0.5% 78.59% 20ms 0.5% Node::IsDeleted 0 0% 78.59% 20ms 0.5% NodesOnlyMesh::Clear (inline) 0 0% 78.59% 20ms 0.5% OutputFileHandler::OpenOutputFile 1ms 0.025% 78.62% 20ms 0.5% tbb::detail::r1::cancel_group_execution 19ms 0.48% 79.09% 20ms 0.5% vtkObjectBase::Delete