File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3750ms, 80.08% of 4683ms total Dropped 735 nodes (cum <= 23.41ms) flat flat% sum% cum cum% 0 0% 0% 4475ms 95.56% __libc_start_call_main 0 0% 0% 4475ms 95.56% __libc_start_main_impl 0 0% 0% 4475ms 95.56% _start 0 0% 0% 4457ms 95.17% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4457ms 95.17% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4457ms 95.17% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4457ms 95.17% main 0 0% 0% 4418ms 94.34% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4418ms 94.34% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4418ms 94.34% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4407ms 94.11% AbstractCellBasedSimulation::Solve 0 0% 0% 4106ms 87.68% AbstractCellPopulation::WriteResultsToFiles 7ms 0.15% 0.15% 3888ms 83.02% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.15% 1960ms 41.85% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.17% 1689ms 36.07% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.19% 1238ms 26.44% vtkPolygon::New 2ms 0.043% 0.23% 1236ms 26.39% vtkPolygon::vtkPolygon 9ms 0.19% 0.43% 902ms 19.26% vtkCell::vtkCell 4ms 0.085% 0.51% 788ms 16.83% vtkPoints::New 19ms 0.41% 0.92% 747ms 15.95% vtkPoints::vtkPoints 3ms 0.064% 0.98% 678ms 14.48% VertexMeshWriter::WriteFiles 34ms 0.73% 1.71% 658ms 14.05% operator new 203ms 4.33% 6.04% 634ms 13.54% __GI___libc_malloc 59ms 1.26% 7.30% 633ms 13.52% std::ostream::_M_insert 1ms 0.021% 7.32% 633ms 13.52% std::ostream::operator<< (inline) 1ms 0.021% 7.35% 596ms 12.73% vtkTriangle::New 3ms 0.064% 7.41% 593ms 12.66% vtkLine::New 9ms 0.19% 7.60% 584ms 12.47% vtkTriangle::vtkTriangle 2ms 0.043% 7.64% 581ms 12.41% vtkQuad::New 1ms 0.021% 7.67% 579ms 12.36% vtkQuad::vtkQuad 9ms 0.19% 7.86% 566ms 12.09% vtkLine::vtkLine 0 0% 7.86% 561ms 11.98% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.86% 561ms 11.98% vtkXMLWriterBase::Write 0 0% 7.86% 560ms 11.96% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.86% 559ms 11.94% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.86% 558ms 11.92% vtkExecutive::CallAlgorithm 0 0% 7.86% 557ms 11.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.86% 556ms 11.87% vtkCompositeDataPipeline::ExecuteData 0 0% 7.86% 556ms 11.87% vtkXMLUnstructuredDataWriter::ProcessRequest 39ms 0.83% 8.69% 508ms 10.85% std::num_put::_M_insert_float 0 0% 8.69% 501ms 10.70% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.69% 501ms 10.70% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 117ms 2.50% 11.19% 467ms 9.97% __GI___libc_free 21ms 0.45% 11.64% 445ms 9.50% vtkPoints::SetDataType 0 0% 11.64% 442ms 9.44% vtkXMLWriter::WriteBinaryData 0 0% 11.64% 440ms 9.40% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.64% 440ms 9.40% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.64% 424ms 9.05% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 8ms 0.17% 11.81% 406ms 8.67% std::__cxx11::collate::do_transform 2ms 0.043% 11.85% 401ms 8.56% vtkPolygon::~vtkPolygon 3ms 0.064% 11.92% 389ms 8.31% __vsnprintf_internal (inline) 0 0% 11.92% 388ms 8.29% ___vsnprintf 62ms 1.32% 13.24% 377ms 8.05% __printf_buffer 246ms 5.25% 18.49% 356ms 7.60% _int_malloc 201ms 4.29% 22.78% 349ms 7.45% _int_free 0 0% 22.78% 339ms 7.24% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.78% 338ms 7.22% VtkMeshWriter::WriteFiles 0 0% 22.78% 324ms 6.92% vtkXMLWriter::WritePointsAppendedData 5ms 0.11% 22.89% 314ms 6.71% vtkCell::~vtkCell 56ms 1.20% 24.09% 310ms 6.62% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 24.09% 291ms 6.21% OnLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.15% 24.24% 291ms 6.21% PottsBasedCellPopulation::UpdateCellLocations 1ms 0.021% 24.26% 288ms 6.15% __printf_fp_spec (inline) 9ms 0.19% 24.45% 287ms 6.13% __printf_fp_l_buffer 42ms 0.9% 25.35% 287ms 6.13% std::__new_allocator::allocate (inline) 0 0% 25.35% 286ms 6.11% std::allocator_traits::allocate (inline) 124ms 2.65% 27.99% 268ms 5.72% __printf_fp_buffer_1 4ms 0.085% 28.08% 245ms 5.23% std::__new_allocator::deallocate (inline) 0 0% 28.08% 243ms 5.19% std::allocator_traits::deallocate (inline) 4ms 0.085% 28.17% 232ms 4.95% vtkBase64OutputStream::Write 18ms 0.38% 28.55% 226ms 4.83% vtkBase64OutputStream::EncodeTriplet 16ms 0.34% 28.89% 224ms 4.78% vtkFloatArray::New 0 0% 28.89% 219ms 4.68% vtkXMLWriter::WriteCompressionBlock 3ms 0.064% 28.96% 217ms 4.63% vtkPoints::~vtkPoints 0 0% 28.96% 206ms 4.40% compress2 47ms 1.00% 29.96% 206ms 4.40% crc32 0 0% 29.96% 206ms 4.40% deflate 0 0% 29.96% 206ms 4.40% vtkDataCompressor::Compress 0 0% 29.96% 206ms 4.40% vtkZLibDataCompressor::CompressBuffer 19ms 0.41% 30.37% 191ms 4.08% std::_Rb_tree::_Rb_tree 0 0% 30.37% 191ms 4.08% std::set::set (inline) 43ms 0.92% 31.28% 187ms 3.99% std::ostream::write 1ms 0.021% 31.30% 184ms 3.93% tbb::detail::r1::parallel_pipeline 3ms 0.064% 31.37% 180ms 3.84% vtkQuad::~vtkQuad 0 0% 31.37% 179ms 3.82% std::_Rb_tree::_M_create_node (inline) 0 0% 31.37% 178ms 3.80% vtkFloatArray::vtkFloatArray 0 0% 31.37% 175ms 3.74% vtkTriangle::~vtkTriangle 0 0% 31.37% 174ms 3.72% clone3 0 0% 31.37% 174ms 3.72% start_thread 1ms 0.021% 31.39% 173ms 3.69% vtkLine::GetParametricCenter 0 0% 31.39% 170ms 3.63% std::_Rb_tree::_M_get_node (inline) 1ms 0.021% 31.41% 168ms 3.59% NodesOnlyMesh::ConstructNodesWithoutMesh 84ms 1.79% 33.21% 166ms 3.54% std::basic_filebuf::xsputn 0 0% 33.21% 165ms 3.52% VertexMesh::~VertexMesh 0 0% 33.21% 163ms 3.48% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.021% 33.23% 161ms 3.44% tbb::detail::r1::reset 0 0% 33.23% 159ms 3.40% std::_Rb_tree::_Alloc_node::operator() (inline) 47ms 1.00% 34.23% 157ms 3.35% std::_Rb_tree::_M_erase 82ms 1.75% 35.98% 156ms 3.33% malloc_consolidate 73ms 1.56% 37.54% 154ms 3.29% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.043% 37.58% 153ms 3.27% VertexMesh::VertexMesh 0 0% 37.58% 152ms 3.25% std::_Rb_tree::~_Rb_tree (inline) 150ms 3.20% 40.79% 151ms 3.22% [libz.so.1.3] 4ms 0.085% 40.87% 150ms 3.20% vtkIdList::AllocateInternal 0 0% 40.87% 147ms 3.14% std::vector::~vector (partial-inline) 10ms 0.21% 41.08% 146ms 3.12% std::_Rb_tree::_M_copy (inline) 6ms 0.13% 41.21% 142ms 3.03% std::_Vector_base::_M_deallocate (inline) 1ms 0.021% 41.23% 142ms 3.03% vtkDataArray::CreateDataArray 0 0% 41.23% 141ms 3.01% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.13% 41.36% 140ms 2.99% MutableElement::BuildEdges 1ms 0.021% 41.38% 138ms 2.95% NodeLocationWriter::VisitAnyPopulation 10ms 0.21% 41.60% 137ms 2.93% vtkTypeFloat64Array::New 15ms 0.32% 41.92% 134ms 2.86% std::vector::_M_default_append 2ms 0.043% 41.96% 133ms 2.84% vtkDoubleArray::vtkDoubleArray 4ms 0.085% 42.05% 133ms 2.84% vtkFloatArray::~vtkFloatArray 3ms 0.064% 42.11% 130ms 2.78% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 11ms 0.23% 42.34% 130ms 2.78% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.34% 120ms 2.56% std::set::~set (inline) 5ms 0.11% 42.45% 119ms 2.54% EdgeHelper::GetEdgeFromNodes 0 0% 42.45% 119ms 2.54% EdgeHelper::~EdgeHelper (inline) 5ms 0.11% 42.56% 118ms 2.52% std::_Vector_base::~_Vector_base (inline) 0 0% 42.56% 116ms 2.48% std::_Vector_base::_M_allocate (inline) 64ms 1.37% 43.92% 110ms 2.35% vtkObjectBase::UnRegisterInternal 0 0% 43.92% 110ms 2.35% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 43.92% 107ms 2.28% std::_Rb_tree::_M_drop_node (inline) 21ms 0.45% 44.37% 107ms 2.28% vtkObject::vtkObject 0 0% 44.37% 106ms 2.26% std::_Rb_tree::_M_put_node (inline) 0 0% 44.37% 102ms 2.18% CellPropertyCollection::GetPropertiesType (inline) 102ms 2.18% 46.55% 102ms 2.18% unlink_chunk 97ms 2.07% 48.62% 97ms 2.07% __strcmp_avx2 0 0% 48.62% 97ms 2.07% vtkXMLWriter::WritePointDataAppendedData 3ms 0.064% 48.69% 95ms 2.03% std::map::operator[] (partial-inline) 24ms 0.51% 49.20% 93ms 1.99% std::__ostream_insert 1ms 0.021% 49.22% 92ms 1.96% std::operator<< (inline) 1ms 0.021% 49.24% 90ms 1.92% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 5ms 0.11% 49.35% 90ms 1.92% _int_free_maybe_consolidate 1ms 0.021% 49.37% 90ms 1.92% vtkIdList::Allocate 41ms 0.88% 50.25% 90ms 1.92% vtkTypeFloat64Array::PrintSelf 5ms 0.11% 50.35% 88ms 1.88% vtkAOSDataArrayTemplate::DataElementChanged 57ms 1.22% 51.57% 85ms 1.82% std::basic_streambuf::xsputn 1ms 0.021% 51.59% 84ms 1.79% AbstractCellProperty::IsSubType (inline) 28ms 0.6% 52.19% 84ms 1.79% hack_digit 16ms 0.34% 52.53% 83ms 1.77% __dynamic_cast 4ms 0.085% 52.62% 81ms 1.73% CellPropertyCollection::HasProperty 0 0% 52.62% 80ms 1.71% Cell::HasCellProperty (inline) 3ms 0.064% 52.68% 80ms 1.71% vtkDoubleArray::~vtkDoubleArray 79ms 1.69% 54.37% 79ms 1.69% __GI_sched_yield 1ms 0.021% 54.39% 76ms 1.62% AbstractCellProperty::IsType (inline) 0 0% 54.39% 76ms 1.62% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 12ms 0.26% 54.64% 75ms 1.60% vtkDataArray::vtkDataArray 8ms 0.17% 54.82% 73ms 1.56% AbstractCellPopulation::GetCellUsingLocationIndex 27ms 0.58% 55.39% 73ms 1.56% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.064% 55.46% 73ms 1.56% std::vector::push_back (inline) 26ms 0.56% 56.01% 72ms 1.54% vtkObject::Modified 0 0% 56.01% 66ms 1.41% tcache_get (inline) 66ms 1.41% 57.42% 66ms 1.41% tcache_get_n (inline) 0 0% 57.42% 65ms 1.39% PottsMesh::GetMooreNeighbouringNodeIndices 22ms 0.47% 57.89% 63ms 1.35% vtkAbstractArray::vtkAbstractArray 1ms 0.021% 57.91% 63ms 1.35% vtkIdList::New 4ms 0.085% 58.00% 62ms 1.32% std::_Rb_tree::_M_insert_unique 0 0% 58.00% 62ms 1.32% std::set::insert (inline) 7ms 0.15% 58.15% 61ms 1.30% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 58.15% 58ms 1.24% std::_Rb_tree::lower_bound (inline) 0 0% 58.15% 58ms 1.24% std::map::lower_bound (inline) 1ms 0.021% 58.17% 57ms 1.22% Cell::GetCellProliferativeType 0 0% 58.17% 56ms 1.20% boost::numeric::ublas::vector_assign (inline) 0 0% 58.17% 55ms 1.17% NodesOnlyMesh::SetUpBoxCollection 7ms 0.15% 58.32% 53ms 1.13% AbstractCellProperty::IsSame 21ms 0.45% 58.77% 53ms 1.13% std::_Hashtable::clear 9ms 0.19% 58.96% 52ms 1.11% std::vector::_M_realloc_insert 5ms 0.11% 59.06% 50ms 1.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 59.06% 49ms 1.05% NodesOnlyMesh::~NodesOnlyMesh 5ms 0.11% 59.17% 49ms 1.05% VertexMeshWriter::GetNextNode 1ms 0.021% 59.19% 47ms 1.00% DistributedBoxCollection::IsOwned 47ms 1.00% 60.20% 47ms 1.00% __GI___writev 0 0% 60.20% 47ms 1.00% std::__basic_file::xsputn_2 0 0% 60.20% 47ms 1.00% vtkDataArray::ComputeRange 9ms 0.19% 60.39% 47ms 1.00% vtkSOADataArrayTemplate::FillTypedComponent 2ms 0.043% 60.43% 46ms 0.98% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 24ms 0.51% 60.94% 46ms 0.98% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 60.94% 46ms 0.98% VertexMesh::Clear 26ms 0.56% 61.50% 46ms 0.98% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.15% 61.65% 46ms 0.98% std::type_info::operator== (inline) 46ms 0.98% 62.63% 46ms 0.98% vtkObject::~vtkObject 14ms 0.3% 62.93% 45ms 0.96% vtkDataArray::~vtkDataArray 39ms 0.83% 63.76% 45ms 0.96% vtkObject::ObjectFinalize 44ms 0.94% 64.70% 44ms 0.94% __memcpy_avx_unaligned_erms 9ms 0.19% 64.89% 44ms 0.94% std::num_put::_M_insert_int 15ms 0.32% 65.21% 43ms 0.92% boost::numeric::ublas::indexing_vector_assign 3ms 0.064% 65.28% 43ms 0.92% vtkDataArrayPrivate::DoComputeVectorRange 43ms 0.92% 66.20% 43ms 0.92% vtkObjectBase::Delete 0 0% 66.20% 42ms 0.9% vtkDoubleArray::New 42ms 0.9% 67.09% 42ms 0.9% vtkTimeStamp::Modified 41ms 0.88% 67.97% 41ms 0.88% [libvtkCommonCore-9.3.so.9.3] 41ms 0.88% 68.84% 41ms 0.88% vtkObjectBase::~vtkObjectBase 39ms 0.83% 69.68% 39ms 0.83% [libstdc++.so.6.0.33] 0 0% 69.68% 39ms 0.83% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.11% 69.78% 39ms 0.83% vtkAOSDataArrayTemplate::InsertTuple 4ms 0.085% 69.87% 38ms 0.81% tbb::detail::r1::cancel_group_execution 7ms 0.15% 70.02% 38ms 0.81% vtk::detail::smp::vtkSMPToolsImpl::For 37ms 0.79% 70.81% 37ms 0.79% __memset_avx2_unaligned_erms 37ms 0.79% 71.60% 37ms 0.79% __mpn_divrem 0 0% 71.60% 37ms 0.79% std::_Destroy (inline) 0 0% 71.60% 37ms 0.79% std::_Destroy_aux::__destroy (inline) 7ms 0.15% 71.75% 36ms 0.77% _int_free_merge_chunk 36ms 0.77% 72.52% 36ms 0.77% boost::numeric::ublas::c_vector::operator() 36ms 0.77% 73.29% 36ms 0.77% std::codecvt::do_always_noconv 36ms 0.77% 74.06% 36ms 0.77% std::ostream::sentry::sentry 36ms 0.77% 74.82% 36ms 0.77% vtkObjectBase::vtkObjectBase 0 0% 74.82% 35ms 0.75% CxxTest::RealWorldDescription::setUp 0 0% 74.82% 35ms 0.75% PetscInitialize 0 0% 74.82% 35ms 0.75% PetscSetup::setUpWorld 0 0% 74.82% 35ms 0.75% PetscSetupUtils::CommonSetup 0 0% 74.82% 35ms 0.75% PetscSetupUtils::InitialisePetsc 0 0% 74.82% 35ms 0.75% _dl_init 0 0% 74.82% 35ms 0.75% call_init (inline) 0 0% 74.82% 34ms 0.73% PMPI_Init_thread 0 0% 74.82% 34ms 0.73% _dl_start_user 0 0% 74.82% 34ms 0.73% ompi_mpi_init 0 0% 74.82% 34ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 0 0% 74.82% 33ms 0.7% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 74.82% 32ms 0.68% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 74.82% 32ms 0.68% Cell::GetCellId 0 0% 74.82% 32ms 0.68% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 74.82% 32ms 0.68% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.82% 32ms 0.68% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 74.82% 32ms 0.68% OutputFileHandler::OpenOutputFile 5ms 0.11% 74.93% 32ms 0.68% boost::serialization::singleton::get_instance 0 0% 74.93% 32ms 0.68% std::map::~map (inline) 3ms 0.064% 74.99% 32ms 0.68% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 74.99% 31ms 0.66% PottsBasedCellPopulation::AcceptCellWriter 2ms 0.043% 75.04% 31ms 0.66% VtkMeshWriter::MakeVtkMesh 31ms 0.66% 75.70% 31ms 0.66% std::_Rb_tree_increment 0 0% 75.70% 31ms 0.66% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 75.70% 30ms 0.64% std::basic_filebuf::open 0 0% 75.70% 30ms 0.64% std::less::operator() (inline) 0 0% 75.70% 30ms 0.64% std::make_unique (inline) 30ms 0.64% 76.34% 30ms 0.64% std::operator< (inline) 1ms 0.021% 76.36% 29ms 0.62% 0 0% 76.36% 29ms 0.62% CellIdWriter::GetCellDataForVtkOutput 5ms 0.11% 76.47% 29ms 0.62% vtkIdList::~vtkIdList 9ms 0.19% 76.66% 29ms 0.62% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 28ms 0.6% 77.26% 28ms 0.6% __GI___libc_write 0 0% 77.26% 28ms 0.6% std::__basic_file::xsputn 0 0% 77.26% 28ms 0.6% std::basic_filebuf::_M_convert_to_external 0 0% 77.26% 28ms 0.6% std::basic_filebuf::overflow 28ms 0.6% 77.86% 28ms 0.6% tcache_put (inline) 0 0% 77.86% 27ms 0.58% _IO_new_file_fopen 0 0% 77.86% 27ms 0.58% _IO_new_fopen 0 0% 77.86% 27ms 0.58% __GI__IO_file_open 0 0% 77.86% 27ms 0.58% __fopen_internal (inline) 0 0% 77.86% 27ms 0.58% std::__basic_file::open 25ms 0.53% 78.39% 26ms 0.56% __libc_open64 19ms 0.41% 78.80% 26ms 0.56% _int_free_create_chunk (inline) 0 0% 78.80% 26ms 0.56% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.80% 25ms 0.53% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 78.80% 25ms 0.53% std::_Rb_tree_header::_Rb_tree_header (inline) 6ms 0.13% 78.92% 25ms 0.53% std::__new_allocator::construct (inline) 0 0% 78.92% 25ms 0.53% std::allocator_traits::construct (inline) 1ms 0.021% 78.95% 24ms 0.51% Node::SetRadius 24ms 0.51% 79.46% 24ms 0.51% std::_Rb_tree::_S_right (inline) 5ms 0.11% 79.56% 24ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.51% 80.08% 24ms 0.51% std::_Rb_tree_header::_M_reset (inline)