File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3896ms, 79.53% of 4899ms total Dropped 826 nodes (cum <= 24.50ms) flat flat% sum% cum cum% 0 0% 0% 4699ms 95.92% __libc_start_call_main 0 0% 0% 4699ms 95.92% __libc_start_main_impl 0 0% 0% 4699ms 95.92% _start 0 0% 0% 4679ms 95.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4679ms 95.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4679ms 95.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4679ms 95.51% main 0 0% 0% 4636ms 94.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4636ms 94.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4636ms 94.63% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4625ms 94.41% AbstractCellBasedSimulation::Solve 0 0% 0% 4265ms 87.06% AbstractCellPopulation::WriteResultsToFiles 11ms 0.22% 0.22% 4056ms 82.79% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.22% 2012ms 41.07% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.041% 0.27% 1726ms 35.23% VertexMeshWriter::MakeVtkMesh 0 0% 0.27% 1303ms 26.60% vtkPolygon::New 0 0% 0.27% 1302ms 26.58% vtkPolygon::vtkPolygon 2ms 0.041% 0.31% 911ms 18.60% vtkCell::vtkCell 2ms 0.041% 0.35% 769ms 15.70% vtkPoints::New 11ms 0.22% 0.57% 719ms 14.68% vtkPoints::vtkPoints 0 0% 0.57% 711ms 14.51% VertexMeshWriter::WriteFiles 25ms 0.51% 1.08% 691ms 14.10% operator new 218ms 4.45% 5.53% 673ms 13.74% __GI___libc_malloc 3ms 0.061% 5.59% 660ms 13.47% std::ostream::operator<< (inline) 56ms 1.14% 6.74% 659ms 13.45% std::ostream::_M_insert 1ms 0.02% 6.76% 590ms 12.04% vtkLine::New 3ms 0.061% 6.82% 583ms 11.90% vtkQuad::New 0 0% 6.82% 579ms 11.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.82% 579ms 11.82% vtkXMLWriterBase::Write 1ms 0.02% 6.84% 577ms 11.78% vtkDemandDrivenPipeline::ProcessRequest 2ms 0.041% 6.88% 577ms 11.78% vtkQuad::vtkQuad 4ms 0.082% 6.96% 574ms 11.72% vtkLine::vtkLine 0 0% 6.96% 570ms 11.64% vtkExecutive::CallAlgorithm 0 0% 6.96% 569ms 11.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.96% 568ms 11.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.96% 567ms 11.57% vtkCompositeDataPipeline::ExecuteData 1ms 0.02% 6.98% 566ms 11.55% vtkTriangle::New 0 0% 6.98% 565ms 11.53% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.061% 7.04% 558ms 11.39% vtkTriangle::vtkTriangle 41ms 0.84% 7.88% 518ms 10.57% std::num_put::_M_insert_float 0 0% 7.88% 503ms 10.27% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.88% 503ms 10.27% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 124ms 2.53% 10.41% 465ms 9.49% __GI___libc_free 0 0% 10.41% 444ms 9.06% vtkXMLWriter::WriteBinaryData 34ms 0.69% 11.10% 441ms 9.00% vtkPoints::SetDataType 1ms 0.02% 11.12% 437ms 8.92% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.12% 436ms 8.90% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.12% 435ms 8.88% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.22% 11.35% 411ms 8.39% std::__cxx11::collate::do_transform 1ms 0.02% 11.37% 395ms 8.06% __vsnprintf_internal (inline) 1ms 0.02% 11.39% 394ms 8.04% ___vsnprintf 61ms 1.25% 12.64% 388ms 7.92% __printf_buffer 237ms 4.84% 17.47% 386ms 7.88% _int_malloc 0 0% 17.47% 367ms 7.49% vtkPolygon::~vtkPolygon 0 0% 17.47% 352ms 7.19% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.47% 348ms 7.10% VtkMeshWriter::WriteFiles 0 0% 17.47% 343ms 7.00% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.12% 17.60% 343ms 7.00% PottsBasedCellPopulation::UpdateCellLocations 189ms 3.86% 21.45% 338ms 6.90% _int_free 0 0% 21.45% 332ms 6.78% vtkXMLWriter::WritePointsAppendedData 12ms 0.24% 21.70% 304ms 6.21% __printf_fp_l_buffer 0 0% 21.70% 304ms 6.21% __printf_fp_spec (inline) 48ms 0.98% 22.68% 296ms 6.04% std::__new_allocator::allocate (inline) 0 0% 22.68% 294ms 6.00% std::allocator_traits::allocate (inline) 6ms 0.12% 22.80% 279ms 5.70% vtkCell::~vtkCell 34ms 0.69% 23.49% 274ms 5.59% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 129ms 2.63% 26.13% 273ms 5.57% __printf_fp_buffer_1 5ms 0.1% 26.23% 270ms 5.51% std::__new_allocator::deallocate (inline) 0 0% 26.23% 266ms 5.43% std::allocator_traits::deallocate (inline) 1ms 0.02% 26.25% 224ms 4.57% std::set::set (inline) 0 0% 26.25% 224ms 4.57% vtkXMLWriter::WriteCompressionBlock 18ms 0.37% 26.62% 223ms 4.55% std::_Rb_tree::_Rb_tree 3ms 0.061% 26.68% 219ms 4.47% vtkBase64OutputStream::Write 11ms 0.22% 26.90% 211ms 4.31% vtkBase64OutputStream::EncodeTriplet 0 0% 26.90% 209ms 4.27% vtkDataCompressor::Compress 0 0% 26.90% 207ms 4.23% compress2 0 0% 26.90% 207ms 4.23% vtkZLibDataCompressor::CompressBuffer 122ms 2.49% 29.39% 206ms 4.20% malloc_consolidate 0 0% 29.39% 205ms 4.18% VertexMesh::~VertexMesh 41ms 0.84% 30.23% 205ms 4.18% crc32 0 0% 30.23% 205ms 4.18% deflate 10ms 0.2% 30.43% 201ms 4.10% vtkIdList::AllocateInternal 10ms 0.2% 30.64% 190ms 3.88% std::_Rb_tree::~_Rb_tree (inline) 0 0% 30.64% 188ms 3.84% std::_Rb_tree::_M_create_node (inline) 83ms 1.69% 32.33% 187ms 3.82% std::basic_filebuf::xsputn 47ms 0.96% 33.29% 187ms 3.82% std::ostream::write 75ms 1.53% 34.82% 185ms 3.78% std::_Rb_tree::_M_erase 2ms 0.041% 34.86% 185ms 3.78% vtkPoints::~vtkPoints 3ms 0.061% 34.93% 183ms 3.74% vtkFloatArray::New 5ms 0.1% 35.03% 173ms 3.53% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.041% 35.07% 172ms 3.51% std::vector::~vector (partial-inline) 5ms 0.1% 35.17% 171ms 3.49% std::_Vector_base::_M_deallocate (inline) 0 0% 35.17% 169ms 3.45% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.17% 169ms 3.45% std::_Rb_tree::_M_get_node (inline) 2ms 0.041% 35.21% 169ms 3.45% tbb::detail::r1::parallel_pipeline 1ms 0.02% 35.23% 168ms 3.43% vtkLine::GetParametricCenter 0 0% 35.23% 164ms 3.35% vtkQuad::~vtkQuad 0 0% 35.23% 163ms 3.33% clone3 0 0% 35.23% 163ms 3.33% start_thread 2ms 0.041% 35.27% 161ms 3.29% vtkFloatArray::vtkFloatArray 158ms 3.23% 38.50% 160ms 3.27% [libz.so.1.3] 0 0% 38.50% 159ms 3.25% vtkTriangle::~vtkTriangle 0 0% 38.50% 158ms 3.23% VertexMesh::VertexMesh 11ms 0.22% 38.72% 157ms 3.20% std::vector::_M_default_append 3ms 0.061% 38.78% 156ms 3.18% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 12ms 0.24% 39.03% 156ms 3.18% std::_Rb_tree::_M_copy (inline) 0 0% 39.03% 151ms 3.08% tbb::detail::r1::reset 0 0% 39.03% 146ms 2.98% EdgeHelper::~EdgeHelper (inline) 0 0% 39.03% 146ms 2.98% vtkIdList::Allocate 67ms 1.37% 40.40% 143ms 2.92% tbb::detail::r1::wait_bounded_queue_monitor 10ms 0.2% 40.60% 141ms 2.88% std::_Rb_tree::_M_clone_node (inline) 2ms 0.041% 40.64% 140ms 2.86% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 40.64% 138ms 2.82% NodeLocationWriter::VisitAnyPopulation 0 0% 40.64% 138ms 2.82% VertexMesh::GenerateEdgesFromElements (inline) 5ms 0.1% 40.74% 137ms 2.80% MutableElement::BuildEdges 1ms 0.02% 40.76% 137ms 2.80% std::_Vector_base::~_Vector_base (inline) 0 0% 40.76% 133ms 2.71% std::set::~set (inline) 4ms 0.082% 40.85% 132ms 2.69% vtkDataArray::CreateDataArray 1ms 0.02% 40.87% 126ms 2.57% std::_Vector_base::_M_allocate (inline) 30ms 0.61% 41.48% 126ms 2.57% vtkObject::vtkObject 2ms 0.041% 41.52% 122ms 2.49% vtkFloatArray::~vtkFloatArray 10ms 0.2% 41.72% 121ms 2.47% vtkTypeFloat64Array::New 5ms 0.1% 41.82% 120ms 2.45% vtkDoubleArray::vtkDoubleArray 1ms 0.02% 41.85% 118ms 2.41% EdgeHelper::GetEdgeFromNodes 2ms 0.041% 41.89% 110ms 2.25% CellPropertyCollection::GetPropertiesType (inline) 110ms 2.25% 44.13% 110ms 2.25% unlink_chunk 0 0% 44.13% 107ms 2.18% std::_Rb_tree::_M_drop_node (inline) 12ms 0.24% 44.38% 103ms 2.10% _int_free_maybe_consolidate 4ms 0.082% 44.46% 102ms 2.08% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 44.46% 100ms 2.04% std::_Rb_tree::_M_put_node (inline) 99ms 2.02% 46.48% 99ms 2.02% __strcmp_avx2 0 0% 46.48% 99ms 2.02% vtkXMLWriter::WritePointDataAppendedData 4ms 0.082% 46.56% 98ms 2.00% vtkIdList::New 0 0% 46.56% 97ms 1.98% Cell::HasCellProperty (inline) 56ms 1.14% 47.70% 97ms 1.98% vtkTypeFloat64Array::PrintSelf 6ms 0.12% 47.83% 96ms 1.96% CellPropertyCollection::HasProperty 47ms 0.96% 48.79% 93ms 1.90% hack_digit 1ms 0.02% 48.81% 92ms 1.88% AbstractCellProperty::IsSubType (inline) 25ms 0.51% 49.32% 92ms 1.88% std::__ostream_insert 3ms 0.061% 49.38% 90ms 1.84% AbstractCellProperty::IsType (inline) 17ms 0.35% 49.72% 90ms 1.84% __dynamic_cast 3ms 0.061% 49.79% 89ms 1.82% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.02% 49.81% 88ms 1.80% std::operator<< (inline) 61ms 1.25% 51.05% 88ms 1.80% vtkObjectBase::UnRegisterInternal 31ms 0.63% 51.68% 87ms 1.78% vtkObject::Modified 3ms 0.061% 51.75% 83ms 1.69% std::map::operator[] (partial-inline) 8ms 0.16% 51.91% 81ms 1.65% vtkAOSDataArrayTemplate::DataElementChanged 76ms 1.55% 53.46% 76ms 1.55% __GI_sched_yield 23ms 0.47% 53.93% 72ms 1.47% std::_Rb_tree::_M_lower_bound (inline) 0 0% 53.93% 71ms 1.45% NodesOnlyMesh::SetUpBoxCollection 1ms 0.02% 53.95% 70ms 1.43% Cell::GetCellProliferativeType 1ms 0.02% 53.97% 69ms 1.41% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 52ms 1.06% 55.03% 68ms 1.39% std::basic_streambuf::xsputn 1ms 0.02% 55.05% 67ms 1.37% std::vector::push_back (inline) 0 0% 55.05% 65ms 1.33% tcache_get (inline) 65ms 1.33% 56.38% 65ms 1.33% tcache_get_n (inline) 1ms 0.02% 56.40% 64ms 1.31% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.18% 56.58% 64ms 1.31% AbstractCellProperty::IsSame 64ms 1.31% 57.89% 64ms 1.31% [libvtkCommonCore-9.3.so.9.3] 3ms 0.061% 57.95% 64ms 1.31% std::_Rb_tree::_M_insert_unique 0 0% 57.95% 64ms 1.31% std::set::insert (inline) 0 0% 57.95% 63ms 1.29% PottsMesh::GetMooreNeighbouringNodeIndices 7ms 0.14% 58.09% 63ms 1.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 58.09% 63ms 1.29% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 12ms 0.24% 58.34% 62ms 1.27% std::num_put::_M_insert_int 1ms 0.02% 58.36% 59ms 1.20% VertexMesh::Clear 9ms 0.18% 58.54% 59ms 1.20% VertexMeshWriter::GetNextNode 6ms 0.12% 58.67% 59ms 1.20% vtkDataArray::vtkDataArray 1ms 0.02% 58.69% 57ms 1.16% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.02% 58.71% 57ms 1.16% boost::numeric::ublas::vector_assign (inline) 0 0% 58.71% 57ms 1.16% std::map::~map (inline) 56ms 1.14% 59.85% 56ms 1.14% __GI___writev 23ms 0.47% 60.32% 56ms 1.14% std::_Hashtable::clear 0 0% 60.32% 56ms 1.14% std::__basic_file::xsputn_2 2ms 0.041% 60.36% 56ms 1.14% vtkDoubleArray::~vtkDoubleArray 16ms 0.33% 60.69% 55ms 1.12% std::type_info::operator== (inline) 54ms 1.10% 61.79% 54ms 1.10% vtkTimeStamp::Modified 22ms 0.45% 62.24% 50ms 1.02% vtkAbstractArray::vtkAbstractArray 30ms 0.61% 62.85% 49ms 1.00% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 62.85% 49ms 1.00% std::_Rb_tree::lower_bound (inline) 0 0% 62.85% 49ms 1.00% std::map::lower_bound (inline) 0 0% 62.85% 48ms 0.98% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 62.87% 48ms 0.98% std::_Rb_tree_header::_Rb_tree_header (inline) 48ms 0.98% 63.85% 48ms 0.98% std::codecvt::do_always_noconv 48ms 0.98% 64.83% 48ms 0.98% vtkObject::~vtkObject 47ms 0.96% 65.79% 47ms 0.96% std::_Rb_tree_header::_M_reset (inline) 5ms 0.1% 65.89% 46ms 0.94% std::vector::_M_realloc_insert 11ms 0.22% 66.12% 46ms 0.94% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.082% 66.20% 45ms 0.92% std::_Rb_tree::_M_insert_ (inline) 1ms 0.02% 66.22% 45ms 0.92% vtkDataArray::ComputeRange 15ms 0.31% 66.52% 43ms 0.88% boost::numeric::ublas::indexing_vector_assign 1ms 0.02% 66.54% 41ms 0.84% DistributedBoxCollection::SetupLocalBoxesHalfOnly 41ms 0.84% 67.38% 41ms 0.84% __memcpy_avx_unaligned_erms 0 0% 67.38% 41ms 0.84% _dl_init 0 0% 67.38% 41ms 0.84% call_init (inline) 0 0% 67.38% 39ms 0.8% CxxTest::RealWorldDescription::setUp 23ms 0.47% 67.85% 39ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.85% 39ms 0.8% DistributedBoxCollection::IsOwned 0 0% 67.85% 39ms 0.8% PetscInitialize 0 0% 67.85% 39ms 0.8% PetscSetup::setUpWorld 0 0% 67.85% 39ms 0.8% PetscSetupUtils::CommonSetup 0 0% 67.85% 39ms 0.8% PetscSetupUtils::InitialisePetsc 39ms 0.8% 68.65% 39ms 0.8% vtkObjectBase::~vtkObjectBase 0 0% 68.65% 38ms 0.78% PMPI_Init_thread 38ms 0.78% 69.42% 38ms 0.78% __GI___libc_write 0 0% 69.42% 38ms 0.78% ompi_mpi_init 0 0% 69.42% 38ms 0.78% std::_Destroy (inline) 0 0% 69.42% 38ms 0.78% std::_Destroy_aux::__destroy (inline) 1ms 0.02% 69.44% 38ms 0.78% std::basic_filebuf::overflow 6ms 0.12% 69.57% 38ms 0.78% vtkDataArrayPrivate::DoComputeVectorRange 11ms 0.22% 69.79% 38ms 0.78% vtkIdList::~vtkIdList 0 0% 69.79% 37ms 0.76% _dl_start_user 0 0% 69.79% 37ms 0.76% std::__basic_file::xsputn 13ms 0.27% 70.06% 37ms 0.76% std::__new_allocator::construct (inline) 0 0% 70.06% 37ms 0.76% std::allocator_traits::construct (inline) 0 0% 70.06% 37ms 0.76% std::basic_filebuf::_M_convert_to_external 0 0% 70.06% 37ms 0.76% std::make_unique (inline) 0 0% 70.06% 36ms 0.73% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.06% 36ms 0.73% NodesOnlyMesh::ClearBoxCollection (inline) 36ms 0.73% 70.79% 36ms 0.73% __memset_avx2_unaligned_erms 36ms 0.73% 71.52% 36ms 0.73% std::_Rb_tree_increment 0 0% 71.52% 36ms 0.73% std::basic_filebuf::open 8ms 0.16% 71.69% 35ms 0.71% vtkDataArray::~vtkDataArray 10ms 0.2% 71.89% 35ms 0.71% vtkIdList::vtkIdList 35ms 0.71% 72.61% 35ms 0.71% vtkObjectBase::vtkObjectBase 1ms 0.02% 72.63% 34ms 0.69% 1ms 0.02% 72.65% 34ms 0.69% VertexElement::~VertexElement 34ms 0.69% 73.34% 34ms 0.69% __mpn_divrem 34ms 0.69% 74.04% 34ms 0.69% std::ostream::sentry::sentry 34ms 0.69% 74.73% 34ms 0.69% vtkObjectBase::Delete 0 0% 74.73% 33ms 0.67% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 74.73% 33ms 0.67% _IO_new_fopen 0 0% 74.73% 33ms 0.67% __fopen_internal (inline) 0 0% 74.73% 33ms 0.67% std::__basic_file::open 10ms 0.2% 74.93% 32ms 0.65% _int_free_merge_chunk 0 0% 74.93% 32ms 0.65% std::less::operator() (inline) 32ms 0.65% 75.59% 32ms 0.65% std::operator< (inline) 7ms 0.14% 75.73% 32ms 0.65% vtkAOSDataArrayTemplate::InsertTuple 6ms 0.12% 75.85% 32ms 0.65% vtkAbstractArray::~vtkAbstractArray 1ms 0.02% 75.87% 32ms 0.65% vtkDoubleArray::New 1ms 0.02% 75.89% 31ms 0.63% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 75.89% 31ms 0.63% _IO_new_file_fopen 0 0% 75.89% 31ms 0.63% __GI__IO_file_open 3ms 0.061% 75.95% 31ms 0.63% boost::serialization::singleton::get_instance 0 0% 75.95% 31ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 30ms 0.61% 76.57% 30ms 0.61% __libc_open64 0 0% 76.57% 30ms 0.61% vtk::detail::smp::vtkSMPToolsImplForTBB 29ms 0.59% 77.16% 29ms 0.59% [libstdc++.so.6.0.33] 8ms 0.16% 77.32% 29ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.12% 77.44% 29ms 0.59% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 77.44% 28ms 0.57% Cell::GetCellId 26ms 0.53% 77.98% 28ms 0.57% std::num_put::do_put 0 0% 77.98% 27ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.98% 27ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 2ms 0.041% 78.02% 27ms 0.55% std::ostream::flush 1ms 0.02% 78.04% 27ms 0.55% tbb::detail::r1::cancel_group_execution 21ms 0.43% 78.46% 27ms 0.55% vtkObject::ObjectFinalize 0 0% 78.46% 26ms 0.53% OutputFileHandler::OpenOutputFile 0 0% 78.46% 26ms 0.53% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.46% 26ms 0.53% std::unique_ptr::~unique_ptr (inline) 0 0% 78.46% 26ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 1ms 0.02% 78.49% 25ms 0.51% Node::AddElement 25ms 0.51% 79.00% 25ms 0.51% Node::GetNumContainingElements 0 0% 79.00% 25ms 0.51% VtkMeshWriter::MakeVtkMesh 25ms 0.51% 79.51% 25ms 0.51% [libchaste_cell_based.so] 0 0% 79.51% 25ms 0.51% orte_init 1ms 0.02% 79.53% 25ms 0.51% std::_Rb_tree::find (inline) 0 0% 79.53% 25ms 0.51% std::basic_filebuf::sync 0 0% 79.53% 25ms 0.51% std::default_delete::operator() (inline) 0 0% 79.53% 25ms 0.51% std::map::find (inline) 0 0% 79.53% 25ms 0.51% std::vector::vector (partial-inline)