File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3752ms, 79.02% of 4748ms total Dropped 709 nodes (cum <= 23.74ms) flat flat% sum% cum cum% 0 0% 0% 4552ms 95.87% __libc_start_call_main 0 0% 0% 4552ms 95.87% __libc_start_main_impl 0 0% 0% 4552ms 95.87% _start 0 0% 0% 4534ms 95.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4534ms 95.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4534ms 95.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4534ms 95.49% main 0 0% 0% 4496ms 94.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4496ms 94.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4496ms 94.69% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4485ms 94.46% AbstractCellBasedSimulation::Solve 0 0% 0% 4183ms 88.10% AbstractCellPopulation::WriteResultsToFiles 14ms 0.29% 0.29% 3966ms 83.53% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.29% 2024ms 42.63% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.063% 0.36% 1747ms 36.79% VertexMeshWriter::MakeVtkMesh 0 0% 0.36% 1295ms 27.27% vtkPolygon::New 2ms 0.042% 0.4% 1294ms 27.25% vtkPolygon::vtkPolygon 4ms 0.084% 0.48% 921ms 19.40% vtkCell::vtkCell 3ms 0.063% 0.55% 790ms 16.64% vtkPoints::New 12ms 0.25% 0.8% 742ms 15.63% vtkPoints::vtkPoints 1ms 0.021% 0.82% 688ms 14.49% VertexMeshWriter::WriteFiles 64ms 1.35% 2.17% 670ms 14.11% std::ostream::_M_insert 0 0% 2.17% 668ms 14.07% std::ostream::operator<< (inline) 34ms 0.72% 2.89% 622ms 13.10% operator new 2ms 0.042% 2.93% 601ms 12.66% vtkQuad::New 182ms 3.83% 6.76% 598ms 12.59% __GI___libc_malloc 2ms 0.042% 6.80% 596ms 12.55% vtkQuad::vtkQuad 1ms 0.021% 6.82% 592ms 12.47% vtkLine::New 5ms 0.11% 6.93% 580ms 12.22% vtkTriangle::New 9ms 0.19% 7.12% 573ms 12.07% vtkLine::vtkLine 9ms 0.19% 7.31% 570ms 12.01% vtkTriangle::vtkTriangle 1ms 0.021% 7.33% 568ms 11.96% vtkXMLWriterBase::Write 0 0% 7.33% 567ms 11.94% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.33% 566ms 11.92% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.33% 566ms 11.92% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.33% 566ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.33% 565ms 11.90% vtkCompositeDataPipeline::ExecuteData 0 0% 7.33% 565ms 11.90% vtkExecutive::CallAlgorithm 0 0% 7.33% 565ms 11.90% vtkXMLUnstructuredDataWriter::ProcessRequest 43ms 0.91% 8.24% 535ms 11.27% std::num_put::_M_insert_float 110ms 2.32% 10.55% 513ms 10.80% __GI___libc_free 0 0% 10.55% 505ms 10.64% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.55% 505ms 10.64% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 24ms 0.51% 11.06% 471ms 9.92% vtkPoints::SetDataType 0 0% 11.06% 458ms 9.65% vtkXMLWriter::WriteBinaryData 0 0% 11.06% 451ms 9.50% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.06% 450ms 9.48% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.06% 443ms 9.33% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.23% 11.29% 433ms 9.12% std::__cxx11::collate::do_transform 0 0% 11.29% 405ms 8.53% ___vsnprintf 0 0% 11.29% 405ms 8.53% __vsnprintf_internal (inline) 63ms 1.33% 12.62% 401ms 8.45% __printf_buffer 247ms 5.20% 17.82% 401ms 8.45% _int_free 0 0% 17.82% 401ms 8.45% vtkPolygon::~vtkPolygon 223ms 4.70% 22.51% 350ms 7.37% _int_malloc 0 0% 22.51% 340ms 7.16% vtkXMLWriter::WritePointsAppendedData 8ms 0.17% 22.68% 338ms 7.12% vtkCell::~vtkCell 0 0% 22.68% 335ms 7.06% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.68% 331ms 6.97% VtkMeshWriter::WriteFiles 6ms 0.13% 22.81% 318ms 6.70% __printf_fp_l_buffer 0 0% 22.81% 318ms 6.70% __printf_fp_spec (inline) 43ms 0.91% 23.72% 302ms 6.36% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 149ms 3.14% 26.85% 299ms 6.30% __printf_fp_buffer_1 0 0% 26.85% 292ms 6.15% OnLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.17% 27.02% 292ms 6.15% PottsBasedCellPopulation::UpdateCellLocations 3ms 0.063% 27.09% 274ms 5.77% std::__new_allocator::deallocate (inline) 0 0% 27.09% 272ms 5.73% std::allocator_traits::deallocate (inline) 37ms 0.78% 27.86% 253ms 5.33% std::__new_allocator::allocate (inline) 0 0% 27.86% 252ms 5.31% std::allocator_traits::allocate (inline) 0 0% 27.86% 236ms 4.97% vtkXMLWriter::WriteCompressionBlock 0 0% 27.86% 225ms 4.74% vtkDataCompressor::Compress 0 0% 27.86% 224ms 4.72% compress2 0 0% 27.86% 224ms 4.72% vtkZLibDataCompressor::CompressBuffer 46ms 0.97% 28.83% 221ms 4.65% crc32 0 0% 28.83% 221ms 4.65% deflate 7ms 0.15% 28.98% 221ms 4.65% vtkBase64OutputStream::Write 20ms 0.42% 29.40% 211ms 4.44% vtkBase64OutputStream::EncodeTriplet 7ms 0.15% 29.55% 210ms 4.42% vtkPoints::~vtkPoints 1ms 0.021% 29.57% 192ms 4.04% vtkLine::GetParametricCenter 1ms 0.021% 29.59% 181ms 3.81% vtkTriangle::~vtkTriangle 106ms 2.23% 31.82% 180ms 3.79% malloc_consolidate 37ms 0.78% 32.60% 180ms 3.79% std::_Rb_tree::_M_erase 1ms 0.021% 32.62% 178ms 3.75% vtkFloatArray::New 1ms 0.021% 32.65% 178ms 3.75% vtkQuad::~vtkQuad 3ms 0.063% 32.71% 176ms 3.71% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.063% 32.77% 176ms 3.71% vtkIdList::AllocateInternal 2ms 0.042% 32.81% 171ms 3.60% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 32.81% 171ms 3.60% tbb::detail::r1::parallel_pipeline 35ms 0.74% 33.55% 169ms 3.56% std::ostream::write 2ms 0.042% 33.59% 168ms 3.54% std::set::set (inline) 13ms 0.27% 33.87% 166ms 3.50% std::_Rb_tree::_Rb_tree 160ms 3.37% 37.24% 165ms 3.48% [libz.so.1.3] 0 0% 37.24% 164ms 3.45% VertexMesh::~VertexMesh 0 0% 37.24% 161ms 3.39% clone3 0 0% 37.24% 161ms 3.39% start_thread 3ms 0.063% 37.30% 158ms 3.33% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 37.30% 157ms 3.31% std::_Rb_tree::_M_create_node (inline) 2ms 0.042% 37.34% 156ms 3.29% vtkFloatArray::vtkFloatArray 0 0% 37.34% 154ms 3.24% tbb::detail::r1::reset 0 0% 37.34% 147ms 3.10% VertexMesh::VertexMesh 0 0% 37.34% 147ms 3.10% std::set::~set (inline) 4ms 0.084% 37.43% 147ms 3.10% vtkDataArray::CreateDataArray 1ms 0.021% 37.45% 147ms 3.10% vtkDoubleArray::vtkDoubleArray 2ms 0.042% 37.49% 145ms 3.05% std::_Vector_base::_M_deallocate (inline) 73ms 1.54% 39.03% 145ms 3.05% std::basic_filebuf::xsputn 0 0% 39.03% 144ms 3.03% std::vector::~vector (inline) 0 0% 39.03% 143ms 3.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 39.03% 143ms 3.01% std::_Rb_tree::_M_get_node (inline) 0 0% 39.03% 142ms 2.99% NodeLocationWriter::VisitAnyPopulation 35ms 0.74% 39.76% 142ms 2.99% vtkObject::vtkObject 8ms 0.17% 39.93% 141ms 2.97% MutableElement::BuildEdges 0 0% 39.93% 141ms 2.97% VertexMesh::GenerateEdgesFromElements (inline) 16ms 0.34% 40.27% 140ms 2.95% std::vector::_M_default_append 61ms 1.28% 41.55% 138ms 2.91% tbb::detail::r1::wait_bounded_queue_monitor 4ms 0.084% 41.64% 138ms 2.91% vtkFloatArray::~vtkFloatArray 0 0% 41.64% 136ms 2.86% std::_Rb_tree::_M_drop_node (inline) 6ms 0.13% 41.76% 133ms 2.80% vtkTypeFloat64Array::New 2ms 0.042% 41.81% 132ms 2.78% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.81% 129ms 2.72% std::_Rb_tree::_M_put_node (inline) 9ms 0.19% 42.00% 128ms 2.70% std::_Rb_tree::_M_copy (inline) 2ms 0.042% 42.04% 121ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.063% 42.10% 118ms 2.49% EdgeHelper::GetEdgeFromNodes 0 0% 42.10% 118ms 2.49% EdgeHelper::~EdgeHelper (inline) 4ms 0.084% 42.19% 118ms 2.49% vtkTypeFloat64Array::vtkTypeFloat64Array 11ms 0.23% 42.42% 116ms 2.44% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.42% 116ms 2.44% std::_Vector_base::~_Vector_base (inline) 115ms 2.42% 44.84% 115ms 2.42% __strcmp_avx2 1ms 0.021% 44.86% 114ms 2.40% vtkIdList::Allocate 1ms 0.021% 44.88% 110ms 2.32% std::_Vector_base::_M_allocate (inline) 67ms 1.41% 46.29% 108ms 2.27% vtkObjectBase::UnRegisterInternal 21ms 0.44% 46.74% 101ms 2.13% __dynamic_cast 0 0% 46.74% 100ms 2.11% AbstractCellProperty::IsSubType (inline) 0 0% 46.74% 99ms 2.09% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 46.76% 98ms 2.06% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 7ms 0.15% 46.90% 98ms 2.06% _int_free_maybe_consolidate 29ms 0.61% 47.51% 98ms 2.06% vtkObject::Modified 97ms 2.04% 49.56% 97ms 2.04% unlink_chunk 40ms 0.84% 50.40% 94ms 1.98% std::__ostream_insert 2ms 0.042% 50.44% 93ms 1.96% std::map::operator[] (partial-inline) 47ms 0.99% 51.43% 92ms 1.94% hack_digit 2ms 0.042% 51.47% 90ms 1.90% std::operator<< (inline) 42ms 0.88% 52.36% 89ms 1.87% vtkTypeFloat64Array::PrintSelf 1ms 0.021% 52.38% 85ms 1.79% AbstractCellProperty::IsType (inline) 3ms 0.063% 52.44% 85ms 1.79% CellPropertyCollection::HasProperty 0 0% 52.44% 84ms 1.77% Cell::HasCellProperty (inline) 6ms 0.13% 52.57% 84ms 1.77% vtkAOSDataArrayTemplate::DataElementChanged 80ms 1.68% 54.25% 80ms 1.68% __GI_sched_yield 6ms 0.13% 54.38% 79ms 1.66% boost::numeric::ublas::c_vector::c_vector (partial-inline) 29ms 0.61% 54.99% 74ms 1.56% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 55.01% 72ms 1.52% boost::numeric::ublas::vector_assign (inline) 0 0% 55.01% 69ms 1.45% Cell::GetCellProliferativeType 6ms 0.13% 55.14% 69ms 1.45% vtkDataArray::vtkDataArray 6ms 0.13% 55.27% 69ms 1.45% vtkDoubleArray::~vtkDoubleArray 8ms 0.17% 55.43% 68ms 1.43% vtkIdList::New 0 0% 55.43% 65ms 1.37% NodesOnlyMesh::SetUpBoxCollection 46ms 0.97% 56.40% 65ms 1.37% std::basic_streambuf::xsputn 38ms 0.8% 57.20% 64ms 1.35% std::_Hashtable::clear 11ms 0.23% 57.43% 62ms 1.31% AbstractCellProperty::IsSame 3ms 0.063% 57.50% 62ms 1.31% std::vector::push_back (inline) 13ms 0.27% 57.77% 62ms 1.31% vtkAbstractArray::vtkAbstractArray 62ms 1.31% 59.08% 62ms 1.31% vtkTimeStamp::Modified 0 0% 59.08% 62ms 1.31% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 59.08% 60ms 1.26% tcache_get (inline) 60ms 1.26% 60.34% 60ms 1.26% tcache_get_n (inline) 0 0% 60.34% 59ms 1.24% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 60.36% 58ms 1.22% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 60.36% 57ms 1.20% std::_Rb_tree::lower_bound (inline) 0 0% 60.36% 57ms 1.20% std::map::lower_bound (inline) 55ms 1.16% 61.52% 55ms 1.16% [libvtkCommonCore-9.3.so.9.3] 0 0% 61.52% 53ms 1.12% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.021% 61.54% 52ms 1.10% std::_Rb_tree::_M_insert_unique 0 0% 61.54% 52ms 1.10% std::set::insert (inline) 17ms 0.36% 61.90% 51ms 1.07% std::type_info::operator== (inline) 18ms 0.38% 62.28% 50ms 1.05% boost::numeric::ublas::indexing_vector_assign 48ms 1.01% 63.29% 48ms 1.01% [libstdc++.so.6.0.33] 47ms 0.99% 64.28% 48ms 1.01% __GI___writev 22ms 0.46% 64.74% 48ms 1.01% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.74% 48ms 1.01% std::__basic_file::xsputn_2 5ms 0.11% 64.85% 48ms 1.01% vtkDataArray::~vtkDataArray 9ms 0.19% 65.04% 47ms 0.99% std::num_put::_M_insert_int 3ms 0.063% 65.10% 46ms 0.97% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 2ms 0.042% 65.14% 46ms 0.97% VertexMesh::Clear 46ms 0.97% 66.11% 46ms 0.97% vtkObject::~vtkObject 3ms 0.063% 66.18% 45ms 0.95% std::vector::_M_realloc_insert 45ms 0.95% 67.12% 45ms 0.95% vtkObjectBase::Delete 3ms 0.063% 67.19% 44ms 0.93% std::_Rb_tree::_M_insert_ (inline) 2ms 0.042% 67.23% 42ms 0.88% vtkDoubleArray::New 41ms 0.86% 68.09% 41ms 0.86% std::ostream::sentry::sentry 37ms 0.78% 68.87% 41ms 0.86% vtkObject::ObjectFinalize 8ms 0.17% 69.04% 40ms 0.84% vtkSOADataArrayTemplate::FillTypedComponent 2ms 0.042% 69.08% 39ms 0.82% VertexMeshWriter::GetNextNode 0 0% 69.08% 39ms 0.82% _dl_init 0 0% 69.08% 39ms 0.82% call_init (inline) 6ms 0.13% 69.21% 39ms 0.82% vtkIdList::~vtkIdList 6ms 0.13% 69.33% 38ms 0.8% DistributedBoxCollection::SetupLocalBoxesHalfOnly 38ms 0.8% 70.13% 38ms 0.8% __memcpy_avx_unaligned_erms 1ms 0.021% 70.16% 36ms 0.76% DistributedBoxCollection::IsOwned 1ms 0.021% 70.18% 35ms 0.74% CellProliferativeTypesWriter::GetCellDataForVtkOutput 20ms 0.42% 70.60% 35ms 0.74% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 70.60% 35ms 0.74% _dl_start_user 0 0% 70.60% 34ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 70.60% 34ms 0.72% PetscSetup::setUpWorld 0 0% 70.60% 34ms 0.72% PetscSetupUtils::CommonSetup 0 0% 70.60% 34ms 0.72% std::_Destroy (inline) 0 0% 70.60% 34ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.60% 34ms 0.72% std::basic_filebuf::open 0 0% 70.60% 33ms 0.7% Cell::GetMutationState 0 0% 70.60% 33ms 0.7% PMPI_Init_thread 0 0% 70.60% 33ms 0.7% PetscInitialize 0 0% 70.60% 33ms 0.7% PetscSetupUtils::InitialisePetsc 0 0% 70.60% 33ms 0.7% ompi_mpi_init 0 0% 70.60% 33ms 0.7% std::_Destroy_aux::__destroy (inline) 1ms 0.021% 70.62% 33ms 0.7% std::make_unique (inline) 0 0% 70.62% 32ms 0.67% Cell::GetCellId 32ms 0.67% 71.29% 32ms 0.67% __mpn_divrem 32ms 0.67% 71.97% 32ms 0.67% boost::numeric::ublas::c_vector::operator() 3ms 0.063% 72.03% 32ms 0.67% boost::serialization::singleton::get_instance 7ms 0.15% 72.18% 32ms 0.67% vtkAOSDataArrayTemplate::InsertTuple 1ms 0.021% 72.20% 32ms 0.67% vtkDataArray::ComputeRange 4ms 0.084% 72.28% 32ms 0.67% vtkDataArrayPrivate::DoComputeVectorRange 32ms 0.67% 72.96% 32ms 0.67% vtkObjectBase::vtkObjectBase 0 0% 72.96% 31ms 0.65% DistributedBoxCollection::~DistributedBoxCollection 0 0% 72.96% 31ms 0.65% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 72.96% 31ms 0.65% _IO_new_file_fopen 0 0% 72.96% 31ms 0.65% _IO_new_fopen 1ms 0.021% 72.98% 31ms 0.65% __GI__IO_file_open 0 0% 72.98% 31ms 0.65% __fopen_internal (inline) 0 0% 72.98% 31ms 0.65% std::__basic_file::open 0 0% 72.98% 31ms 0.65% std::less::operator() (inline) 31ms 0.65% 73.63% 31ms 0.65% std::operator< (inline) 31ms 0.65% 74.28% 31ms 0.65% tcache_put (inline) 31ms 0.65% 74.94% 31ms 0.65% vtkObjectBase::~vtkObjectBase 0 0% 74.94% 30ms 0.63% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 74.94% 30ms 0.63% OutputFileHandler::OpenOutputFile 1ms 0.021% 74.96% 30ms 0.63% PottsBasedCellPopulation::AcceptCellWriter 30ms 0.63% 75.59% 30ms 0.63% __libc_open64 0 0% 75.59% 30ms 0.63% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 75.59% 29ms 0.61% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 75.61% 29ms 0.61% Node::SetRadius 8ms 0.17% 75.78% 29ms 0.61% _int_free_merge_chunk 0 0% 75.78% 29ms 0.61% std::map::~map (inline) 21ms 0.44% 76.22% 29ms 0.61% std::num_put::do_put 1ms 0.021% 76.24% 28ms 0.59% 0 0% 76.24% 28ms 0.59% Node::ConstructNodeAttributes (inline) 28ms 0.59% 76.83% 28ms 0.59% __memset_avx2_unaligned_erms 0 0% 76.83% 28ms 0.59% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 76.85% 28ms 0.59% tbb::detail::r1::cancel_group_execution 10ms 0.21% 77.06% 28ms 0.59% vtkAbstractArray::~vtkAbstractArray 0 0% 77.06% 27ms 0.57% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 26ms 0.55% 77.61% 26ms 0.55% __GI___libc_write 2ms 0.042% 77.65% 26ms 0.55% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 77.65% 26ms 0.55% std::__basic_file::xsputn 10ms 0.21% 77.86% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 77.86% 26ms 0.55% std::allocator_traits::construct (inline) 0 0% 77.86% 26ms 0.55% std::basic_filebuf::_M_convert_to_external 0 0% 77.86% 26ms 0.55% std::basic_filebuf::overflow 25ms 0.53% 78.39% 25ms 0.53% std::_Rb_tree_increment 4ms 0.084% 78.48% 25ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 78.48% 24ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.48% 24ms 0.51% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.042% 78.52% 24ms 0.51% std::_Rb_tree_header::_Rb_tree_header (inline) 24ms 0.51% 79.02% 24ms 0.51% std::codecvt::do_always_noconv