File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3169ms, 78.93% of 4015ms total Dropped 722 nodes (cum <= 20.07ms) flat flat% sum% cum cum% 0 0% 0% 3842ms 95.69% __libc_start_call_main 0 0% 0% 3842ms 95.69% __libc_start_main_impl 0 0% 0% 3842ms 95.69% _start 0 0% 0% 3826ms 95.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3826ms 95.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3826ms 95.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3826ms 95.29% main 0 0% 0% 3783ms 94.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3783ms 94.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3783ms 94.22% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3774ms 94.00% AbstractCellBasedSimulation::Solve 0 0% 0% 3456ms 86.08% AbstractCellPopulation::WriteResultsToFiles 9ms 0.22% 0.22% 3289ms 81.92% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.22% 1631ms 40.62% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.22% 1404ms 34.97% VertexMeshWriter::MakeVtkMesh 0 0% 0.22% 1073ms 26.72% vtkPolygon::New 0 0% 0.22% 1071ms 26.67% vtkPolygon::vtkPolygon 11ms 0.27% 0.5% 728ms 18.13% vtkCell::vtkCell 1ms 0.025% 0.52% 636ms 15.84% vtkPoints::New 8ms 0.2% 0.72% 597ms 14.87% vtkPoints::vtkPoints 0 0% 0.72% 563ms 14.02% VertexMeshWriter::WriteFiles 54ms 1.34% 2.07% 526ms 13.10% std::ostream::_M_insert 0 0% 2.07% 525ms 13.08% std::ostream::operator<< (inline) 26ms 0.65% 2.71% 506ms 12.60% operator new 145ms 3.61% 6.33% 488ms 12.15% __GI___libc_malloc 0 0% 6.33% 485ms 12.08% vtkQuad::New 4ms 0.1% 6.43% 483ms 12.03% vtkQuad::vtkQuad 2ms 0.05% 6.48% 477ms 11.88% vtkLine::New 1ms 0.025% 6.50% 471ms 11.73% vtkTriangle::New 1ms 0.025% 6.53% 468ms 11.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.53% 468ms 11.66% vtkXMLWriterBase::Write 0 0% 6.53% 466ms 11.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.53% 465ms 11.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.53% 465ms 11.58% vtkDemandDrivenPipeline::ProcessRequest 10ms 0.25% 6.77% 465ms 11.58% vtkLine::vtkLine 0 0% 6.77% 464ms 11.56% vtkCompositeDataPipeline::ExecuteData 3ms 0.075% 6.85% 464ms 11.56% vtkTriangle::vtkTriangle 0 0% 6.85% 463ms 11.53% vtkExecutive::CallAlgorithm 0 0% 6.85% 463ms 11.53% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 6.85% 413ms 10.29% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 6.85% 413ms 10.29% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 32ms 0.8% 7.65% 406ms 10.11% std::num_put::_M_insert_float 86ms 2.14% 9.79% 395ms 9.84% __GI___libc_free 31ms 0.77% 10.56% 368ms 9.17% vtkPoints::SetDataType 0 0% 10.56% 364ms 9.07% vtkXMLWriter::WriteBinaryData 0 0% 10.56% 357ms 8.89% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.56% 356ms 8.87% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.56% 344ms 8.57% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 15ms 0.37% 10.93% 323ms 8.04% std::__cxx11::collate::do_transform 0 0% 10.93% 307ms 7.65% OnLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.05% 10.98% 307ms 7.65% PottsBasedCellPopulation::UpdateCellLocations 165ms 4.11% 15.09% 306ms 7.62% _int_free 191ms 4.76% 19.85% 299ms 7.45% _int_malloc 2ms 0.05% 19.90% 293ms 7.30% ___vsnprintf 0 0% 19.90% 291ms 7.25% __vsnprintf_internal (inline) 51ms 1.27% 21.17% 287ms 7.15% __printf_buffer 0 0% 21.17% 282ms 7.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 21.17% 282ms 7.02% vtkPolygon::~vtkPolygon 0 0% 21.17% 281ms 7.00% VtkMeshWriter::WriteFiles 0 0% 21.17% 262ms 6.53% vtkXMLWriter::WritePointsAppendedData 61ms 1.52% 22.69% 259ms 6.45% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 2ms 0.05% 22.74% 231ms 5.75% std::__new_allocator::deallocate (inline) 0 0% 22.74% 230ms 5.73% std::allocator_traits::deallocate (inline) 5ms 0.12% 22.86% 228ms 5.68% vtkCell::~vtkCell 50ms 1.25% 24.11% 223ms 5.55% std::__new_allocator::allocate (inline) 0 0% 24.11% 223ms 5.55% std::allocator_traits::allocate (inline) 1ms 0.025% 24.13% 223ms 5.55% std::set::set (inline) 24ms 0.6% 24.73% 222ms 5.53% std::_Rb_tree::_Rb_tree 11ms 0.27% 25.01% 213ms 5.31% __printf_fp_l_buffer 0 0% 25.01% 213ms 5.31% __printf_fp_spec (inline) 0 0% 25.01% 189ms 4.71% VertexMesh::~VertexMesh 80ms 1.99% 27.00% 189ms 4.71% __printf_fp_buffer_1 0 0% 27.00% 183ms 4.56% vtkXMLWriter::WriteCompressionBlock 4ms 0.1% 27.10% 176ms 4.38% vtkBase64OutputStream::Write 0 0% 27.10% 175ms 4.36% compress2 0 0% 27.10% 175ms 4.36% vtkDataCompressor::Compress 0 0% 27.10% 175ms 4.36% vtkZLibDataCompressor::CompressBuffer 0 0% 27.10% 174ms 4.33% deflate 37ms 0.92% 28.02% 173ms 4.31% crc32 106ms 2.64% 30.66% 171ms 4.26% malloc_consolidate 13ms 0.32% 30.98% 170ms 4.23% vtkBase64OutputStream::EncodeTriplet 5ms 0.12% 31.11% 170ms 4.23% vtkFloatArray::New 69ms 1.72% 32.83% 168ms 4.18% std::_Rb_tree::_M_erase 0 0% 32.83% 161ms 4.01% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.05% 32.88% 154ms 3.84% tbb::detail::r1::parallel_pipeline 3ms 0.075% 32.95% 152ms 3.79% vtkFloatArray::vtkFloatArray 4ms 0.1% 33.05% 148ms 3.69% vtkPoints::~vtkPoints 11ms 0.27% 33.33% 147ms 3.66% std::_Rb_tree::_M_copy (inline) 4ms 0.1% 33.42% 146ms 3.64% vtkIdList::AllocateInternal 0 0% 33.42% 143ms 3.56% clone3 0 0% 33.42% 143ms 3.56% start_thread 0 0% 33.42% 142ms 3.54% std::vector::~vector (inline) 3ms 0.075% 33.50% 141ms 3.51% std::_Vector_base::_M_deallocate (inline) 0 0% 33.50% 139ms 3.46% std::_Rb_tree::_M_create_node (inline) 3ms 0.075% 33.57% 138ms 3.44% tbb::detail::r1::reset 37ms 0.92% 34.50% 136ms 3.39% std::ostream::write 0 0% 34.50% 135ms 3.36% EdgeHelper::~EdgeHelper (inline) 1ms 0.025% 34.52% 133ms 3.31% VertexMesh::VertexMesh 3ms 0.075% 34.60% 132ms 3.29% NodesOnlyMesh::ConstructNodesWithoutMesh 129ms 3.21% 37.81% 132ms 3.29% [libz.so.1.3] 0 0% 37.81% 132ms 3.29% std::_Rb_tree::_Alloc_node::operator() (inline) 17ms 0.42% 38.23% 132ms 3.29% std::_Rb_tree::_M_clone_node (inline) 0 0% 38.23% 131ms 3.26% std::_Rb_tree::_M_get_node (inline) 2ms 0.05% 38.28% 130ms 3.24% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 66ms 1.64% 39.93% 126ms 3.14% std::basic_filebuf::xsputn 54ms 1.34% 41.27% 122ms 3.04% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 41.27% 120ms 2.99% std::_Vector_base::~_Vector_base (inline) 0 0% 41.27% 119ms 2.96% vtkQuad::~vtkQuad 4ms 0.1% 41.37% 118ms 2.94% MutableElement::BuildEdges 0 0% 41.37% 118ms 2.94% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.025% 41.39% 118ms 2.94% vtkDataArray::CreateDataArray 1ms 0.025% 41.42% 118ms 2.94% vtkTriangle::~vtkTriangle 1ms 0.025% 41.44% 114ms 2.84% vtkLine::GetParametricCenter 0 0% 41.44% 111ms 2.76% std::set::~set (inline) 2ms 0.05% 41.49% 110ms 2.74% vtkDoubleArray::vtkDoubleArray 6ms 0.15% 41.64% 109ms 2.71% vtkTypeFloat64Array::New 40ms 1% 42.64% 109ms 2.71% vtkTypeFloat64Array::PrintSelf 8ms 0.2% 42.84% 106ms 2.64% std::vector::_M_default_append 4ms 0.1% 42.94% 106ms 2.64% vtkFloatArray::~vtkFloatArray 0 0% 42.94% 106ms 2.64% vtkIdList::Allocate 2ms 0.05% 42.99% 106ms 2.64% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.025% 43.01% 104ms 2.59% EdgeHelper::GetEdgeFromNodes 0 0% 43.01% 104ms 2.59% NodeLocationWriter::VisitAnyPopulation 19ms 0.47% 43.49% 99ms 2.47% vtkObject::vtkObject 4ms 0.1% 43.59% 98ms 2.44% _int_free_maybe_consolidate 0 0% 43.59% 95ms 2.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.59% 91ms 2.27% std::_Vector_base::_M_allocate (inline) 91ms 2.27% 45.85% 91ms 2.27% unlink_chunk 0 0% 45.85% 90ms 2.24% std::_Rb_tree::_M_put_node (inline) 6ms 0.15% 46.00% 90ms 2.24% vtkTypeFloat64Array::vtkTypeFloat64Array 84ms 2.09% 48.09% 84ms 2.09% __strcmp_evex 31ms 0.77% 48.87% 82ms 2.04% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.42% 49.29% 81ms 2.02% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 49.29% 79ms 1.97% CellPropertyCollection::GetPropertiesType (inline) 46ms 1.15% 50.44% 79ms 1.97% vtkObjectBase::UnRegisterInternal 0 0% 50.44% 78ms 1.94% vtkXMLWriter::WritePointDataAppendedData 0 0% 50.44% 75ms 1.87% PottsMesh::GetMooreNeighbouringNodeIndices 56ms 1.39% 51.83% 75ms 1.87% std::_Hashtable::clear 2ms 0.05% 51.88% 75ms 1.87% std::map::operator[] (partial-inline) 74ms 1.84% 53.72% 74ms 1.84% __GI_sched_yield 0 0% 53.72% 73ms 1.82% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 3ms 0.075% 53.80% 70ms 1.74% std::vector::push_back (inline) 0 0% 53.80% 67ms 1.67% Cell::HasCellProperty (inline) 3ms 0.075% 53.87% 67ms 1.67% CellPropertyCollection::HasProperty 29ms 0.72% 54.60% 67ms 1.67% hack_digit 22ms 0.55% 55.14% 66ms 1.64% vtkObject::Modified 0 0% 55.14% 66ms 1.64% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 55.14% 64ms 1.59% AbstractCellProperty::IsSubType (inline) 22ms 0.55% 55.69% 64ms 1.59% __dynamic_cast 2ms 0.05% 55.74% 63ms 1.57% std::operator<< (inline) 0 0% 55.74% 61ms 1.52% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.025% 55.77% 61ms 1.52% AbstractCellProperty::IsType (inline) 20ms 0.5% 56.26% 61ms 1.52% std::__ostream_insert 0 0% 56.26% 60ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 56.26% 60ms 1.49% std::map::lower_bound (inline) 3ms 0.075% 56.34% 57ms 1.42% vtkDataArray::vtkDataArray 1ms 0.025% 56.36% 54ms 1.34% VertexMesh::Clear 0 0% 56.36% 53ms 1.32% NodesOnlyMesh::SetUpBoxCollection 5ms 0.12% 56.49% 53ms 1.32% std::vector::_M_realloc_insert 15ms 0.37% 56.86% 53ms 1.32% vtkAbstractArray::vtkAbstractArray 1ms 0.025% 56.89% 53ms 1.32% vtkDoubleArray::~vtkDoubleArray 0 0% 56.89% 50ms 1.25% std::map::~map (inline) 4ms 0.1% 56.99% 50ms 1.25% vtkIdList::New 0 0% 56.99% 49ms 1.22% NodesOnlyMesh::~NodesOnlyMesh 49ms 1.22% 58.21% 49ms 1.22% __memcpy_avx512_unaligned_erms 0 0% 58.21% 49ms 1.22% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.025% 58.23% 49ms 1.22% std::_Rb_tree_header::_Rb_tree_header (inline) 9ms 0.22% 58.46% 48ms 1.20% AbstractCellProperty::IsSame 47ms 1.17% 59.63% 47ms 1.17% std::_Rb_tree_header::_M_reset (inline) 0 0% 59.63% 45ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 3ms 0.075% 59.70% 44ms 1.10% boost::numeric::ublas::c_vector::c_vector (partial-inline) 26ms 0.65% 60.35% 44ms 1.10% std::basic_streambuf::xsputn 42ms 1.05% 61.39% 42ms 1.05% [libvtkCommonCore-9.3.so.9.3] 0 0% 61.39% 41ms 1.02% Cell::GetCellProliferativeType 41ms 1.02% 62.42% 41ms 1.02% Node::GetIndex 1ms 0.025% 62.44% 41ms 1.02% VertexMeshWriter::GetNextNode 0 0% 62.44% 41ms 1.02% boost::numeric::ublas::vector_assign (inline) 7ms 0.17% 62.62% 41ms 1.02% std::num_put::_M_insert_int 1ms 0.025% 62.64% 41ms 1.02% vtkDoubleArray::New 0 0% 62.64% 40ms 1% CxxTest::RealWorldDescription::setUp 0 0% 62.64% 40ms 1% PetscInitialize 0 0% 62.64% 40ms 1% PetscSetup::setUpWorld 0 0% 62.64% 40ms 1% PetscSetupUtils::CommonSetup 0 0% 62.64% 40ms 1% PetscSetupUtils::InitialisePetsc 40ms 1% 63.64% 40ms 1% vtkTimeStamp::Modified 0 0% 63.64% 39ms 0.97% PMPI_Init_thread 39ms 0.97% 64.61% 39ms 0.97% __GI___writev 0 0% 64.61% 39ms 0.97% ompi_mpi_init 0 0% 64.61% 39ms 0.97% std::_Rb_tree::_M_insert_unique 0 0% 64.61% 39ms 0.97% std::__basic_file::xsputn_2 0 0% 64.61% 39ms 0.97% std::set::insert (inline) 6ms 0.15% 64.76% 39ms 0.97% std::type_info::operator== (inline) 0 0% 64.76% 39ms 0.97% tcache_get (inline) 39ms 0.97% 65.73% 39ms 0.97% tcache_get_n (inline) 0 0% 65.73% 37ms 0.92% 0 0% 65.73% 37ms 0.92% _dl_init 0 0% 65.73% 37ms 0.92% call_init (inline) 0 0% 65.73% 37ms 0.92% std::make_unique (inline) 36ms 0.9% 66.63% 36ms 0.9% vtkObjectBase::vtkObjectBase 3ms 0.075% 66.70% 35ms 0.87% VertexMeshWriter::GetNextElement 35ms 0.87% 67.57% 35ms 0.87% [libstdc++.so.6.0.33] 1ms 0.025% 67.60% 35ms 0.87% std::less::operator() (inline) 34ms 0.85% 68.44% 34ms 0.85% std::operator< (inline) 5ms 0.12% 68.57% 34ms 0.85% vtkIdList::~vtkIdList 28ms 0.7% 69.27% 32ms 0.8% vtkObject::ObjectFinalize 1ms 0.025% 69.29% 31ms 0.77% DistributedBoxCollection::IsOwned 3ms 0.075% 69.36% 31ms 0.77% DistributedBoxCollection::SetupLocalBoxesHalfOnly 12ms 0.3% 69.66% 31ms 0.77% boost::numeric::ublas::indexing_vector_assign 31ms 0.77% 70.44% 31ms 0.77% std::ostream::sentry::sentry 4ms 0.1% 70.54% 31ms 0.77% vtkAOSDataArrayTemplate::InsertTuple 0 0% 70.54% 31ms 0.77% vtkDataArray::ComputeRange 5ms 0.12% 70.66% 31ms 0.77% vtkDataArrayPrivate::DoComputeVectorRange 20ms 0.5% 71.16% 30ms 0.75% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.16% 30ms 0.75% DistributedBoxCollection::~DistributedBoxCollection 1ms 0.025% 71.18% 30ms 0.75% Edge::Edge 0 0% 71.18% 30ms 0.75% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 71.18% 30ms 0.75% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 71.18% 30ms 0.75% _dl_start_user 10ms 0.25% 71.43% 30ms 0.75% _int_free_merge_chunk 30ms 0.75% 72.18% 30ms 0.75% vtkObject::~vtkObject 1ms 0.025% 72.20% 29ms 0.72% Cell::GetMutationState 5ms 0.12% 72.33% 29ms 0.72% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 72.33% 28ms 0.7% Edge::SetNodes (inline) 1ms 0.025% 72.35% 28ms 0.7% VtkMeshWriter::MakeVtkMesh 14ms 0.35% 72.70% 28ms 0.7% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.7% 73.40% 28ms 0.7% __mpn_divrem 6ms 0.15% 73.55% 28ms 0.7% vtkDataArray::~vtkDataArray 0 0% 73.55% 27ms 0.67% std::basic_filebuf::open 0 0% 73.55% 26ms 0.65% _IO_new_fopen 0 0% 73.55% 26ms 0.65% __fopen_internal (inline) 26ms 0.65% 74.20% 26ms 0.65% __memset_avx512_unaligned_erms 2ms 0.05% 74.25% 26ms 0.65% std::_Rb_tree::_M_insert_ (inline) 0 0% 74.25% 26ms 0.65% std::__basic_file::open 0 0% 74.25% 26ms 0.65% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 74.25% 25ms 0.62% _IO_new_file_fopen 0 0% 74.25% 25ms 0.62% __GI__IO_file_open 25ms 0.62% 74.87% 25ms 0.62% __libc_open64 0 0% 74.87% 25ms 0.62% orte_init 0 0% 74.87% 24ms 0.6% std::_Destroy (inline) 0 0% 74.87% 24ms 0.6% std::_Destroy_aux::__destroy (inline) 24ms 0.6% 75.47% 24ms 0.6% std::_Rb_tree_increment 1ms 0.025% 75.49% 24ms 0.6% std::__basic_file::xsputn 0 0% 75.49% 24ms 0.6% std::basic_filebuf::_M_convert_to_external 0 0% 75.49% 24ms 0.6% std::basic_filebuf::overflow 0 0% 75.49% 24ms 0.6% tbb::detail::r1::cancel_group_execution 6ms 0.15% 75.64% 24ms 0.6% vtkAOSDataArrayTemplate::AllocateTuples 24ms 0.6% 76.24% 24ms 0.6% vtkObjectBase::~vtkObjectBase 1ms 0.025% 76.26% 23ms 0.57% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 23ms 0.57% 76.84% 23ms 0.57% __GI___libc_write 23ms 0.57% 77.41% 23ms 0.57% std::_Rb_tree::_S_right (inline) 1ms 0.025% 77.43% 23ms 0.57% std::_Rb_tree::find (inline) 0 0% 77.43% 23ms 0.57% std::map::find (inline) 2ms 0.05% 77.48% 23ms 0.57% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 77.48% 22ms 0.55% PottsBasedCellPopulation::AcceptCellWriter 22ms 0.55% 78.03% 22ms 0.55% boost::numeric::ublas::c_vector::operator() 1ms 0.025% 78.06% 22ms 0.55% boost::serialization::singleton::get_instance 8ms 0.2% 78.26% 22ms 0.55% std::__new_allocator::construct (inline) 0 0% 78.26% 22ms 0.55% std::allocator_traits::construct (inline) 0 0% 78.26% 21ms 0.52% Cell::GetCellId 21ms 0.52% 78.78% 21ms 0.52% Node::GetNumContainingElements 1ms 0.025% 78.80% 21ms 0.52% Node::~Node 1ms 0.025% 78.83% 21ms 0.52% OutputFileHandler::OpenOutputFile 0 0% 78.83% 21ms 0.52% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 4ms 0.1% 78.93% 21ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 78.93% 21ms 0.52% vtkXMLUnstructuredDataWriter::WriteHeader