File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3916ms, 78.79% of 4970ms total Dropped 778 nodes (cum <= 24.85ms) flat flat% sum% cum cum% 0 0% 0% 4765ms 95.88% __libc_start_call_main 0 0% 0% 4765ms 95.88% __libc_start_main_impl 0 0% 0% 4765ms 95.88% _start 0 0% 0% 4742ms 95.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4742ms 95.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4742ms 95.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4742ms 95.41% main 0 0% 0% 4702ms 94.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4702ms 94.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4702ms 94.61% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4691ms 94.39% AbstractCellBasedSimulation::Solve 0 0% 0% 4377ms 88.07% AbstractCellPopulation::WriteResultsToFiles 19ms 0.38% 0.38% 4127ms 83.04% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.38% 2002ms 40.28% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.04% 0.42% 1727ms 34.75% VertexMeshWriter::MakeVtkMesh 1ms 0.02% 0.44% 1311ms 26.38% vtkPolygon::New 2ms 0.04% 0.48% 1309ms 26.34% vtkPolygon::vtkPolygon 2ms 0.04% 0.52% 924ms 18.59% vtkCell::vtkCell 1ms 0.02% 0.54% 805ms 16.20% VertexMeshWriter::WriteFiles 3ms 0.06% 0.6% 781ms 15.71% vtkPoints::New 57ms 1.15% 1.75% 763ms 15.35% std::ostream::_M_insert 1ms 0.02% 1.77% 761ms 15.31% std::ostream::operator<< (inline) 16ms 0.32% 2.09% 740ms 14.89% vtkPoints::vtkPoints 35ms 0.7% 2.80% 664ms 13.36% operator new 1ms 0.02% 2.82% 641ms 12.90% vtkQuad::New 5ms 0.1% 2.92% 637ms 12.82% vtkQuad::vtkQuad 198ms 3.98% 6.90% 636ms 12.80% __GI___libc_malloc 53ms 1.07% 7.97% 631ms 12.70% std::num_put::_M_insert_float 1ms 0.02% 7.99% 599ms 12.05% vtkLine::New 0 0% 7.99% 596ms 11.99% vtkTriangle::New 0 0% 7.99% 589ms 11.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.99% 589ms 11.85% vtkXMLWriterBase::Write 0 0% 7.99% 586ms 11.79% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.99% 585ms 11.77% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.99% 585ms 11.77% vtkExecutive::CallAlgorithm 13ms 0.26% 8.25% 585ms 11.77% vtkTriangle::vtkTriangle 16ms 0.32% 8.57% 584ms 11.75% vtkLine::vtkLine 0 0% 8.57% 583ms 11.73% vtkCompositeDataPipeline::ExecuteData 0 0% 8.57% 583ms 11.73% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.57% 583ms 11.73% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.57% 521ms 10.48% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.57% 521ms 10.48% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 151ms 3.04% 11.61% 509ms 10.24% __GI___libc_free 14ms 0.28% 11.89% 497ms 10.00% std::__cxx11::collate::do_transform 28ms 0.56% 12.45% 480ms 9.66% vtkPoints::SetDataType 4ms 0.08% 12.54% 465ms 9.36% ___vsnprintf 0 0% 12.54% 461ms 9.28% __vsnprintf_internal (inline) 49ms 0.99% 13.52% 456ms 9.18% __printf_buffer 0 0% 13.52% 454ms 9.13% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.02% 13.54% 453ms 9.11% vtkXMLWriter::WriteBinaryData 0 0% 13.54% 441ms 8.87% vtkXMLWriter::WriteBinaryDataBlock 0 0% 13.54% 441ms 8.87% vtkXMLWriter::WriteBinaryDataInternal 2ms 0.04% 13.58% 383ms 7.71% __printf_fp_spec (inline) 18ms 0.36% 13.94% 381ms 7.67% __printf_fp_l_buffer 0 0% 13.94% 372ms 7.48% vtkPolygon::~vtkPolygon 231ms 4.65% 18.59% 369ms 7.42% _int_malloc 0 0% 18.59% 368ms 7.40% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 18.59% 365ms 7.34% VtkMeshWriter::WriteFiles 230ms 4.63% 23.22% 358ms 7.20% _int_free 167ms 3.36% 26.58% 348ms 7.00% __printf_fp_buffer_1 0 0% 26.58% 338ms 6.80% vtkXMLWriter::WritePointsAppendedData 0 0% 26.58% 305ms 6.14% OnLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.16% 26.74% 305ms 6.14% PottsBasedCellPopulation::UpdateCellLocations 4ms 0.08% 26.82% 303ms 6.10% vtkCell::~vtkCell 55ms 1.11% 27.93% 299ms 6.02% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 42ms 0.85% 28.77% 266ms 5.35% std::__new_allocator::allocate (inline) 0 0% 28.77% 264ms 5.31% std::allocator_traits::allocate (inline) 2ms 0.04% 28.81% 261ms 5.25% std::__new_allocator::deallocate (inline) 0 0% 28.81% 258ms 5.19% std::allocator_traits::deallocate (inline) 0 0% 28.81% 237ms 4.77% vtkXMLWriter::WriteCompressionBlock 0 0% 28.81% 225ms 4.53% compress2 0 0% 28.81% 225ms 4.53% vtkDataCompressor::Compress 0 0% 28.81% 225ms 4.53% vtkZLibDataCompressor::CompressBuffer 71ms 1.43% 30.24% 222ms 4.47% crc32 0 0% 30.24% 222ms 4.47% deflate 10ms 0.2% 30.44% 214ms 4.31% vtkBase64OutputStream::Write 13ms 0.26% 30.70% 204ms 4.10% vtkBase64OutputStream::EncodeTriplet 7ms 0.14% 30.85% 192ms 3.86% vtkPoints::~vtkPoints 72ms 1.45% 32.29% 188ms 3.78% std::_Rb_tree::_M_erase 6ms 0.12% 32.41% 185ms 3.72% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.02% 32.43% 183ms 3.68% std::set::set (inline) 115ms 2.31% 34.75% 182ms 3.66% malloc_consolidate 20ms 0.4% 35.15% 182ms 3.66% std::_Rb_tree::_Rb_tree 4ms 0.08% 35.23% 182ms 3.66% vtkFloatArray::New 0 0% 35.23% 181ms 3.64% VertexMesh::~VertexMesh 0 0% 35.23% 175ms 3.52% tbb::detail::r1::parallel_pipeline 6ms 0.12% 35.35% 175ms 3.52% vtkIdList::AllocateInternal 0 0% 35.35% 174ms 3.50% NodeLocationWriter::VisitAnyPopulation 1ms 0.02% 35.37% 174ms 3.50% vtkQuad::~vtkQuad 64ms 1.29% 36.66% 172ms 3.46% std::ostream::write 0 0% 36.66% 168ms 3.38% clone3 0 0% 36.66% 168ms 3.38% start_thread 0 0% 36.66% 167ms 3.36% tbb::detail::r1::reset 71ms 1.43% 38.09% 167ms 3.36% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 38.09% 160ms 3.22% vtkLine::GetParametricCenter 2ms 0.04% 38.13% 158ms 3.18% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.02% 38.15% 158ms 3.18% VertexMesh::VertexMesh 5ms 0.1% 38.25% 158ms 3.18% std::_Vector_base::_M_deallocate (inline) 9ms 0.18% 38.43% 158ms 3.18% std::vector::_M_default_append 3ms 0.06% 38.49% 157ms 3.16% vtkFloatArray::vtkFloatArray 1ms 0.02% 38.51% 156ms 3.14% vtkTriangle::~vtkTriangle 2ms 0.04% 38.55% 153ms 3.08% vtkDataArray::CreateDataArray 0 0% 38.55% 152ms 3.06% std::_Rb_tree::_M_create_node (inline) 1ms 0.02% 38.57% 151ms 3.04% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.08% 38.65% 149ms 3.00% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.02% 38.67% 147ms 2.96% vtkDoubleArray::vtkDoubleArray 1ms 0.02% 38.69% 144ms 2.90% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.02% 38.71% 144ms 2.90% std::vector::~vector (inline) 9ms 0.18% 38.89% 143ms 2.88% MutableElement::BuildEdges 0 0% 38.89% 143ms 2.88% std::_Rb_tree::_M_get_node (inline) 0 0% 38.89% 141ms 2.84% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.06% 38.95% 138ms 2.78% vtkTypeFloat64Array::New 69ms 1.39% 40.34% 137ms 2.76% std::__ostream_insert 133ms 2.68% 43.02% 134ms 2.70% [libz.so.1.3] 8ms 0.16% 43.18% 134ms 2.70% std::_Rb_tree::_M_copy (inline) 0 0% 43.18% 132ms 2.66% std::operator<< (inline) 0 0% 43.18% 132ms 2.66% std::set::~set (inline) 0 0% 43.18% 131ms 2.64% EdgeHelper::~EdgeHelper (inline) 5ms 0.1% 43.28% 129ms 2.60% vtkFloatArray::~vtkFloatArray 55ms 1.11% 44.39% 126ms 2.54% std::basic_filebuf::xsputn 30ms 0.6% 44.99% 126ms 2.54% vtkObject::vtkObject 2ms 0.04% 45.03% 124ms 2.49% vtkIdList::Allocate 1ms 0.02% 45.05% 122ms 2.45% EdgeHelper::GetEdgeFromNodes 10ms 0.2% 45.25% 121ms 2.43% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.25% 121ms 2.43% std::_Vector_base::_M_allocate (inline) 0 0% 45.25% 121ms 2.43% vtkTypeFloat64Array::vtkTypeFloat64Array 55ms 1.11% 46.36% 115ms 2.31% hack_digit 0 0% 46.36% 115ms 2.31% vtkXMLWriter::WritePointDataAppendedData 0 0% 46.36% 114ms 2.29% std::_Vector_base::~_Vector_base (inline) 0 0% 46.36% 113ms 2.27% std::_Rb_tree::_M_drop_node (inline) 5ms 0.1% 46.46% 108ms 2.17% std::map::operator[] (partial-inline) 106ms 2.13% 48.59% 106ms 2.13% __strcmp_avx2 0 0% 48.59% 105ms 2.11% std::_Rb_tree::_M_put_node (inline) 0 0% 48.59% 104ms 2.09% CellPropertyCollection::GetPropertiesType (inline) 56ms 1.13% 49.72% 97ms 1.95% vtkTypeFloat64Array::PrintSelf 94ms 1.89% 51.61% 94ms 1.89% __GI_sched_yield 11ms 0.22% 51.83% 94ms 1.89% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.02% 51.85% 93ms 1.87% AbstractCellProperty::IsSubType (inline) 24ms 0.48% 52.33% 92ms 1.85% __dynamic_cast 5ms 0.1% 52.43% 90ms 1.81% AbstractCellPopulation::GetCellUsingLocationIndex 30ms 0.6% 53.04% 90ms 1.81% vtkObject::Modified 89ms 1.79% 54.83% 89ms 1.79% unlink_chunk 1ms 0.02% 54.85% 88ms 1.77% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 71ms 1.43% 56.28% 87ms 1.75% std::basic_streambuf::xsputn 5ms 0.1% 56.38% 85ms 1.71% _int_free_maybe_consolidate 0 0% 56.38% 79ms 1.59% Cell::HasCellProperty (inline) 6ms 0.12% 56.50% 79ms 1.59% CellPropertyCollection::HasProperty 46ms 0.93% 57.42% 78ms 1.57% vtkObjectBase::UnRegisterInternal 4ms 0.08% 57.51% 75ms 1.51% AbstractCellProperty::IsType (inline) 3ms 0.06% 57.57% 72ms 1.45% std::vector::push_back (inline) 20ms 0.4% 57.97% 71ms 1.43% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.08% 58.05% 71ms 1.43% vtkIdList::New 6ms 0.12% 58.17% 66ms 1.33% boost::numeric::ublas::c_vector::c_vector (inline) 44ms 0.89% 59.05% 64ms 1.29% std::_Hashtable::clear 5ms 0.1% 59.15% 64ms 1.29% vtkDoubleArray::~vtkDoubleArray 0 0% 59.15% 64ms 1.29% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 59.15% 62ms 1.25% std::_Rb_tree::lower_bound (inline) 0 0% 59.15% 62ms 1.25% std::map::lower_bound (inline) 0 0% 59.15% 61ms 1.23% tcache_get (inline) 61ms 1.23% 60.38% 61ms 1.23% tcache_get_n (inline) 0 0% 60.38% 59ms 1.19% boost::numeric::ublas::vector_assign (inline) 1ms 0.02% 60.40% 58ms 1.17% Cell::GetCellProliferativeType 0 0% 60.40% 58ms 1.17% NodesOnlyMesh::~NodesOnlyMesh 5ms 0.1% 60.50% 58ms 1.17% std::vector::_M_realloc_insert 0 0% 60.50% 57ms 1.15% NodesOnlyMesh::SetUpBoxCollection 0 0% 60.50% 56ms 1.13% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 15ms 0.3% 60.80% 56ms 1.13% std::num_put::_M_insert_int 55ms 1.11% 61.91% 55ms 1.11% vtkTimeStamp::Modified 9ms 0.18% 62.09% 54ms 1.09% AbstractCellProperty::IsSame 0 0% 62.09% 54ms 1.09% std::_Rb_tree::_M_insert_unique 0 0% 62.09% 54ms 1.09% std::set::insert (inline) 0 0% 62.09% 53ms 1.07% std::map::~map (inline) 0 0% 62.09% 52ms 1.05% vtkDataArray::ComputeRange 0 0% 62.09% 50ms 1.01% VertexMesh::Clear 4ms 0.08% 62.17% 50ms 1.01% vtkDataArray::vtkDataArray 0 0% 62.17% 49ms 0.99% PottsMesh::GetMooreNeighbouringNodeIndices 48ms 0.97% 63.14% 48ms 0.97% __GI___writev 29ms 0.58% 63.72% 48ms 0.97% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.72% 47ms 0.95% std::__basic_file::xsputn_2 46ms 0.93% 64.65% 46ms 0.93% [libvtkCommonCore-9.3.so.9.3] 5ms 0.1% 64.75% 45ms 0.91% std::type_info::operator== (inline) 18ms 0.36% 65.11% 44ms 0.89% boost::numeric::ublas::indexing_vector_assign 43ms 0.87% 65.98% 43ms 0.87% std::ostream::sentry::sentry 8ms 0.16% 66.14% 42ms 0.85% vtkAbstractArray::vtkAbstractArray 12ms 0.24% 66.38% 42ms 0.85% vtkIdList::~vtkIdList 41ms 0.82% 67.20% 42ms 0.85% vtkObjectBase::Delete 1ms 0.02% 67.22% 41ms 0.82% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.08% 67.30% 40ms 0.8% std::_Rb_tree::_M_insert_ (inline) 5ms 0.1% 67.40% 40ms 0.8% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 67.40% 39ms 0.78% std::make_unique (inline) 0 0% 67.40% 38ms 0.76% _dl_init 0 0% 67.40% 38ms 0.76% call_init (inline) 38ms 0.76% 68.17% 38ms 0.76% vtkObjectBase::~vtkObjectBase 37ms 0.74% 68.91% 37ms 0.74% __memcpy_avx_unaligned_erms 0 0% 68.91% 37ms 0.74% _dl_start_user 0 0% 68.91% 37ms 0.74% std::_Destroy (inline) 0 0% 68.91% 37ms 0.74% std::_Destroy_aux::__destroy (inline) 4ms 0.08% 68.99% 37ms 0.74% vtkDataArray::~vtkDataArray 5ms 0.1% 69.09% 36ms 0.72% VertexMeshWriter::GetNextNode 0 0% 69.09% 36ms 0.72% std::basic_filebuf::open 36ms 0.72% 69.82% 36ms 0.72% vtkObject::~vtkObject 0 0% 69.82% 35ms 0.7% Cell::GetMutationState 0 0% 69.82% 35ms 0.7% CxxTest::RealWorldDescription::setUp 0 0% 69.82% 35ms 0.7% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.82% 35ms 0.7% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 69.82% 35ms 0.7% PMPI_Init_thread 0 0% 69.82% 35ms 0.7% PetscInitialize 0 0% 69.82% 35ms 0.7% PetscSetup::setUpWorld 0 0% 69.82% 35ms 0.7% PetscSetupUtils::CommonSetup 0 0% 69.82% 35ms 0.7% PetscSetupUtils::InitialisePetsc 0 0% 69.82% 35ms 0.7% ompi_mpi_init 0 0% 69.82% 34ms 0.68% OutputFileHandler::OpenOutputFile 3ms 0.06% 69.88% 34ms 0.68% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 69.88% 34ms 0.68% VtkMeshWriter::MakeVtkMesh 13ms 0.26% 70.14% 34ms 0.68% _int_free_merge_chunk 1ms 0.02% 70.16% 34ms 0.68% std::less::operator() (inline) 1ms 0.02% 70.18% 34ms 0.68% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.02% 70.20% 34ms 0.68% vtkDoubleArray::New 1ms 0.02% 70.22% 33ms 0.66% 0 0% 70.22% 33ms 0.66% _IO_new_file_fopen 0 0% 70.22% 33ms 0.66% _IO_new_fopen 0 0% 70.22% 33ms 0.66% __fopen_internal (inline) 0 0% 70.22% 33ms 0.66% boost::serialization::singleton::get_instance 0 0% 70.22% 33ms 0.66% std::__basic_file::open 33ms 0.66% 70.89% 33ms 0.66% std::operator< (inline) 0 0% 70.89% 32ms 0.64% __GI__IO_file_open 32ms 0.64% 71.53% 32ms 0.64% __mpn_divrem 0 0% 71.53% 32ms 0.64% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.02% 71.55% 31ms 0.62% DistributedBoxCollection::SetupLocalBoxesHalfOnly 31ms 0.62% 72.17% 31ms 0.62% __libc_open64 1ms 0.02% 72.19% 30ms 0.6% std::__basic_file::xsputn 0 0% 72.19% 30ms 0.6% std::basic_filebuf::_M_convert_to_external 0 0% 72.19% 30ms 0.6% std::basic_filebuf::overflow 0 0% 72.19% 30ms 0.6% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.1% 72.29% 30ms 0.6% vtkAOSDataArrayTemplate::InsertTuple 0 0% 72.29% 29ms 0.58% DistributedBoxCollection::IsOwned 29ms 0.58% 72.88% 29ms 0.58% __GI___libc_write 29ms 0.58% 73.46% 29ms 0.58% std::_Rb_tree_insert_and_rebalance 20ms 0.4% 73.86% 29ms 0.58% std::num_put::do_put 0 0% 73.86% 28ms 0.56% CellProliferativeTypesWriter::GetCellDataForVtkOutput 18ms 0.36% 74.23% 28ms 0.56% DistributedBoxCollection::CalculateContainingBox (inline) 28ms 0.56% 74.79% 28ms 0.56% Node::GetIndex 28ms 0.56% 75.35% 28ms 0.56% __mpn_mul_1 25ms 0.5% 75.86% 28ms 0.56% __printf_buffer_write 0 0% 75.86% 28ms 0.56% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 28ms 0.56% 76.42% 28ms 0.56% std::_Rb_tree_header::_M_reset (inline) 0 0% 76.42% 28ms 0.56% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.02% 76.44% 27ms 0.54% Node::ConstructNodeAttributes (inline) 0 0% 76.44% 27ms 0.54% Node::SetRadius 0 0% 76.44% 27ms 0.54% __GI___get_nprocs 27ms 0.54% 76.98% 27ms 0.54% __memset_avx2_unaligned_erms 0 0% 76.98% 27ms 0.54% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 76.98% 27ms 0.54% read_sysfs_file 0 0% 76.98% 27ms 0.54% std::thread::hardware_concurrency 2ms 0.04% 77.02% 27ms 0.54% tbb::detail::r1::cancel_group_execution 23ms 0.46% 77.48% 27ms 0.54% vtkObject::ObjectFinalize 2ms 0.04% 77.53% 26ms 0.52% VertexMeshWriter::GetNextElement 0 0% 77.53% 26ms 0.52% std::basic_ofstream::basic_ofstream (inline) 26ms 0.52% 78.05% 26ms 0.52% vtkObjectBase::vtkObjectBase 0 0% 78.05% 25ms 0.5% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.06% 78.11% 25ms 0.5% __cxa_finalize 0 0% 78.11% 25ms 0.5% _dl_call_fini 1ms 0.02% 78.13% 25ms 0.5% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 78.13% 25ms 0.5% orte_init 0 0% 78.13% 25ms 0.5% std::_Rb_tree::_Auto_node::_M_insert (inline) 2ms 0.04% 78.17% 25ms 0.5% std::_Rb_tree::_M_insert_node (inline) 25ms 0.5% 78.67% 25ms 0.5% std::_Rb_tree_increment 0 0% 78.67% 25ms 0.5% std::basic_filebuf::close 0 0% 78.67% 25ms 0.5% std::basic_ofstream::open (inline) 6ms 0.12% 78.79% 25ms 0.5% vtk::detail::smp::vtkSMPToolsImpl::For