File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3644ms, 76.78% of 4746ms total Dropped 737 nodes (cum <= 23.73ms) flat flat% sum% cum cum% 0 0% 0% 4507ms 94.96% __libc_start_call_main 0 0% 0% 4507ms 94.96% __libc_start_main_impl 0 0% 0% 4507ms 94.96% _start 0 0% 0% 4489ms 94.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4489ms 94.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4489ms 94.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4489ms 94.58% main 0 0% 0% 4454ms 93.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4454ms 93.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4454ms 93.85% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4443ms 93.62% AbstractCellBasedSimulation::Solve 0 0% 0% 4178ms 88.03% AbstractCellPopulation::WriteResultsToFiles 15ms 0.32% 0.32% 3942ms 83.06% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.32% 1974ms 41.59% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.042% 0.36% 1703ms 35.88% VertexMeshWriter::MakeVtkMesh 0 0% 0.36% 1266ms 26.68% vtkPolygon::New 2ms 0.042% 0.4% 1265ms 26.65% vtkPolygon::vtkPolygon 7ms 0.15% 0.55% 922ms 19.43% vtkCell::vtkCell 6ms 0.13% 0.67% 777ms 16.37% vtkPoints::New 0 0% 0.67% 747ms 15.74% VertexMeshWriter::WriteFiles 13ms 0.27% 0.95% 717ms 15.11% vtkPoints::vtkPoints 58ms 1.22% 2.17% 713ms 15.02% std::ostream::_M_insert 0 0% 2.17% 713ms 15.02% std::ostream::operator<< (inline) 44ms 0.93% 3.10% 681ms 14.35% operator new 217ms 4.57% 7.67% 641ms 13.51% __GI___libc_malloc 1ms 0.021% 7.69% 621ms 13.08% vtkLine::New 10ms 0.21% 7.90% 598ms 12.60% vtkLine::vtkLine 0 0% 7.90% 592ms 12.47% vtkQuad::New 4ms 0.084% 7.99% 591ms 12.45% vtkQuad::vtkQuad 24ms 0.51% 8.49% 579ms 12.20% std::num_put::_M_insert_float 0 0% 8.49% 568ms 11.97% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.49% 568ms 11.97% vtkXMLWriterBase::Write 0 0% 8.49% 567ms 11.95% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.021% 8.51% 565ms 11.90% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.51% 565ms 11.90% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.51% 564ms 11.88% vtkCompositeDataPipeline::ExecuteData 0 0% 8.51% 564ms 11.88% vtkExecutive::CallAlgorithm 0 0% 8.51% 564ms 11.88% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.021% 8.53% 560ms 11.80% vtkTriangle::New 3ms 0.063% 8.60% 553ms 11.65% vtkTriangle::vtkTriangle 0 0% 8.60% 507ms 10.68% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.60% 507ms 10.68% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 141ms 2.97% 11.57% 504ms 10.62% __GI___libc_free 9ms 0.19% 11.76% 469ms 9.88% std::__cxx11::collate::do_transform 0 0% 11.76% 440ms 9.27% vtkXMLWriter::WriteBinaryData 10ms 0.21% 11.97% 436ms 9.19% ___vsnprintf 0 0% 11.97% 436ms 9.19% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.97% 436ms 9.19% vtkXMLWriter::WriteBinaryDataInternal 36ms 0.76% 12.73% 434ms 9.14% vtkPoints::SetDataType 0 0% 12.73% 426ms 8.98% __vsnprintf_internal (inline) 0 0% 12.73% 422ms 8.89% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 51ms 1.07% 13.80% 417ms 8.79% __printf_buffer 5ms 0.11% 13.91% 381ms 8.03% vtkPolygon::~vtkPolygon 230ms 4.85% 18.75% 362ms 7.63% _int_free 257ms 5.42% 24.17% 358ms 7.54% _int_malloc 0 0% 24.17% 347ms 7.31% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.17% 343ms 7.23% VtkMeshWriter::WriteFiles 2ms 0.042% 24.21% 330ms 6.95% __printf_fp_spec (inline) 14ms 0.29% 24.50% 328ms 6.91% __printf_fp_l_buffer 0 0% 24.50% 319ms 6.72% vtkXMLWriter::WritePointsAppendedData 4ms 0.084% 24.59% 307ms 6.47% vtkCell::~vtkCell 163ms 3.43% 28.02% 306ms 6.45% __printf_fp_buffer_1 37ms 0.78% 28.80% 278ms 5.86% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 30ms 0.63% 29.44% 271ms 5.71% std::__new_allocator::allocate (inline) 0 0% 29.44% 270ms 5.69% std::allocator_traits::allocate (inline) 1ms 0.021% 29.46% 262ms 5.52% std::__new_allocator::deallocate (inline) 0 0% 29.46% 257ms 5.42% std::allocator_traits::deallocate (inline) 0 0% 29.46% 254ms 5.35% OnLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.19% 29.65% 254ms 5.35% PottsBasedCellPopulation::UpdateCellLocations 5ms 0.11% 29.75% 226ms 4.76% vtkBase64OutputStream::Write 18ms 0.38% 30.13% 221ms 4.66% vtkBase64OutputStream::EncodeTriplet 0 0% 30.13% 218ms 4.59% vtkXMLWriter::WriteCompressionBlock 0 0% 30.13% 212ms 4.47% tbb::detail::r1::parallel_pipeline 0 0% 30.13% 210ms 4.42% vtkDataCompressor::Compress 9ms 0.19% 30.32% 210ms 4.42% vtkPoints::~vtkPoints 0 0% 30.32% 209ms 4.40% compress2 0 0% 30.32% 209ms 4.40% vtkZLibDataCompressor::CompressBuffer 1ms 0.021% 30.34% 207ms 4.36% deflate 51ms 1.07% 31.42% 206ms 4.34% crc32 0 0% 31.42% 202ms 4.26% clone3 0 0% 31.42% 202ms 4.26% start_thread 1ms 0.021% 31.44% 199ms 4.19% tbb::detail::r1::reset 87ms 1.83% 33.27% 198ms 4.17% tbb::detail::r1::wait_bounded_queue_monitor 77ms 1.62% 34.89% 187ms 3.94% std::ostream::write 7ms 0.15% 35.04% 178ms 3.75% vtkFloatArray::New 1ms 0.021% 35.06% 178ms 3.75% vtkTriangle::~vtkTriangle 1ms 0.021% 35.08% 170ms 3.58% vtkQuad::~vtkQuad 2ms 0.042% 35.12% 166ms 3.50% vtkLine::GetParametricCenter 90ms 1.90% 37.02% 161ms 3.39% malloc_consolidate 0 0% 37.02% 158ms 3.33% VertexMesh::VertexMesh 2ms 0.042% 37.06% 158ms 3.33% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 37.06% 154ms 3.24% NodeLocationWriter::VisitAnyPopulation 30ms 0.63% 37.69% 154ms 3.24% std::_Rb_tree::_M_erase 2ms 0.042% 37.74% 153ms 3.22% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.021% 37.76% 152ms 3.20% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 37.76% 152ms 3.20% std::_Rb_tree::_M_create_node (inline) 5ms 0.11% 37.86% 151ms 3.18% std::_Rb_tree::_Rb_tree 0 0% 37.86% 151ms 3.18% std::set::set (inline) 0 0% 37.86% 150ms 3.16% std::vector::~vector (inline) 7ms 0.15% 38.01% 149ms 3.14% MutableElement::BuildEdges 0 0% 38.01% 149ms 3.14% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.021% 38.03% 147ms 3.10% std::_Vector_base::_M_deallocate (inline) 3ms 0.063% 38.10% 147ms 3.10% vtkIdList::AllocateInternal 0 0% 38.10% 146ms 3.08% std::_Rb_tree::_M_get_node (inline) 143ms 3.01% 41.11% 145ms 3.06% [libz.so.1.3] 1ms 0.021% 41.13% 145ms 3.06% vtkFloatArray::vtkFloatArray 17ms 0.36% 41.49% 143ms 3.01% std::vector::_M_default_append 0 0% 41.49% 141ms 2.97% VertexMesh::~VertexMesh 0 0% 41.49% 141ms 2.97% std::set::~set (inline) 1ms 0.021% 41.51% 138ms 2.91% vtkDataArray::CreateDataArray 1ms 0.021% 41.53% 134ms 2.82% vtkDoubleArray::vtkDoubleArray 6ms 0.13% 41.66% 132ms 2.78% vtkTypeFloat64Array::New 0 0% 41.66% 131ms 2.76% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.063% 41.72% 130ms 2.74% EdgeHelper::GetEdgeFromNodes 14ms 0.29% 42.01% 125ms 2.63% std::_Rb_tree::_M_copy (inline) 0 0% 42.01% 124ms 2.61% std::_Vector_base::_M_allocate (inline) 66ms 1.39% 43.40% 122ms 2.57% std::basic_filebuf::xsputn 4ms 0.084% 43.49% 121ms 2.55% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 121ms 2.55% 46.04% 121ms 2.55% __strcmp_avx2 1ms 0.021% 46.06% 121ms 2.55% std::_Vector_base::~_Vector_base (inline) 0 0% 46.06% 115ms 2.42% std::_Rb_tree::_M_drop_node (inline) 3ms 0.063% 46.12% 115ms 2.42% vtkFloatArray::~vtkFloatArray 111ms 2.34% 48.46% 111ms 2.34% __GI_sched_yield 0 0% 48.46% 111ms 2.34% std::_Rb_tree::_M_put_node (inline) 2ms 0.042% 48.50% 111ms 2.34% vtkTypeFloat64Array::vtkTypeFloat64Array 18ms 0.38% 48.88% 108ms 2.28% std::_Rb_tree::_M_clone_node (inline) 29ms 0.61% 49.49% 108ms 2.28% vtkObject::vtkObject 61ms 1.29% 50.78% 106ms 2.23% vtkTypeFloat64Array::PrintSelf 0 0% 50.78% 105ms 2.21% CellPropertyCollection::GetPropertiesType (inline) 42ms 0.88% 51.66% 105ms 2.21% std::__ostream_insert 2ms 0.042% 51.71% 104ms 2.19% std::operator<< (inline) 0 0% 51.71% 103ms 2.17% vtkXMLWriter::WritePointDataAppendedData 0 0% 51.71% 98ms 2.06% EdgeHelper::~EdgeHelper (inline) 2ms 0.042% 51.75% 96ms 2.02% vtkIdList::Allocate 1ms 0.021% 51.77% 95ms 2.00% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 51.79% 94ms 1.98% AbstractCellProperty::IsSubType (inline) 5ms 0.11% 51.90% 93ms 1.96% _int_free_maybe_consolidate 17ms 0.36% 52.25% 92ms 1.94% __dynamic_cast 92ms 1.94% 54.19% 92ms 1.94% unlink_chunk 64ms 1.35% 55.54% 91ms 1.92% std::basic_streambuf::xsputn 4ms 0.084% 55.63% 86ms 1.81% CellPropertyCollection::HasProperty 3ms 0.063% 55.69% 86ms 1.81% std::map::operator[] (partial-inline) 0 0% 55.69% 85ms 1.79% Cell::HasCellProperty (inline) 0 0% 55.69% 85ms 1.79% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 28ms 0.59% 56.28% 84ms 1.77% vtkObject::Modified 14ms 0.29% 56.57% 82ms 1.73% vtkAOSDataArrayTemplate::DataElementChanged 4ms 0.084% 56.66% 81ms 1.71% vtkIdList::New 7ms 0.15% 56.81% 80ms 1.69% vtkDoubleArray::~vtkDoubleArray 6ms 0.13% 56.93% 77ms 1.62% AbstractCellProperty::IsType (inline) 45ms 0.95% 57.88% 74ms 1.56% hack_digit 40ms 0.84% 58.72% 73ms 1.54% vtkObjectBase::UnRegisterInternal 3ms 0.063% 58.79% 71ms 1.50% std::vector::push_back (inline) 5ms 0.11% 58.89% 66ms 1.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.084% 58.98% 64ms 1.35% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.98% 62ms 1.31% boost::numeric::ublas::vector_assign (inline) 7ms 0.15% 59.12% 59ms 1.24% AbstractCellProperty::IsSame 0 0% 59.12% 58ms 1.22% vtkDataArray::ComputeRange 0 0% 59.12% 56ms 1.18% Cell::GetCellProliferativeType 19ms 0.4% 59.52% 56ms 1.18% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.38% 59.90% 55ms 1.16% std::num_put::_M_insert_int 5ms 0.11% 60.01% 55ms 1.16% std::vector::_M_realloc_insert 55ms 1.16% 61.17% 55ms 1.16% vtkTimeStamp::Modified 54ms 1.14% 62.31% 54ms 1.14% [libvtkCommonCore-9.3.so.9.3] 1ms 0.021% 62.33% 54ms 1.14% std::_Rb_tree::_M_insert_unique 0 0% 62.33% 54ms 1.14% std::set::insert (inline) 0 0% 62.33% 54ms 1.14% tcache_get (inline) 54ms 1.14% 63.46% 54ms 1.14% tcache_get_n (inline) 1ms 0.021% 63.49% 52ms 1.10% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 26ms 0.55% 64.03% 52ms 1.10% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.15% 64.18% 52ms 1.10% std::type_info::operator== (inline) 5ms 0.11% 64.29% 52ms 1.10% vtkDataArray::vtkDataArray 3ms 0.063% 64.35% 51ms 1.07% VertexMeshWriter::GetNextNode 4ms 0.084% 64.43% 51ms 1.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 64.43% 49ms 1.03% NodesOnlyMesh::~NodesOnlyMesh 0 0% 64.43% 46ms 0.97% NodesOnlyMesh::SetUpBoxCollection 46ms 0.97% 65.40% 46ms 0.97% __memcpy_avx_unaligned_erms 15ms 0.32% 65.72% 44ms 0.93% boost::numeric::ublas::indexing_vector_assign 12ms 0.25% 65.97% 44ms 0.93% vtkAbstractArray::vtkAbstractArray 1ms 0.021% 65.99% 44ms 0.93% vtkDoubleArray::New 43ms 0.91% 66.90% 44ms 0.93% vtkObjectBase::Delete 3ms 0.063% 66.96% 43ms 0.91% VertexMesh::Clear 6ms 0.13% 67.09% 43ms 0.91% vtkAOSDataArrayTemplate::InsertTuple 0 0% 67.09% 42ms 0.88% std::_Rb_tree::_M_emplace_hint_unique 0 0% 67.09% 42ms 0.88% vtk::detail::smp::vtkSMPToolsImplForTBB 26ms 0.55% 67.64% 41ms 0.86% std::_Hashtable::clear 0 0% 67.64% 41ms 0.86% std::_Rb_tree::lower_bound (inline) 0 0% 67.64% 41ms 0.86% std::map::lower_bound (inline) 1ms 0.021% 67.66% 41ms 0.86% vtkDataArrayPrivate::DoComputeVectorRange 41ms 0.86% 68.52% 41ms 0.86% vtkObjectBase::~vtkObjectBase 0 0% 68.52% 40ms 0.84% std::make_unique (inline) 3ms 0.063% 68.58% 40ms 0.84% tbb::detail::r1::cancel_group_execution 6ms 0.13% 68.71% 40ms 0.84% vtkDataArray::~vtkDataArray 0 0% 68.71% 39ms 0.82% PottsMesh::GetMooreNeighbouringNodeIndices 39ms 0.82% 69.53% 39ms 0.82% std::ostream::sentry::sentry 1ms 0.021% 69.55% 37ms 0.78% VtkMeshWriter::MakeVtkMesh 37ms 0.78% 70.33% 37ms 0.78% __GI___writev 0 0% 70.33% 37ms 0.78% _dl_init 0 0% 70.33% 37ms 0.78% _dl_start_user 0 0% 70.33% 37ms 0.78% call_init (inline) 0 0% 70.33% 37ms 0.78% std::__basic_file::xsputn_2 3ms 0.063% 70.40% 37ms 0.78% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.021% 70.42% 36ms 0.76% Cell::GetMutationState 1ms 0.021% 70.44% 36ms 0.76% Node::ConstructNodeAttributes (inline) 0 0% 70.44% 36ms 0.76% Node::SetRadius 3ms 0.063% 70.50% 36ms 0.76% boost::serialization::singleton::get_instance 0 0% 70.50% 35ms 0.74% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 70.50% 35ms 0.74% std::_Destroy (inline) 0 0% 70.50% 35ms 0.74% std::_Destroy_aux::__destroy (inline) 0 0% 70.50% 34ms 0.72% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.50% 34ms 0.72% NodesOnlyMesh::ClearBoxCollection (inline) 6ms 0.13% 70.63% 34ms 0.72% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 70.63% 33ms 0.7% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 70.63% 33ms 0.7% PottsBasedCellPopulation::AcceptCellWriter 0 0% 70.63% 33ms 0.7% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 70.63% 32ms 0.67% CxxTest::RealWorldDescription::setUp 23ms 0.48% 71.11% 32ms 0.67% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.11% 32ms 0.67% DistributedBoxCollection::IsOwned 0 0% 71.11% 32ms 0.67% PetscInitialize 0 0% 71.11% 32ms 0.67% PetscSetup::setUpWorld 0 0% 71.11% 32ms 0.67% PetscSetupUtils::CommonSetup 0 0% 71.11% 32ms 0.67% PetscSetupUtils::InitialisePetsc 0 0% 71.11% 31ms 0.65% PMPI_Init_thread 5ms 0.11% 71.22% 31ms 0.65% __find_specmb (inline) 0 0% 71.22% 31ms 0.65% ompi_mpi_init 0 0% 71.22% 31ms 0.65% std::less::operator() (inline) 31ms 0.65% 71.87% 31ms 0.65% std::operator< (inline) 0 0% 71.87% 30ms 0.63% 11ms 0.23% 72.10% 30ms 0.63% _int_free_merge_chunk 0 0% 72.10% 30ms 0.63% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 30ms 0.63% 72.73% 30ms 0.63% vtkDataArray::Modified 30ms 0.63% 73.37% 30ms 0.63% vtkObject::~vtkObject 0 0% 73.37% 29ms 0.61% Cell::GetCellId 0 0% 73.37% 29ms 0.61% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.042% 73.41% 29ms 0.61% boost::serialization::void_cast_detail::void_caster::recursive_register 28ms 0.59% 74.00% 28ms 0.59% __GI___libc_write 0 0% 74.00% 28ms 0.59% std::__basic_file::xsputn 0 0% 74.00% 28ms 0.59% std::basic_filebuf::_M_convert_to_external 0 0% 74.00% 28ms 0.59% std::basic_filebuf::overflow 4ms 0.084% 74.08% 28ms 0.59% vtkIdList::~vtkIdList 0 0% 74.08% 27ms 0.57% Edge::Edge 0 0% 74.08% 27ms 0.57% Edge::SetNodes (inline) 0 0% 74.08% 27ms 0.57% OutputFileHandler::OpenOutputFile 0 0% 74.08% 27ms 0.57% std::basic_filebuf::open 0 0% 74.08% 27ms 0.57% std::default_delete::operator() (inline) 0 0% 74.08% 27ms 0.57% std::unique_ptr::~unique_ptr (inline) 20ms 0.42% 74.50% 27ms 0.57% vtkObject::ObjectFinalize 0 0% 74.50% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 1ms 0.021% 74.53% 25ms 0.53% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 74.55% 25ms 0.53% DistributedBoxCollection::SetupLocalBoxesHalfOnly 3ms 0.063% 74.61% 25ms 0.53% Node::GetPoint 25ms 0.53% 75.14% 25ms 0.53% vtkObjectBase::vtkObjectBase 5ms 0.11% 75.24% 24ms 0.51% NodeAttributes::NodeAttributes 24ms 0.51% 75.75% 24ms 0.51% [libstdc++.so.6.0.33] 24ms 0.51% 76.25% 24ms 0.51% __GI___uselocale 24ms 0.51% 76.76% 24ms 0.51% __strchrnul_avx2 1ms 0.021% 76.78% 24ms 0.51% std::__basic_file::open