File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3813ms, 79.08% of 4822ms total Dropped 711 nodes (cum <= 24.11ms) flat flat% sum% cum cum% 0 0% 0% 4581ms 95.00% __libc_start_call_main 0 0% 0% 4581ms 95.00% __libc_start_main_impl 0 0% 0% 4581ms 95.00% _start 0 0% 0% 4565ms 94.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4565ms 94.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4565ms 94.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4565ms 94.67% main 0 0% 0% 4530ms 93.94% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4530ms 93.94% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4530ms 93.94% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4520ms 93.74% AbstractCellBasedSimulation::Solve 0 0% 0% 4238ms 87.89% AbstractCellPopulation::WriteResultsToFiles 17ms 0.35% 0.35% 4003ms 83.02% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.35% 1967ms 40.79% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.37% 1709ms 35.44% VertexMeshWriter::MakeVtkMesh 0 0% 0.37% 1278ms 26.50% vtkPolygon::New 4ms 0.083% 0.46% 1274ms 26.42% vtkPolygon::vtkPolygon 13ms 0.27% 0.73% 903ms 18.73% vtkCell::vtkCell 2ms 0.041% 0.77% 760ms 15.76% VertexMeshWriter::WriteFiles 1ms 0.021% 0.79% 752ms 15.60% vtkPoints::New 2ms 0.041% 0.83% 746ms 15.47% std::ostream::operator<< (inline) 49ms 1.02% 1.85% 743ms 15.41% std::ostream::_M_insert 9ms 0.19% 2.03% 712ms 14.77% vtkPoints::vtkPoints 47ms 0.97% 3.01% 681ms 14.12% operator new 211ms 4.38% 7.38% 642ms 13.31% __GI___libc_malloc 37ms 0.77% 8.15% 617ms 12.80% std::num_put::_M_insert_float 2ms 0.041% 8.19% 591ms 12.26% vtkLine::New 2ms 0.041% 8.23% 575ms 11.92% vtkQuad::New 5ms 0.1% 8.34% 574ms 11.90% vtkLine::vtkLine 1ms 0.021% 8.36% 573ms 11.88% vtkTriangle::New 2ms 0.041% 8.40% 570ms 11.82% vtkQuad::vtkQuad 9ms 0.19% 8.59% 570ms 11.82% vtkTriangle::vtkTriangle 0 0% 8.59% 567ms 11.76% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.59% 567ms 11.76% vtkXMLWriterBase::Write 0 0% 8.59% 565ms 11.72% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.59% 564ms 11.70% vtkExecutive::CallAlgorithm 0 0% 8.59% 564ms 11.70% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 8.61% 563ms 11.68% vtkCompositeDataPipeline::ExecuteData 0 0% 8.61% 563ms 11.68% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.61% 562ms 11.65% vtkDemandDrivenPipeline::ExecuteData 149ms 3.09% 11.70% 506ms 10.49% __GI___libc_free 0 0% 11.70% 498ms 10.33% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.70% 498ms 10.33% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 12ms 0.25% 11.95% 481ms 9.98% std::__cxx11::collate::do_transform 4ms 0.083% 12.03% 451ms 9.35% ___vsnprintf 0 0% 12.03% 448ms 9.29% __vsnprintf_internal (inline) 23ms 0.48% 12.51% 448ms 9.29% vtkPoints::SetDataType 1ms 0.021% 12.53% 444ms 9.21% vtkXMLWriter::WriteBinaryData 0 0% 12.53% 439ms 9.10% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.53% 439ms 9.10% vtkXMLWriter::WriteBinaryDataInternal 37ms 0.77% 13.29% 438ms 9.08% __printf_buffer 0 0% 13.29% 420ms 8.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.041% 13.33% 396ms 8.21% vtkPolygon::~vtkPolygon 1ms 0.021% 13.36% 372ms 7.71% __printf_fp_spec (inline) 15ms 0.31% 13.67% 371ms 7.69% __printf_fp_l_buffer 242ms 5.02% 18.69% 368ms 7.63% _int_malloc 228ms 4.73% 23.41% 355ms 7.36% _int_free 0 0% 23.41% 350ms 7.26% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.41% 350ms 7.26% VtkMeshWriter::WriteFiles 172ms 3.57% 26.98% 335ms 6.95% __printf_fp_buffer_1 4ms 0.083% 27.06% 325ms 6.74% vtkCell::~vtkCell 0 0% 27.06% 309ms 6.41% vtkXMLWriter::WritePointsAppendedData 40ms 0.83% 27.89% 300ms 6.22% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 39ms 0.81% 28.70% 283ms 5.87% std::__new_allocator::allocate (inline) 0 0% 28.70% 281ms 5.83% std::allocator_traits::allocate (inline) 0 0% 28.70% 277ms 5.74% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.1% 28.81% 277ms 5.74% PottsBasedCellPopulation::UpdateCellLocations 5ms 0.1% 28.91% 273ms 5.66% std::__new_allocator::deallocate (inline) 0 0% 28.91% 272ms 5.64% std::allocator_traits::deallocate (inline) 6ms 0.12% 29.03% 237ms 4.91% vtkPoints::~vtkPoints 0 0% 29.03% 235ms 4.87% vtkXMLWriter::WriteCompressionBlock 0 0% 29.03% 222ms 4.60% vtkDataCompressor::Compress 0 0% 29.03% 221ms 4.58% compress2 0 0% 29.03% 221ms 4.58% vtkZLibDataCompressor::CompressBuffer 1ms 0.021% 29.05% 219ms 4.54% deflate 60ms 1.24% 30.30% 218ms 4.52% crc32 0 0% 30.30% 217ms 4.50% tbb::detail::r1::parallel_pipeline 7ms 0.15% 30.44% 209ms 4.33% vtkBase64OutputStream::Write 0 0% 30.44% 206ms 4.27% clone3 0 0% 30.44% 206ms 4.27% start_thread 2ms 0.041% 30.49% 206ms 4.27% tbb::detail::r1::reset 6ms 0.12% 30.61% 204ms 4.23% vtkIdList::AllocateInternal 82ms 1.70% 32.31% 203ms 4.21% tbb::detail::r1::wait_bounded_queue_monitor 14ms 0.29% 32.60% 202ms 4.19% vtkBase64OutputStream::EncodeTriplet 3ms 0.062% 32.66% 192ms 3.98% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.041% 32.70% 185ms 3.84% vtkFloatArray::New 1ms 0.021% 32.73% 181ms 3.75% std::set::set (inline) 13ms 0.27% 32.99% 180ms 3.73% std::_Rb_tree::_Rb_tree 118ms 2.45% 35.44% 178ms 3.69% malloc_consolidate 47ms 0.97% 36.42% 174ms 3.61% std::ostream::write 13ms 0.27% 36.69% 173ms 3.59% std::vector::_M_default_append 0 0% 36.69% 169ms 3.50% vtkQuad::~vtkQuad 0 0% 36.69% 168ms 3.48% vtkFloatArray::vtkFloatArray 3ms 0.062% 36.75% 168ms 3.48% vtkLine::GetParametricCenter 1ms 0.021% 36.77% 165ms 3.42% NodeLocationWriter::VisitAnyPopulation 0 0% 36.77% 164ms 3.40% std::vector::~vector (inline) 0 0% 36.77% 160ms 3.32% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 36.77% 160ms 3.32% VertexMesh::~VertexMesh 2ms 0.041% 36.81% 158ms 3.28% std::_Vector_base::_M_deallocate (inline) 2ms 0.041% 36.85% 158ms 3.28% vtkTriangle::~vtkTriangle 0 0% 36.85% 157ms 3.26% std::_Rb_tree::_M_create_node (inline) 32ms 0.66% 37.52% 157ms 3.26% std::_Rb_tree::_M_erase 1ms 0.021% 37.54% 156ms 3.24% VertexMesh::VertexMesh 0 0% 37.54% 153ms 3.17% std::_Rb_tree::~_Rb_tree (inline) 143ms 2.97% 40.50% 151ms 3.13% [libz.so.1.3] 4ms 0.083% 40.58% 151ms 3.13% vtkDataArray::CreateDataArray 0 0% 40.58% 147ms 3.05% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.58% 147ms 3.05% std::_Rb_tree::_M_get_node (inline) 0 0% 40.58% 146ms 3.03% VertexMesh::GenerateEdgesFromElements (inline) 4ms 0.083% 40.67% 145ms 3.01% MutableElement::BuildEdges 6ms 0.12% 40.79% 140ms 2.90% vtkDoubleArray::vtkDoubleArray 18ms 0.37% 41.17% 137ms 2.84% std::_Rb_tree::_M_copy (inline) 6ms 0.12% 41.29% 137ms 2.84% vtkTypeFloat64Array::New 3ms 0.062% 41.35% 136ms 2.82% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.35% 134ms 2.78% std::_Vector_base::_M_allocate (inline) 0 0% 41.35% 131ms 2.72% EdgeHelper::GetEdgeFromNodes 53ms 1.10% 42.45% 129ms 2.68% std::basic_filebuf::xsputn 0 0% 42.45% 127ms 2.63% std::set::~set (inline) 1ms 0.021% 42.47% 126ms 2.61% vtkIdList::Allocate 27ms 0.56% 43.03% 125ms 2.59% vtkObject::vtkObject 1ms 0.021% 43.05% 124ms 2.57% std::_Vector_base::~_Vector_base (inline) 0 0% 43.05% 121ms 2.51% std::_Rb_tree::_M_drop_node (inline) 119ms 2.47% 45.52% 119ms 2.47% __GI_sched_yield 3ms 0.062% 45.58% 116ms 2.41% vtkFloatArray::~vtkFloatArray 5ms 0.1% 45.69% 116ms 2.41% vtkTypeFloat64Array::vtkTypeFloat64Array 9ms 0.19% 45.87% 115ms 2.38% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.87% 115ms 2.38% std::_Rb_tree::_M_put_node (inline) 54ms 1.12% 46.99% 114ms 2.36% std::__ostream_insert 1ms 0.021% 47.01% 110ms 2.28% CellPropertyCollection::GetPropertiesType (inline) 0 0% 47.01% 109ms 2.26% EdgeHelper::~EdgeHelper (inline) 0 0% 47.01% 109ms 2.26% vtkXMLWriter::WritePointDataAppendedData 2ms 0.041% 47.06% 108ms 2.24% std::operator<< (inline) 105ms 2.18% 49.23% 105ms 2.18% __strcmp_avx2 50ms 1.04% 50.27% 101ms 2.09% hack_digit 1ms 0.021% 50.29% 97ms 2.01% AbstractCellProperty::IsSubType (inline) 18ms 0.37% 50.66% 96ms 1.99% __dynamic_cast 2ms 0.041% 50.71% 95ms 1.97% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 28ms 0.58% 51.29% 95ms 1.97% vtkObject::Modified 70ms 1.45% 52.74% 92ms 1.91% std::basic_streambuf::xsputn 4ms 0.083% 52.82% 92ms 1.91% std::map::operator[] (partial-inline) 6ms 0.12% 52.94% 92ms 1.91% vtkDoubleArray::~vtkDoubleArray 58ms 1.20% 54.15% 92ms 1.91% vtkObjectBase::UnRegisterInternal 46ms 0.95% 55.10% 88ms 1.82% vtkTypeFloat64Array::PrintSelf 5ms 0.1% 55.21% 85ms 1.76% _int_free_maybe_consolidate 0 0% 55.21% 80ms 1.66% Cell::HasCellProperty (inline) 5ms 0.1% 55.31% 80ms 1.66% CellPropertyCollection::HasProperty 9ms 0.19% 55.50% 79ms 1.64% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 55.50% 78ms 1.62% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 6ms 0.12% 55.62% 77ms 1.60% AbstractCellProperty::IsType (inline) 8ms 0.17% 55.79% 75ms 1.56% vtkIdList::New 72ms 1.49% 57.28% 72ms 1.49% unlink_chunk 19ms 0.39% 57.67% 69ms 1.43% std::_Rb_tree::_M_lower_bound (inline) 0 0% 57.67% 68ms 1.41% Cell::GetCellProliferativeType 6ms 0.12% 57.80% 68ms 1.41% std::vector::push_back (inline) 7ms 0.15% 57.94% 68ms 1.41% vtkDataArray::vtkDataArray 4ms 0.083% 58.03% 64ms 1.33% AbstractCellPopulation::GetCellUsingLocationIndex 63ms 1.31% 59.33% 63ms 1.31% vtkTimeStamp::Modified 5ms 0.1% 59.44% 61ms 1.27% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.021% 59.46% 61ms 1.27% std::_Rb_tree::_M_insert_unique 0 0% 59.46% 61ms 1.27% std::set::insert (inline) 0 0% 59.46% 59ms 1.22% NodesOnlyMesh::SetUpBoxCollection 0 0% 59.46% 59ms 1.22% NodesOnlyMesh::~NodesOnlyMesh 10ms 0.21% 59.66% 58ms 1.20% vtkDataArray::~vtkDataArray 0 0% 59.66% 57ms 1.18% tcache_get (inline) 57ms 1.18% 60.85% 57ms 1.18% tcache_get_n (inline) 13ms 0.27% 61.12% 57ms 1.18% vtkAbstractArray::vtkAbstractArray 0 0% 61.12% 56ms 1.16% PottsMesh::GetMooreNeighbouringNodeIndices 8ms 0.17% 61.28% 55ms 1.14% AbstractCellProperty::IsSame 1ms 0.021% 61.30% 54ms 1.12% boost::numeric::ublas::vector_assign (inline) 1ms 0.021% 61.32% 52ms 1.08% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 4ms 0.083% 61.41% 52ms 1.08% std::_Rb_tree::_M_insert_ (inline) 0 0% 61.41% 51ms 1.06% VertexMesh::Clear 23ms 0.48% 61.88% 51ms 1.06% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.88% 51ms 1.06% std::_Rb_tree::lower_bound (inline) 0 0% 61.88% 51ms 1.06% std::map::lower_bound (inline) 11ms 0.23% 62.11% 51ms 1.06% vtkSOADataArrayTemplate::FillTypedComponent 10ms 0.21% 62.32% 50ms 1.04% std::num_put::_M_insert_int 9ms 0.19% 62.51% 47ms 0.97% std::type_info::operator== (inline) 0 0% 62.51% 46ms 0.95% std::_Destroy (inline) 0 0% 62.51% 46ms 0.95% std::_Destroy_aux::__destroy (inline) 45ms 0.93% 63.44% 45ms 0.93% [libvtkCommonCore-9.3.so.9.3] 45ms 0.93% 64.37% 45ms 0.93% std::ostream::sentry::sentry 3ms 0.062% 64.43% 45ms 0.93% std::vector::_M_realloc_insert 43ms 0.89% 65.33% 43ms 0.89% __GI___writev 0 0% 65.33% 43ms 0.89% std::__basic_file::xsputn_2 1ms 0.021% 65.35% 43ms 0.89% vtkDataArray::ComputeRange 26ms 0.54% 65.89% 42ms 0.87% std::_Hashtable::clear 36ms 0.75% 66.63% 41ms 0.85% std::num_put::do_put 2ms 0.041% 66.67% 40ms 0.83% VertexMeshWriter::GetNextNode 40ms 0.83% 67.50% 40ms 0.83% vtkObject::~vtkObject 26ms 0.54% 68.04% 39ms 0.81% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.04% 39ms 0.81% DistributedBoxCollection::IsOwned 0 0% 68.04% 39ms 0.81% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.04% 39ms 0.81% NodesOnlyMesh::ClearBoxCollection (inline) 12ms 0.25% 68.29% 39ms 0.81% boost::numeric::ublas::indexing_vector_assign 1ms 0.021% 68.31% 39ms 0.81% std::make_unique (inline) 7ms 0.15% 68.46% 38ms 0.79% vtkIdList::~vtkIdList 37ms 0.77% 69.22% 37ms 0.77% __memcpy_avx_unaligned_erms 2ms 0.041% 69.27% 37ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.083% 69.35% 37ms 0.77% std::less::operator() (inline) 7ms 0.15% 69.49% 37ms 0.77% tbb::detail::r1::cancel_group_execution 0 0% 69.49% 37ms 0.77% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 69.49% 37ms 0.77% vtkDoubleArray::New 37ms 0.77% 70.26% 37ms 0.77% vtkObjectBase::vtkObjectBase 0 0% 70.26% 35ms 0.73% _dl_init 0 0% 70.26% 35ms 0.73% _dl_start_user 0 0% 70.26% 35ms 0.73% call_init (inline) 34ms 0.71% 70.97% 34ms 0.71% vtkObjectBase::Delete 33ms 0.68% 71.65% 33ms 0.68% std::codecvt::do_always_noconv 33ms 0.68% 72.34% 33ms 0.68% std::operator< (inline) 4ms 0.083% 72.42% 33ms 0.68% vtkAOSDataArrayTemplate::InsertTuple 0 0% 72.42% 32ms 0.66% CxxTest::RealWorldDescription::setUp 0 0% 72.42% 32ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 72.42% 32ms 0.66% PetscInitialize 0 0% 72.42% 32ms 0.66% PetscSetup::setUpWorld 0 0% 72.42% 32ms 0.66% PetscSetupUtils::CommonSetup 0 0% 72.42% 32ms 0.66% PetscSetupUtils::InitialisePetsc 32ms 0.66% 73.08% 32ms 0.66% __mpn_divrem 1ms 0.021% 73.10% 32ms 0.66% std::basic_filebuf::_M_convert_to_external 0 0% 73.10% 32ms 0.66% std::basic_filebuf::overflow 32ms 0.66% 73.77% 32ms 0.66% vtkObjectBase::~vtkObjectBase 0 0% 73.77% 31ms 0.64% PMPI_Init_thread 31ms 0.64% 74.41% 31ms 0.64% __GI___libc_write 0 0% 74.41% 31ms 0.64% ompi_mpi_init 0 0% 74.41% 31ms 0.64% std::__basic_file::xsputn 0 0% 74.41% 30ms 0.62% Cell::GetCellId 0 0% 74.41% 30ms 0.62% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.041% 74.45% 30ms 0.62% std::_Rb_tree_header::_Rb_tree_header (inline) 30ms 0.62% 75.07% 30ms 0.62% std::_Rb_tree_insert_and_rebalance 2ms 0.041% 75.11% 30ms 0.62% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 75.11% 29ms 0.6% CellIdWriter::GetCellDataForVtkOutput 0 0% 75.11% 29ms 0.6% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 75.13% 29ms 0.6% VtkMeshWriter::MakeVtkMesh 4ms 0.083% 75.22% 29ms 0.6% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 75.22% 28ms 0.58% Node::ConstructNodeAttributes (inline) 0 0% 75.22% 28ms 0.58% Node::SetRadius 4ms 0.083% 75.30% 28ms 0.58% boost::serialization::singleton::get_instance 28ms 0.58% 75.88% 28ms 0.58% operator delete 28ms 0.58% 76.46% 28ms 0.58% std::_Rb_tree_header::_M_reset (inline) 28ms 0.58% 77.04% 28ms 0.58% tcache_put (inline) 28ms 0.58% 77.62% 28ms 0.58% vtkDataArray::Modified 0 0% 77.62% 27ms 0.56% std::default_delete::operator() (inline) 0 0% 77.62% 27ms 0.56% std::unique_ptr::~unique_ptr (inline) 23ms 0.48% 78.10% 27ms 0.56% vtkObject::ObjectFinalize 26ms 0.54% 78.64% 26ms 0.54% __memset_avx2_unaligned_erms 0 0% 78.64% 26ms 0.54% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 5ms 0.1% 78.74% 26ms 0.54% std::__new_allocator::construct (inline) 0 0% 78.74% 26ms 0.54% std::allocator_traits::construct (inline) 0 0% 78.74% 26ms 0.54% std::map::~map (inline) 8ms 0.17% 78.91% 26ms 0.54% vtkAbstractArray::~vtkAbstractArray 0 0% 78.91% 26ms 0.54% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 78.91% 25ms 0.52% 0 0% 78.91% 25ms 0.52% Edge::Edge 0 0% 78.91% 25ms 0.52% Edge::SetNodes (inline) 2ms 0.041% 78.95% 25ms 0.52% PottsMesh::GetVonNeumannNeighbouringNodeIndices 6ms 0.12% 79.08% 25ms 0.52% _int_free_merge_chunk