File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3776ms, 80.53% of 4689ms total Dropped 714 nodes (cum <= 23.45ms) flat flat% sum% cum cum% 0 0% 0% 4486ms 95.67% __libc_start_call_main 0 0% 0% 4486ms 95.67% __libc_start_main_impl 0 0% 0% 4486ms 95.67% _start 0 0% 0% 4467ms 95.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4467ms 95.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4467ms 95.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4467ms 95.27% main 0 0% 0% 4425ms 94.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4425ms 94.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4425ms 94.37% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4414ms 94.14% AbstractCellBasedSimulation::Solve 0 0% 0% 4114ms 87.74% AbstractCellPopulation::WriteResultsToFiles 9ms 0.19% 0.19% 3899ms 83.15% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.19% 1967ms 41.95% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.21% 1699ms 36.23% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.23% 1251ms 26.68% vtkPolygon::New 1ms 0.021% 0.26% 1250ms 26.66% vtkPolygon::vtkPolygon 9ms 0.19% 0.45% 880ms 18.77% vtkCell::vtkCell 3ms 0.064% 0.51% 749ms 15.97% vtkPoints::New 12ms 0.26% 0.77% 710ms 15.14% vtkPoints::vtkPoints 0 0% 0.77% 680ms 14.50% VertexMeshWriter::WriteFiles 41ms 0.87% 1.64% 647ms 13.80% operator new 2ms 0.043% 1.68% 633ms 13.50% std::ostream::operator<< (inline) 52ms 1.11% 2.79% 628ms 13.39% std::ostream::_M_insert 188ms 4.01% 6.80% 612ms 13.05% __GI___libc_malloc 0 0% 6.80% 588ms 12.54% vtkQuad::New 6ms 0.13% 6.93% 588ms 12.54% vtkQuad::vtkQuad 2ms 0.043% 6.97% 574ms 12.24% vtkLine::New 0 0% 6.97% 561ms 11.96% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.97% 561ms 11.96% vtkXMLWriterBase::Write 0 0% 6.97% 558ms 11.90% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.97% 557ms 11.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.97% 555ms 11.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.97% 554ms 11.81% vtkCompositeDataPipeline::ExecuteData 0 0% 6.97% 554ms 11.81% vtkExecutive::CallAlgorithm 10ms 0.21% 7.19% 554ms 11.81% vtkLine::vtkLine 0 0% 7.19% 554ms 11.81% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 7.19% 552ms 11.77% vtkTriangle::New 3ms 0.064% 7.25% 547ms 11.67% vtkTriangle::vtkTriangle 47ms 1.00% 8.25% 516ms 11.00% std::num_put::_M_insert_float 0 0% 8.25% 503ms 10.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.25% 503ms 10.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 99ms 2.11% 10.36% 464ms 9.90% __GI___libc_free 0 0% 10.36% 455ms 9.70% vtkXMLWriter::WriteBinaryData 1ms 0.021% 10.39% 451ms 9.62% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.39% 450ms 9.60% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.39% 430ms 9.17% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 23ms 0.49% 10.88% 427ms 9.11% vtkPoints::SetDataType 11ms 0.23% 11.11% 416ms 8.87% std::__cxx11::collate::do_transform 0 0% 11.11% 398ms 8.49% vtkPolygon::~vtkPolygon 4ms 0.085% 11.20% 392ms 8.36% ___vsnprintf 0 0% 11.20% 388ms 8.27% __vsnprintf_internal (inline) 65ms 1.39% 12.58% 383ms 8.17% __printf_buffer 259ms 5.52% 18.11% 377ms 8.04% _int_malloc 216ms 4.61% 22.71% 359ms 7.66% _int_free 1ms 0.021% 22.73% 345ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.73% 339ms 7.23% VtkMeshWriter::WriteFiles 0 0% 22.73% 333ms 7.10% vtkXMLWriter::WritePointsAppendedData 5ms 0.11% 22.84% 320ms 6.82% vtkCell::~vtkCell 45ms 0.96% 23.80% 304ms 6.48% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 1ms 0.021% 23.82% 298ms 6.36% __printf_fp_spec (inline) 13ms 0.28% 24.10% 297ms 6.33% __printf_fp_l_buffer 0 0% 24.10% 288ms 6.14% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.13% 24.23% 288ms 6.14% PottsBasedCellPopulation::UpdateCellLocations 146ms 3.11% 27.34% 276ms 5.89% __printf_fp_buffer_1 34ms 0.73% 28.07% 254ms 5.42% std::__new_allocator::allocate (inline) 0 0% 28.07% 253ms 5.40% std::allocator_traits::allocate (inline) 5ms 0.11% 28.17% 242ms 5.16% std::__new_allocator::deallocate (inline) 0 0% 28.17% 242ms 5.16% std::allocator_traits::deallocate (inline) 0 0% 28.17% 236ms 5.03% vtkXMLWriter::WriteCompressionBlock 0 0% 28.17% 225ms 4.80% vtkDataCompressor::Compress 0 0% 28.17% 223ms 4.76% compress2 0 0% 28.17% 223ms 4.76% vtkZLibDataCompressor::CompressBuffer 44ms 0.94% 29.11% 222ms 4.73% crc32 0 0% 29.11% 222ms 4.73% deflate 3ms 0.064% 29.17% 214ms 4.56% vtkBase64OutputStream::Write 13ms 0.28% 29.45% 210ms 4.48% vtkBase64OutputStream::EncodeTriplet 3ms 0.064% 29.52% 206ms 4.39% vtkFloatArray::New 2ms 0.043% 29.56% 203ms 4.33% vtkPoints::~vtkPoints 0 0% 29.56% 201ms 4.29% vtkQuad::~vtkQuad 2ms 0.043% 29.60% 190ms 4.05% std::set::set (inline) 17ms 0.36% 29.96% 188ms 4.01% std::_Rb_tree::_Rb_tree 43ms 0.92% 30.88% 183ms 3.90% std::ostream::write 107ms 2.28% 33.16% 181ms 3.86% malloc_consolidate 5ms 0.11% 33.27% 179ms 3.82% vtkIdList::AllocateInternal 0 0% 33.27% 179ms 3.82% vtkLine::GetParametricCenter 4ms 0.085% 33.35% 176ms 3.75% vtkFloatArray::vtkFloatArray 2ms 0.043% 33.40% 172ms 3.67% tbb::detail::r1::parallel_pipeline 3ms 0.064% 33.46% 167ms 3.56% vtkTriangle::~vtkTriangle 161ms 3.43% 36.89% 166ms 3.54% [libz.so.1.3] 0 0% 36.89% 165ms 3.52% clone3 0 0% 36.89% 165ms 3.52% start_thread 0 0% 36.89% 161ms 3.43% tbb::detail::r1::reset 1ms 0.021% 36.92% 158ms 3.37% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 36.92% 158ms 3.37% VertexMesh::~VertexMesh 63ms 1.34% 38.26% 156ms 3.33% std::basic_filebuf::xsputn 59ms 1.26% 39.52% 155ms 3.31% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.043% 39.56% 154ms 3.28% VertexMesh::VertexMesh 0 0% 39.56% 152ms 3.24% std::vector::~vector (inline) 0 0% 39.56% 151ms 3.22% std::_Rb_tree::_M_create_node (inline) 5ms 0.11% 39.67% 150ms 3.20% std::_Vector_base::_M_deallocate (inline) 21ms 0.45% 40.12% 149ms 3.18% std::_Rb_tree::_M_copy (inline) 1ms 0.021% 40.14% 149ms 3.18% vtkTypeFloat64Array::~vtkTypeFloat64Array 4ms 0.085% 40.22% 148ms 3.16% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 6ms 0.13% 40.35% 147ms 3.13% MutableElement::BuildEdges 0 0% 40.35% 147ms 3.13% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.043% 40.39% 145ms 3.09% vtkDataArray::CreateDataArray 12ms 0.26% 40.65% 144ms 3.07% std::vector::_M_default_append 0 0% 40.65% 143ms 3.05% std::_Rb_tree::_M_get_node (inline) 37ms 0.79% 41.44% 142ms 3.03% std::_Rb_tree::_M_erase 0 0% 41.44% 138ms 2.94% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.064% 41.50% 138ms 2.94% vtkDoubleArray::vtkDoubleArray 5ms 0.11% 41.61% 137ms 2.92% vtkTypeFloat64Array::New 2ms 0.043% 41.65% 133ms 2.84% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.043% 41.69% 128ms 2.73% EdgeHelper::GetEdgeFromNodes 0 0% 41.69% 126ms 2.69% NodeLocationWriter::VisitAnyPopulation 13ms 0.28% 41.97% 125ms 2.67% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.97% 124ms 2.64% vtkIdList::Allocate 2ms 0.043% 42.01% 122ms 2.60% std::_Vector_base::~_Vector_base (inline) 1ms 0.021% 42.03% 120ms 2.56% vtkFloatArray::~vtkFloatArray 0 0% 42.03% 114ms 2.43% std::set::~set (inline) 30ms 0.64% 42.67% 114ms 2.43% vtkObject::vtkObject 5ms 0.11% 42.78% 114ms 2.43% vtkTypeFloat64Array::vtkTypeFloat64Array 111ms 2.37% 45.15% 111ms 2.37% __strcmp_avx2 0 0% 45.15% 110ms 2.35% std::_Vector_base::_M_allocate (inline) 3ms 0.064% 45.21% 109ms 2.32% std::map::operator[] (partial-inline) 1ms 0.021% 45.23% 106ms 2.26% CellPropertyCollection::GetPropertiesType (inline) 0 0% 45.23% 104ms 2.22% EdgeHelper::~EdgeHelper (inline) 0 0% 45.23% 102ms 2.18% std::_Rb_tree::_M_drop_node (inline) 0 0% 45.23% 97ms 2.07% std::_Rb_tree::_M_put_node (inline) 0 0% 45.23% 97ms 2.07% vtkXMLWriter::WritePointDataAppendedData 0 0% 45.23% 94ms 2.00% Cell::HasCellProperty (inline) 3ms 0.064% 45.30% 94ms 2.00% CellPropertyCollection::HasProperty 0 0% 45.30% 94ms 2.00% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 94ms 2.00% 47.30% 94ms 2.00% __GI_sched_yield 7ms 0.15% 47.45% 91ms 1.94% _int_free_maybe_consolidate 51ms 1.09% 48.54% 91ms 1.94% vtkObjectBase::UnRegisterInternal 2ms 0.043% 48.58% 90ms 1.92% AbstractCellProperty::IsType (inline) 90ms 1.92% 50.50% 90ms 1.92% unlink_chunk 47ms 1.00% 51.50% 90ms 1.92% vtkTypeFloat64Array::PrintSelf 0 0% 51.50% 89ms 1.90% AbstractCellProperty::IsSubType (inline) 16ms 0.34% 51.84% 89ms 1.90% __dynamic_cast 23ms 0.49% 52.34% 86ms 1.83% std::_Rb_tree::_M_lower_bound (inline) 19ms 0.41% 52.74% 84ms 1.79% std::__ostream_insert 6ms 0.13% 52.87% 81ms 1.73% AbstractCellPopulation::GetCellUsingLocationIndex 37ms 0.79% 53.66% 81ms 1.73% hack_digit 2ms 0.043% 53.70% 81ms 1.73% std::operator<< (inline) 47ms 1.00% 54.70% 76ms 1.62% std::basic_streambuf::xsputn 9ms 0.19% 54.89% 75ms 1.60% vtkAOSDataArrayTemplate::DataElementChanged 6ms 0.13% 55.02% 74ms 1.58% vtkIdList::New 0 0% 55.02% 72ms 1.54% Cell::GetCellProliferativeType 3ms 0.064% 55.09% 72ms 1.54% std::vector::push_back (inline) 19ms 0.41% 55.49% 72ms 1.54% vtkObject::Modified 1ms 0.021% 55.51% 71ms 1.51% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 55.51% 70ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 55.51% 70ms 1.49% std::map::lower_bound (inline) 12ms 0.26% 55.77% 67ms 1.43% AbstractCellProperty::IsSame 5ms 0.11% 55.88% 65ms 1.39% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.064% 55.94% 65ms 1.39% vtkDoubleArray::~vtkDoubleArray 0 0% 55.94% 60ms 1.28% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 55.94% 60ms 1.28% NodesOnlyMesh::~NodesOnlyMesh 6ms 0.13% 56.07% 59ms 1.26% VertexMeshWriter::GetNextNode 0 0% 56.07% 59ms 1.26% boost::numeric::ublas::vector_assign (inline) 13ms 0.28% 56.34% 59ms 1.26% vtkDataArray::vtkDataArray 58ms 1.24% 57.58% 58ms 1.24% __GI___writev 0 0% 57.58% 58ms 1.24% std::__basic_file::xsputn_2 57ms 1.22% 58.80% 57ms 1.22% [libvtkCommonCore-9.3.so.9.3] 26ms 0.55% 59.35% 56ms 1.19% __cxxabiv1::__si_class_type_info::__do_dyncast 14ms 0.3% 59.65% 56ms 1.19% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 59.65% 55ms 1.17% NodesOnlyMesh::SetUpBoxCollection 9ms 0.19% 59.84% 55ms 1.17% std::type_info::operator== (inline) 1ms 0.021% 59.86% 54ms 1.15% VertexMesh::Clear 1ms 0.021% 59.88% 52ms 1.11% PottsMesh::GetMooreNeighbouringNodeIndices 51ms 1.09% 60.97% 51ms 1.09% vtkTimeStamp::Modified 24ms 0.51% 61.48% 50ms 1.07% std::_Hashtable::clear 49ms 1.04% 62.53% 49ms 1.04% vtkObject::~vtkObject 47ms 1.00% 63.53% 47ms 1.00% __memcpy_avx_unaligned_erms 12ms 0.26% 63.79% 47ms 1.00% boost::numeric::ublas::indexing_vector_assign 6ms 0.13% 63.92% 47ms 1.00% std::vector::_M_realloc_insert 0 0% 63.92% 47ms 1.00% tcache_get (inline) 47ms 1.00% 64.92% 47ms 1.00% tcache_get_n (inline) 1ms 0.021% 64.94% 45ms 0.96% DistributedBoxCollection::IsOwned 2ms 0.043% 64.98% 45ms 0.96% std::_Rb_tree::_M_insert_unique 0 0% 64.98% 45ms 0.96% std::set::insert (inline) 13ms 0.28% 65.26% 45ms 0.96% vtkAbstractArray::vtkAbstractArray 28ms 0.6% 65.86% 44ms 0.94% DistributedBoxCollection::CalculateContainingBox (inline) 42ms 0.9% 66.75% 44ms 0.94% vtkObjectBase::Delete 0 0% 66.75% 42ms 0.9% _dl_init 0 0% 66.75% 42ms 0.9% call_init (inline) 40ms 0.85% 67.61% 40ms 0.85% [libstdc++.so.6.0.33] 9ms 0.19% 67.80% 40ms 0.85% vtkDataArray::~vtkDataArray 0 0% 67.80% 40ms 0.85% vtkDoubleArray::New 33ms 0.7% 68.50% 40ms 0.85% vtkObject::ObjectFinalize 0 0% 68.50% 39ms 0.83% std::_Destroy (inline) 0 0% 68.50% 39ms 0.83% std::_Destroy_aux::__destroy (inline) 0 0% 68.50% 39ms 0.83% vtkDataArray::ComputeRange 0 0% 68.50% 38ms 0.81% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 68.50% 38ms 0.81% CxxTest::RealWorldDescription::setUp 1ms 0.021% 68.52% 38ms 0.81% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.52% 38ms 0.81% PetscInitialize 0 0% 68.52% 38ms 0.81% PetscSetup::setUpWorld 0 0% 68.52% 38ms 0.81% PetscSetupUtils::CommonSetup 0 0% 68.52% 38ms 0.81% PetscSetupUtils::InitialisePetsc 0 0% 68.52% 38ms 0.81% _dl_start_user 9ms 0.19% 68.71% 38ms 0.81% std::num_put::_M_insert_int 0 0% 68.71% 37ms 0.79% PMPI_Init_thread 0 0% 68.71% 37ms 0.79% ompi_mpi_init 9ms 0.19% 68.91% 37ms 0.79% vtkIdList::~vtkIdList 37ms 0.79% 69.70% 37ms 0.79% vtkObjectBase::~vtkObjectBase 0 0% 69.70% 36ms 0.77% PottsBasedCellPopulation::AcceptCellWriter 2ms 0.043% 69.74% 36ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.021% 69.76% 36ms 0.77% std::make_unique (inline) 0 0% 69.76% 35ms 0.75% OutputFileHandler::OpenOutputFile 35ms 0.75% 70.51% 35ms 0.75% std::codecvt::do_always_noconv 1ms 0.021% 70.53% 35ms 0.75% std::less::operator() (inline) 35ms 0.75% 71.27% 35ms 0.75% vtkObjectBase::vtkObjectBase 0 0% 71.27% 34ms 0.73% DistributedBoxCollection::~DistributedBoxCollection 0 0% 71.27% 34ms 0.73% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 71.27% 34ms 0.73% std::basic_filebuf::open 34ms 0.73% 72.00% 34ms 0.73% std::operator< (inline) 34ms 0.73% 72.72% 34ms 0.73% std::ostream::sentry::sentry 6ms 0.13% 72.85% 32ms 0.68% Node::GetPoint 16ms 0.34% 73.19% 32ms 0.68% _int_free_merge_chunk 3ms 0.064% 73.26% 32ms 0.68% std::_Rb_tree::_M_insert_ (inline) 8ms 0.17% 73.43% 32ms 0.68% vtkAOSDataArrayTemplate::InsertTuple 2ms 0.043% 73.47% 32ms 0.68% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 73.47% 31ms 0.66% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 73.47% 31ms 0.66% VtkMeshWriter::MakeVtkMesh 31ms 0.66% 74.13% 31ms 0.66% __memset_avx2_unaligned_erms 31ms 0.66% 74.79% 31ms 0.66% __mpn_divrem 4ms 0.085% 74.88% 30ms 0.64% boost::serialization::singleton::get_instance 8ms 0.17% 75.05% 30ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.021% 75.07% 30ms 0.64% std::__basic_file::open 0 0% 75.07% 30ms 0.64% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 75.07% 29ms 0.62% _IO_new_file_fopen 0 0% 75.07% 29ms 0.62% _IO_new_fopen 0 0% 75.07% 29ms 0.62% __GI__IO_file_open 0 0% 75.07% 29ms 0.62% __fopen_internal (inline) 29ms 0.62% 75.69% 29ms 0.62% std::_Rb_tree_increment 6ms 0.13% 75.82% 29ms 0.62% std::__new_allocator::construct (inline) 0 0% 75.82% 29ms 0.62% std::allocator_traits::construct (inline) 0 0% 75.82% 28ms 0.6% 28ms 0.6% 76.41% 28ms 0.6% [libchaste_cell_based.so] 28ms 0.6% 77.01% 28ms 0.6% __libc_open64 0 0% 77.01% 28ms 0.6% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 77.01% 28ms 0.6% std::basic_ofstream::basic_ofstream (inline) 1ms 0.021% 77.03% 27ms 0.58% Cell::GetMutationState 27ms 0.58% 77.61% 27ms 0.58% __GI___libc_write 27ms 0.58% 78.18% 27ms 0.58% std::_Rb_tree::_S_right (inline) 0 0% 78.18% 27ms 0.58% std::__basic_file::xsputn 0 0% 78.18% 27ms 0.58% std::basic_filebuf::_M_convert_to_external 0 0% 78.18% 27ms 0.58% std::basic_filebuf::overflow 0 0% 78.18% 27ms 0.58% std::basic_ofstream::open (inline) 0 0% 78.18% 26ms 0.55% NodesOnlyMesh::Clear (inline) 0 0% 78.18% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 19ms 0.41% 78.59% 26ms 0.55% std::num_put::do_put 3ms 0.064% 78.65% 26ms 0.55% tbb::detail::r1::cancel_group_execution 25ms 0.53% 79.19% 25ms 0.53% Node::GetIndex 25ms 0.53% 79.72% 25ms 0.53% boost::numeric::ublas::c_vector::operator() 25ms 0.53% 80.25% 25ms 0.53% vtkDataArray::Modified 0 0% 80.25% 24ms 0.51% Edge::Edge 0 0% 80.25% 24ms 0.51% VertexElement::~VertexElement 0 0% 80.25% 24ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.021% 80.27% 24ms 0.51% std::unique_ptr::~unique_ptr (inline) 6ms 0.13% 80.40% 24ms 0.51% vtkAOSDataArrayTemplate::AllocateTuples 6ms 0.13% 80.53% 24ms 0.51% vtkAbstractArray::~vtkAbstractArray