File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3700ms, 78.92% of 4688ms total Dropped 741 nodes (cum <= 23.44ms) flat flat% sum% cum cum% 0 0% 0% 4499ms 95.97% __libc_start_call_main 0 0% 0% 4499ms 95.97% __libc_start_main_impl 0 0% 0% 4499ms 95.97% _start 0 0% 0% 4481ms 95.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4481ms 95.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4481ms 95.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4481ms 95.58% main 0 0% 0% 4441ms 94.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4441ms 94.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4441ms 94.73% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4430ms 94.50% AbstractCellBasedSimulation::Solve 0 0% 0% 4119ms 87.86% AbstractCellPopulation::WriteResultsToFiles 11ms 0.23% 0.23% 3907ms 83.34% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.23% 1969ms 42.00% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.26% 1691ms 36.07% VertexMeshWriter::MakeVtkMesh 0 0% 0.26% 1250ms 26.66% vtkPolygon::New 1ms 0.021% 0.28% 1249ms 26.64% vtkPolygon::vtkPolygon 4ms 0.085% 0.36% 893ms 19.05% vtkCell::vtkCell 3ms 0.064% 0.43% 793ms 16.92% vtkPoints::New 14ms 0.3% 0.73% 737ms 15.72% vtkPoints::vtkPoints 39ms 0.83% 1.56% 671ms 14.31% operator new 0 0% 1.56% 669ms 14.27% VertexMeshWriter::WriteFiles 49ms 1.05% 2.60% 642ms 13.69% std::ostream::_M_insert 0 0% 2.60% 642ms 13.69% std::ostream::operator<< (inline) 199ms 4.24% 6.85% 637ms 13.59% __GI___libc_malloc 0 0% 6.85% 608ms 12.97% vtkLine::New 0 0% 6.85% 606ms 12.93% vtkQuad::New 5ms 0.11% 6.95% 605ms 12.91% vtkQuad::vtkQuad 11ms 0.23% 7.19% 588ms 12.54% vtkLine::vtkLine 0 0% 7.19% 568ms 12.12% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.19% 568ms 12.12% vtkXMLWriterBase::Write 0 0% 7.19% 566ms 12.07% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.19% 562ms 11.99% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.19% 562ms 11.99% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.19% 561ms 11.97% vtkExecutive::CallAlgorithm 0 0% 7.19% 559ms 11.92% vtkCompositeDataPipeline::ExecuteData 0 0% 7.19% 559ms 11.92% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.043% 7.23% 547ms 11.67% vtkTriangle::New 7ms 0.15% 7.38% 537ms 11.45% vtkTriangle::vtkTriangle 50ms 1.07% 8.45% 524ms 11.18% std::num_put::_M_insert_float 0 0% 8.45% 503ms 10.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.45% 503ms 10.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 129ms 2.75% 11.20% 481ms 10.26% __GI___libc_free 28ms 0.6% 11.80% 457ms 9.75% vtkPoints::SetDataType 0 0% 11.80% 442ms 9.43% vtkXMLWriter::WriteBinaryData 0 0% 11.80% 438ms 9.34% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.80% 437ms 9.32% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.80% 434ms 9.26% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 10ms 0.21% 12.01% 414ms 8.83% std::__cxx11::collate::do_transform 2ms 0.043% 12.05% 390ms 8.32% vtkPolygon::~vtkPolygon 3ms 0.064% 12.12% 389ms 8.30% ___vsnprintf 0 0% 12.12% 386ms 8.23% __vsnprintf_internal (inline) 73ms 1.56% 13.67% 379ms 8.08% __printf_buffer 241ms 5.14% 18.81% 356ms 7.59% _int_malloc 220ms 4.69% 23.51% 349ms 7.44% _int_free 1ms 0.021% 23.53% 345ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.53% 342ms 7.30% VtkMeshWriter::WriteFiles 1ms 0.021% 23.55% 333ms 7.10% vtkXMLWriter::WritePointsAppendedData 3ms 0.064% 23.61% 314ms 6.70% vtkCell::~vtkCell 55ms 1.17% 24.79% 312ms 6.66% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 24.79% 306ms 6.53% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.085% 24.87% 306ms 6.53% PottsBasedCellPopulation::UpdateCellLocations 10ms 0.21% 25.09% 286ms 6.10% __printf_fp_l_buffer 0 0% 25.09% 286ms 6.10% __printf_fp_spec (inline) 41ms 0.87% 25.96% 278ms 5.93% std::__new_allocator::allocate (inline) 0 0% 25.96% 278ms 5.93% std::allocator_traits::allocate (inline) 122ms 2.60% 28.56% 263ms 5.61% __printf_fp_buffer_1 2ms 0.043% 28.60% 254ms 5.42% std::__new_allocator::deallocate (inline) 0 0% 28.60% 252ms 5.38% std::allocator_traits::deallocate (inline) 0 0% 28.60% 227ms 4.84% vtkXMLWriter::WriteCompressionBlock 0 0% 28.60% 219ms 4.67% vtkDataCompressor::Compress 0 0% 28.60% 218ms 4.65% compress2 51ms 1.09% 29.69% 218ms 4.65% crc32 0 0% 29.69% 218ms 4.65% deflate 0 0% 29.69% 218ms 4.65% vtkZLibDataCompressor::CompressBuffer 4ms 0.085% 29.78% 211ms 4.50% vtkBase64OutputStream::Write 10ms 0.21% 29.99% 205ms 4.37% vtkBase64OutputStream::EncodeTriplet 7ms 0.15% 30.14% 204ms 4.35% vtkFloatArray::New 4ms 0.085% 30.23% 192ms 4.10% vtkPoints::~vtkPoints 2ms 0.043% 30.27% 187ms 3.99% std::set::set (inline) 15ms 0.32% 30.59% 185ms 3.95% std::_Rb_tree::_Rb_tree 55ms 1.17% 31.76% 183ms 3.90% std::ostream::write 4ms 0.085% 31.85% 180ms 3.84% vtkIdList::AllocateInternal 2ms 0.043% 31.89% 172ms 3.67% vtkFloatArray::vtkFloatArray 0 0% 31.89% 170ms 3.63% vtkQuad::~vtkQuad 0 0% 31.89% 168ms 3.58% std::_Rb_tree::_M_create_node (inline) 5ms 0.11% 32.00% 167ms 3.56% std::_Rb_tree::~_Rb_tree (inline) 42ms 0.9% 32.89% 166ms 3.54% std::_Rb_tree::_M_erase 5ms 0.11% 33.00% 166ms 3.54% vtkDataArray::CreateDataArray 0 0% 33.00% 164ms 3.50% vtkLine::GetParametricCenter 0 0% 33.00% 163ms 3.48% tbb::detail::r1::parallel_pipeline 5ms 0.11% 33.11% 163ms 3.48% vtkTriangle::~vtkTriangle 2ms 0.043% 33.15% 162ms 3.46% NodesOnlyMesh::ConstructNodesWithoutMesh 96ms 2.05% 35.20% 161ms 3.43% malloc_consolidate 0 0% 35.20% 161ms 3.43% std::_Rb_tree::_M_get_node (inline) 0 0% 35.20% 159ms 3.39% VertexMesh::~VertexMesh 83ms 1.77% 36.97% 156ms 3.33% std::basic_filebuf::xsputn 0 0% 36.97% 155ms 3.31% clone3 0 0% 36.97% 155ms 3.31% start_thread 2ms 0.043% 37.01% 154ms 3.28% VertexMesh::VertexMesh 4ms 0.085% 37.09% 153ms 3.26% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 37.09% 152ms 3.24% std::_Rb_tree::_Alloc_node::operator() (inline) 148ms 3.16% 40.25% 151ms 3.22% [libz.so.1.3] 12ms 0.26% 40.51% 150ms 3.20% std::_Rb_tree::_M_copy (inline) 21ms 0.45% 40.96% 150ms 3.20% std::vector::_M_default_append 1ms 0.021% 40.98% 149ms 3.18% tbb::detail::r1::reset 10ms 0.21% 41.19% 149ms 3.18% vtkTypeFloat64Array::New 3ms 0.064% 41.25% 145ms 3.09% vtkDoubleArray::vtkDoubleArray 0 0% 41.25% 144ms 3.07% std::vector::~vector (inline) 0 0% 41.25% 142ms 3.03% vtkTypeFloat64Array::~vtkTypeFloat64Array 7ms 0.15% 41.40% 141ms 3.01% std::_Vector_base::_M_deallocate (inline) 52ms 1.11% 42.51% 138ms 2.94% tbb::detail::r1::wait_bounded_queue_monitor 6ms 0.13% 42.64% 136ms 2.90% MutableElement::BuildEdges 0 0% 42.64% 136ms 2.90% NodeLocationWriter::VisitAnyPopulation 0 0% 42.64% 136ms 2.90% VertexMesh::GenerateEdgesFromElements (inline) 15ms 0.32% 42.96% 136ms 2.90% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.96% 134ms 2.86% std::set::~set (inline) 2ms 0.043% 43.00% 126ms 2.69% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 43.00% 120ms 2.56% std::_Rb_tree::_M_drop_node (inline) 6ms 0.13% 43.13% 120ms 2.56% vtkFloatArray::~vtkFloatArray 0 0% 43.13% 117ms 2.50% std::_Rb_tree::_M_put_node (inline) 0 0% 43.13% 117ms 2.50% std::_Vector_base::_M_allocate (inline) 1ms 0.021% 43.15% 116ms 2.47% EdgeHelper::GetEdgeFromNodes 0 0% 43.15% 114ms 2.43% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 43.17% 111ms 2.37% CellPropertyCollection::GetPropertiesType (inline) 23ms 0.49% 43.66% 110ms 2.35% vtkObject::vtkObject 108ms 2.30% 45.97% 108ms 2.30% __strcmp_avx2 2ms 0.043% 46.01% 108ms 2.30% std::_Vector_base::~_Vector_base (inline) 0 0% 46.01% 108ms 2.30% vtkIdList::Allocate 0 0% 46.01% 101ms 2.15% vtkXMLWriter::WritePointDataAppendedData 3ms 0.064% 46.08% 100ms 2.13% CellPropertyCollection::HasProperty 2ms 0.043% 46.12% 99ms 2.11% AbstractCellProperty::IsType (inline) 0 0% 46.12% 99ms 2.11% Cell::HasCellProperty (inline) 31ms 0.66% 46.78% 97ms 2.07% std::__ostream_insert 1ms 0.021% 46.80% 94ms 2.01% AbstractCellProperty::IsSubType (inline) 28ms 0.6% 47.40% 94ms 2.01% __dynamic_cast 54ms 1.15% 48.55% 94ms 2.01% vtkObjectBase::UnRegisterInternal 1ms 0.021% 48.57% 93ms 1.98% std::map::operator[] (partial-inline) 1ms 0.021% 48.59% 92ms 1.96% std::operator<< (inline) 92ms 1.96% 50.55% 92ms 1.96% unlink_chunk 44ms 0.94% 51.49% 91ms 1.94% hack_digit 1ms 0.021% 51.51% 90ms 1.92% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 11ms 0.23% 51.75% 87ms 1.86% vtkAOSDataArrayTemplate::DataElementChanged 84ms 1.79% 53.54% 84ms 1.79% __GI_sched_yield 50ms 1.07% 54.61% 83ms 1.77% vtkTypeFloat64Array::PrintSelf 23ms 0.49% 55.10% 81ms 1.73% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.064% 55.16% 78ms 1.66% _int_free_maybe_consolidate 2ms 0.043% 55.20% 74ms 1.58% AbstractCellPopulation::GetCellUsingLocationIndex 13ms 0.28% 55.48% 74ms 1.58% AbstractCellProperty::IsSame 0 0% 55.48% 73ms 1.56% tcache_get (inline) 73ms 1.56% 57.04% 73ms 1.56% tcache_get_n (inline) 50ms 1.07% 58.11% 72ms 1.54% std::basic_streambuf::xsputn 23ms 0.49% 58.60% 68ms 1.45% vtkObject::Modified 2ms 0.043% 58.64% 67ms 1.43% std::vector::push_back (inline) 0 0% 58.64% 67ms 1.43% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1ms 0.021% 58.66% 63ms 1.34% Cell::GetCellProliferativeType 0 0% 58.66% 63ms 1.34% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 58.68% 62ms 1.32% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 7ms 0.15% 58.83% 62ms 1.32% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 58.83% 61ms 1.30% NodesOnlyMesh::~NodesOnlyMesh 11ms 0.23% 59.07% 61ms 1.30% std::type_info::operator== (inline) 1ms 0.021% 59.09% 61ms 1.30% vtkIdList::New 3ms 0.064% 59.15% 60ms 1.28% vtkDoubleArray::~vtkDoubleArray 0 0% 59.15% 59ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 59.15% 59ms 1.26% std::map::lower_bound (inline) 39ms 0.83% 59.98% 58ms 1.24% std::_Hashtable::clear 1ms 0.021% 60.00% 57ms 1.22% std::set::insert (inline) 1ms 0.021% 60.03% 55ms 1.17% DistributedBoxCollection::IsOwned 0 0% 60.03% 55ms 1.17% NodesOnlyMesh::SetUpBoxCollection 1ms 0.021% 60.05% 55ms 1.17% std::_Rb_tree::_M_insert_unique 28ms 0.6% 60.64% 54ms 1.15% DistributedBoxCollection::CalculateContainingBox (inline) 1ms 0.021% 60.67% 54ms 1.15% boost::numeric::ublas::vector_assign (inline) 7ms 0.15% 60.81% 54ms 1.15% vtkDataArray::vtkDataArray 53ms 1.13% 61.95% 53ms 1.13% [libvtkCommonCore-9.3.so.9.3] 10ms 0.21% 62.16% 51ms 1.09% std::num_put::_M_insert_int 4ms 0.085% 62.24% 51ms 1.09% std::vector::_M_realloc_insert 0 0% 62.24% 49ms 1.05% vtkDataArray::ComputeRange 49ms 1.05% 63.29% 49ms 1.05% vtkObject::~vtkObject 11ms 0.23% 63.52% 48ms 1.02% vtkIdList::~vtkIdList 16ms 0.34% 63.87% 47ms 1.00% vtkAbstractArray::vtkAbstractArray 1ms 0.021% 63.89% 45ms 0.96% VertexMesh::Clear 27ms 0.58% 64.46% 45ms 0.96% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.13% 64.59% 43ms 0.92% VertexMeshWriter::GetNextNode 43ms 0.92% 65.51% 43ms 0.92% __GI___writev 43ms 0.92% 66.42% 43ms 0.92% __memcpy_avx_unaligned_erms 0 0% 66.42% 43ms 0.92% std::_Destroy (inline) 0 0% 66.42% 43ms 0.92% std::_Destroy_aux::__destroy (inline) 0 0% 66.42% 43ms 0.92% std::__basic_file::xsputn_2 9ms 0.19% 66.62% 43ms 0.92% vtkSOADataArrayTemplate::FillTypedComponent 43ms 0.92% 67.53% 43ms 0.92% vtkTimeStamp::Modified 42ms 0.9% 68.43% 42ms 0.9% [libstdc++.so.6.0.33] 41ms 0.87% 69.30% 41ms 0.87% boost::numeric::ublas::c_vector::operator() 13ms 0.28% 69.58% 41ms 0.87% boost::numeric::ublas::indexing_vector_assign 5ms 0.11% 69.69% 41ms 0.87% vtkAOSDataArrayTemplate::InsertTuple 7ms 0.15% 69.84% 41ms 0.87% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.021% 69.86% 40ms 0.85% vtk::detail::smp::vtkSMPToolsImplForTBB 30ms 0.64% 70.50% 40ms 0.85% vtkObject::ObjectFinalize 0 0% 70.50% 39ms 0.83% std::less::operator() (inline) 39ms 0.83% 71.33% 39ms 0.83% std::operator< (inline) 10ms 0.21% 71.54% 38ms 0.81% _int_free_merge_chunk 0 0% 71.54% 37ms 0.79% CxxTest::RealWorldDescription::setUp 0 0% 71.54% 37ms 0.79% PetscInitialize 0 0% 71.54% 37ms 0.79% PetscSetup::setUpWorld 0 0% 71.54% 37ms 0.79% PetscSetupUtils::CommonSetup 0 0% 71.54% 37ms 0.79% PetscSetupUtils::InitialisePetsc 37ms 0.79% 72.33% 37ms 0.79% __mpn_divrem 37ms 0.79% 73.12% 37ms 0.79% vtkObjectBase::vtkObjectBase 37ms 0.79% 73.91% 37ms 0.79% vtkObjectBase::~vtkObjectBase 0 0% 73.91% 36ms 0.77% PMPI_Init_thread 0 0% 73.91% 36ms 0.77% _dl_init 0 0% 73.91% 36ms 0.77% call_init (inline) 0 0% 73.91% 36ms 0.77% ompi_mpi_init 3ms 0.064% 73.98% 36ms 0.77% tbb::detail::r1::cancel_group_execution 0 0% 73.98% 35ms 0.75% Cell::GetCellId 4ms 0.085% 74.06% 35ms 0.75% std::_Rb_tree::_M_insert_ (inline) 0 0% 74.06% 34ms 0.73% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.021% 74.08% 34ms 0.73% PottsBasedCellPopulation::AcceptCellWriter 0 0% 74.08% 34ms 0.73% VtkMeshWriter::MakeVtkMesh 0 0% 74.08% 34ms 0.73% _dl_start_user 0 0% 74.08% 33ms 0.7% CellIdWriter::GetCellDataForVtkOutput 0 0% 74.08% 33ms 0.7% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.08% 33ms 0.7% NodesOnlyMesh::ClearBoxCollection (inline) 1ms 0.021% 74.10% 33ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 0 0% 74.10% 33ms 0.7% std::basic_filebuf::open 0 0% 74.10% 33ms 0.7% std::map::~map (inline) 5ms 0.11% 74.21% 33ms 0.7% vtk::detail::smp::vtkSMPToolsImpl::For 1ms 0.021% 74.23% 32ms 0.68% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 74.23% 31ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 7ms 0.15% 74.38% 31ms 0.66% vtkDataArray::~vtkDataArray 30ms 0.64% 75.02% 30ms 0.64% std::codecvt::do_always_noconv 0 0% 75.02% 30ms 0.64% vtkDoubleArray::New 1ms 0.021% 75.04% 29ms 0.62% 0 0% 75.04% 29ms 0.62% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 75.04% 29ms 0.62% _IO_new_file_fopen 0 0% 75.04% 29ms 0.62% _IO_new_fopen 0 0% 75.04% 29ms 0.62% __GI__IO_file_open 0 0% 75.04% 29ms 0.62% __fopen_internal (inline) 29ms 0.62% 75.66% 29ms 0.62% __libc_open64 0 0% 75.66% 29ms 0.62% std::__basic_file::open 1ms 0.021% 75.68% 29ms 0.62% std::unique_ptr::~unique_ptr (inline) 0 0% 75.68% 28ms 0.6% NodesOnlyMesh::Clear (inline) 0 0% 75.68% 28ms 0.6% OutputFileHandler::OpenOutputFile 5ms 0.11% 75.79% 28ms 0.6% boost::serialization::singleton::get_instance 28ms 0.6% 76.39% 28ms 0.6% std::_Rb_tree_increment 0 0% 76.39% 28ms 0.6% std::default_delete::operator() (inline) 0 0% 76.39% 28ms 0.6% std::make_unique (inline) 27ms 0.58% 76.96% 27ms 0.58% std::_Rb_tree::_S_right (inline) 26ms 0.55% 77.52% 26ms 0.55% std::ostream::sentry::sentry 1ms 0.021% 77.54% 26ms 0.55% vtkDataSet::GetCellTypes 0 0% 77.54% 26ms 0.55% vtkUnstructuredGrid::GetDistinctCellTypesArray 1ms 0.021% 77.56% 25ms 0.53% VertexMeshWriter::GetNextElement 25ms 0.53% 78.09% 25ms 0.53% __GI___libc_write 14ms 0.3% 78.39% 25ms 0.53% _int_free_create_chunk (inline) 0 0% 78.39% 25ms 0.53% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.39% 25ms 0.53% std::__basic_file::xsputn 0 0% 78.39% 25ms 0.53% std::basic_filebuf::_M_convert_to_external 0 0% 78.39% 25ms 0.53% std::basic_filebuf::overflow 1ms 0.021% 78.41% 24ms 0.51% Node::AddElement 24ms 0.51% 78.92% 24ms 0.51% [libchaste_cell_based.so] 0 0% 78.92% 24ms 0.51% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.92% 24ms 0.51% orte_init 0 0% 78.92% 24ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange