File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3758ms, 78.24% of 4803ms total Dropped 740 nodes (cum <= 24.02ms) flat flat% sum% cum cum% 0 0% 0% 4586ms 95.48% __libc_start_call_main 0 0% 0% 4586ms 95.48% __libc_start_main_impl 0 0% 0% 4586ms 95.48% _start 0 0% 0% 4568ms 95.11% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4568ms 95.11% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4568ms 95.11% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4568ms 95.11% main 0 0% 0% 4528ms 94.27% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4528ms 94.27% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4528ms 94.27% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4516ms 94.02% AbstractCellBasedSimulation::Solve 0 0% 0% 4195ms 87.34% AbstractCellPopulation::WriteResultsToFiles 18ms 0.37% 0.37% 3975ms 82.76% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.37% 1991ms 41.45% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.37% 1716ms 35.73% VertexMeshWriter::MakeVtkMesh 0 0% 0.37% 1231ms 25.63% vtkPolygon::New 2ms 0.042% 0.42% 1231ms 25.63% vtkPolygon::vtkPolygon 14ms 0.29% 0.71% 862ms 17.95% vtkCell::vtkCell 1ms 0.021% 0.73% 713ms 14.84% vtkPoints::New 0 0% 0.73% 682ms 14.20% VertexMeshWriter::WriteFiles 11ms 0.23% 0.96% 673ms 14.01% vtkPoints::vtkPoints 31ms 0.65% 1.60% 664ms 13.82% operator new 199ms 4.14% 5.75% 641ms 13.35% __GI___libc_malloc 53ms 1.10% 6.85% 623ms 12.97% std::ostream::_M_insert 1ms 0.021% 6.87% 621ms 12.93% std::ostream::operator<< (inline) 1ms 0.021% 6.89% 580ms 12.08% vtkXMLWriterBase::Write 0 0% 6.89% 579ms 12.05% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.89% 572ms 11.91% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.89% 572ms 11.91% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.89% 570ms 11.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.89% 569ms 11.85% vtkCompositeDataPipeline::ExecuteData 0 0% 6.89% 569ms 11.85% vtkExecutive::CallAlgorithm 0 0% 6.89% 569ms 11.85% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 6.89% 568ms 11.83% vtkQuad::New 2ms 0.042% 6.93% 565ms 11.76% vtkQuad::vtkQuad 2ms 0.042% 6.97% 563ms 11.72% vtkLine::New 7ms 0.15% 7.12% 544ms 11.33% vtkLine::vtkLine 121ms 2.52% 9.64% 529ms 11.01% __GI___libc_free 0 0% 9.64% 525ms 10.93% vtkTriangle::New 1ms 0.021% 9.66% 521ms 10.85% vtkTriangle::vtkTriangle 0 0% 9.66% 510ms 10.62% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 9.66% 510ms 10.62% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 47ms 0.98% 10.64% 500ms 10.41% std::num_put::_M_insert_float 3ms 0.062% 10.70% 442ms 9.20% vtkPolygon::~vtkPolygon 0 0% 10.70% 440ms 9.16% vtkXMLWriter::WriteBinaryData 0 0% 10.70% 437ms 9.10% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 10.70% 436ms 9.08% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.70% 436ms 9.08% vtkXMLWriter::WriteBinaryDataInternal 25ms 0.52% 11.22% 415ms 8.64% vtkPoints::SetDataType 258ms 5.37% 16.59% 405ms 8.43% _int_free 8ms 0.17% 16.76% 386ms 8.04% std::__cxx11::collate::do_transform 254ms 5.29% 22.05% 373ms 7.77% _int_malloc 1ms 0.021% 22.07% 363ms 7.56% ___vsnprintf 6ms 0.12% 22.19% 363ms 7.56% vtkCell::~vtkCell 44ms 0.92% 23.11% 362ms 7.54% __printf_buffer 0 0% 23.11% 362ms 7.54% __vsnprintf_internal (inline) 2ms 0.042% 23.15% 354ms 7.37% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.15% 349ms 7.27% VtkMeshWriter::WriteFiles 0 0% 23.15% 329ms 6.85% vtkXMLWriter::WritePointsAppendedData 0 0% 23.15% 312ms 6.50% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 23.17% 312ms 6.50% PottsBasedCellPopulation::UpdateCellLocations 11ms 0.23% 23.40% 294ms 6.12% __printf_fp_l_buffer 0 0% 23.40% 294ms 6.12% __printf_fp_spec (inline) 31ms 0.65% 24.05% 280ms 5.83% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 4ms 0.083% 24.13% 276ms 5.75% std::__new_allocator::deallocate (inline) 0 0% 24.13% 273ms 5.68% std::allocator_traits::deallocate (inline) 41ms 0.85% 24.98% 271ms 5.64% std::__new_allocator::allocate (inline) 0 0% 24.98% 271ms 5.64% std::allocator_traits::allocate (inline) 115ms 2.39% 27.38% 265ms 5.52% __printf_fp_buffer_1 3ms 0.062% 27.44% 226ms 4.71% vtkPoints::~vtkPoints 1ms 0.021% 27.46% 226ms 4.71% vtkXMLWriter::WriteCompressionBlock 7ms 0.15% 27.61% 218ms 4.54% vtkBase64OutputStream::Write 19ms 0.4% 28.00% 210ms 4.37% vtkBase64OutputStream::EncodeTriplet 2ms 0.042% 28.04% 209ms 4.35% std::set::set (inline) 21ms 0.44% 28.48% 207ms 4.31% std::_Rb_tree::_Rb_tree 0 0% 28.48% 206ms 4.29% vtkDataCompressor::Compress 0 0% 28.48% 205ms 4.27% compress2 1ms 0.021% 28.50% 205ms 4.27% vtkQuad::~vtkQuad 0 0% 28.50% 205ms 4.27% vtkZLibDataCompressor::CompressBuffer 2ms 0.042% 28.54% 203ms 4.23% vtkTriangle::~vtkTriangle 1ms 0.021% 28.57% 202ms 4.21% deflate 53ms 1.10% 29.67% 201ms 4.18% crc32 1ms 0.021% 29.69% 196ms 4.08% vtkLine::GetParametricCenter 1ms 0.021% 29.71% 190ms 3.96% tbb::detail::r1::parallel_pipeline 97ms 2.02% 31.73% 185ms 3.85% malloc_consolidate 7ms 0.15% 31.88% 182ms 3.79% vtkFloatArray::New 3ms 0.062% 31.94% 182ms 3.79% vtkIdList::AllocateInternal 0 0% 31.94% 181ms 3.77% clone3 0 0% 31.94% 181ms 3.77% start_thread 2ms 0.042% 31.98% 175ms 3.64% NodesOnlyMesh::ConstructNodesWithoutMesh 53ms 1.10% 33.08% 174ms 3.62% std::ostream::write 2ms 0.042% 33.13% 174ms 3.62% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 33.13% 173ms 3.60% VertexMesh::~VertexMesh 1ms 0.021% 33.15% 169ms 3.52% tbb::detail::r1::reset 0 0% 33.15% 168ms 3.50% std::_Rb_tree::_M_create_node (inline) 4ms 0.083% 33.23% 163ms 3.39% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.083% 33.31% 162ms 3.37% std::_Vector_base::_M_deallocate (inline) 0 0% 33.31% 161ms 3.35% std::vector::~vector (inline) 66ms 1.37% 34.69% 160ms 3.33% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.021% 34.71% 160ms 3.33% vtkFloatArray::vtkFloatArray 33ms 0.69% 35.39% 157ms 3.27% std::_Rb_tree::_M_erase 6ms 0.12% 35.52% 157ms 3.27% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.042% 35.56% 156ms 3.25% VertexMesh::VertexMesh 0 0% 35.56% 155ms 3.23% std::_Rb_tree::_Alloc_node::operator() (inline) 17ms 0.35% 35.92% 155ms 3.23% std::_Rb_tree::_M_copy (inline) 0 0% 35.92% 152ms 3.16% std::_Rb_tree::_M_get_node (inline) 0 0% 35.92% 143ms 2.98% NodeLocationWriter::VisitAnyPopulation 137ms 2.85% 38.77% 142ms 2.96% [libz.so.1.3] 1ms 0.021% 38.79% 142ms 2.96% vtkDataArray::CreateDataArray 65ms 1.35% 40.14% 140ms 2.91% std::basic_filebuf::xsputn 1ms 0.021% 40.16% 135ms 2.81% VertexMesh::GenerateEdgesFromElements (inline) 5ms 0.1% 40.27% 135ms 2.81% std::vector::_M_default_append 5ms 0.1% 40.37% 134ms 2.79% MutableElement::BuildEdges 3ms 0.062% 40.43% 134ms 2.79% vtkTypeFloat64Array::New 12ms 0.25% 40.68% 131ms 2.73% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.68% 129ms 2.69% std::_Vector_base::~_Vector_base (inline) 29ms 0.6% 41.29% 129ms 2.69% vtkObject::vtkObject 0 0% 41.29% 127ms 2.64% std::set::~set (inline) 1ms 0.021% 41.31% 125ms 2.60% vtkDoubleArray::vtkDoubleArray 0 0% 41.31% 123ms 2.56% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 41.33% 120ms 2.50% std::_Vector_base::_M_allocate (inline) 0 0% 41.33% 118ms 2.46% std::_Rb_tree::_M_drop_node (inline) 0 0% 41.33% 118ms 2.46% vtkIdList::Allocate 2ms 0.042% 41.37% 116ms 2.42% vtkFloatArray::~vtkFloatArray 2ms 0.042% 41.41% 115ms 2.39% EdgeHelper::GetEdgeFromNodes 0 0% 41.41% 115ms 2.39% std::_Rb_tree::_M_put_node (inline) 66ms 1.37% 42.79% 113ms 2.35% vtkObjectBase::UnRegisterInternal 34ms 0.71% 43.49% 112ms 2.33% std::__ostream_insert 55ms 1.15% 44.64% 109ms 2.27% vtkTypeFloat64Array::PrintSelf 0 0% 44.64% 107ms 2.23% std::operator<< (inline) 107ms 2.23% 46.87% 107ms 2.23% unlink_chunk 1ms 0.021% 46.89% 107ms 2.23% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 46.89% 106ms 2.21% vtkXMLWriter::WritePointDataAppendedData 103ms 2.14% 49.03% 103ms 2.14% __strcmp_avx2 53ms 1.10% 50.14% 100ms 2.08% hack_digit 1ms 0.021% 50.16% 99ms 2.06% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.12% 50.28% 96ms 2.00% _int_free_maybe_consolidate 94ms 1.96% 52.24% 94ms 1.96% __GI_sched_yield 3ms 0.062% 52.30% 92ms 1.92% std::map::operator[] (partial-inline) 8ms 0.17% 52.47% 91ms 1.89% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.021% 52.49% 89ms 1.85% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 52.49% 88ms 1.83% Cell::HasCellProperty (inline) 4ms 0.083% 52.57% 88ms 1.83% CellPropertyCollection::HasProperty 23ms 0.48% 53.05% 87ms 1.81% vtkObject::Modified 1ms 0.021% 53.07% 86ms 1.79% AbstractCellProperty::IsType (inline) 43ms 0.9% 53.97% 83ms 1.73% std::basic_streambuf::xsputn 1ms 0.021% 53.99% 82ms 1.71% AbstractCellProperty::IsSubType (inline) 3ms 0.062% 54.05% 82ms 1.71% std::vector::push_back (inline) 20ms 0.42% 54.47% 80ms 1.67% __dynamic_cast 3ms 0.062% 54.53% 77ms 1.60% vtkDoubleArray::~vtkDoubleArray 3ms 0.062% 54.59% 76ms 1.58% AbstractCellPopulation::GetCellUsingLocationIndex 27ms 0.56% 55.15% 74ms 1.54% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.083% 55.24% 73ms 1.52% vtkIdList::New 6ms 0.12% 55.36% 70ms 1.46% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 55.36% 70ms 1.46% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 8ms 0.17% 55.53% 69ms 1.44% vtkDataArray::vtkDataArray 0 0% 55.53% 68ms 1.42% NodesOnlyMesh::SetUpBoxCollection 0 0% 55.53% 65ms 1.35% PottsMesh::GetMooreNeighbouringNodeIndices 65ms 1.35% 56.88% 65ms 1.35% [libvtkCommonCore-9.3.so.9.3] 0 0% 56.88% 64ms 1.33% boost::numeric::ublas::vector_assign (inline) 1ms 0.021% 56.90% 64ms 1.33% std::_Rb_tree::_M_insert_unique 0 0% 56.90% 64ms 1.33% std::set::insert (inline) 1ms 0.021% 56.92% 62ms 1.29% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 62ms 1.29% 58.21% 62ms 1.29% vtkTimeStamp::Modified 0 0% 58.21% 61ms 1.27% Cell::GetCellProliferativeType 4ms 0.083% 58.30% 61ms 1.27% std::vector::_M_realloc_insert 0 0% 58.30% 61ms 1.27% tcache_get (inline) 61ms 1.27% 59.57% 61ms 1.27% tcache_get_n (inline) 18ms 0.37% 59.94% 61ms 1.27% vtkAbstractArray::vtkAbstractArray 0 0% 59.94% 60ms 1.25% NodesOnlyMesh::~NodesOnlyMesh 11ms 0.23% 60.17% 59ms 1.23% AbstractCellProperty::IsSame 10ms 0.21% 60.38% 58ms 1.21% VertexMeshWriter::GetNextNode 0 0% 60.38% 57ms 1.19% std::_Rb_tree::lower_bound (inline) 0 0% 60.38% 57ms 1.19% std::map::lower_bound (inline) 56ms 1.17% 61.54% 56ms 1.17% __memcpy_avx_unaligned_erms 18ms 0.37% 61.92% 51ms 1.06% boost::numeric::ublas::indexing_vector_assign 0 0% 61.92% 50ms 1.04% VertexMesh::Clear 9ms 0.19% 62.11% 49ms 1.02% vtkSOADataArrayTemplate::FillTypedComponent 11ms 0.23% 62.34% 48ms 1% std::type_info::operator== (inline) 0 0% 62.34% 48ms 1% vtkDataArray::ComputeRange 41ms 0.85% 63.19% 47ms 0.98% vtkObject::ObjectFinalize 46ms 0.96% 64.15% 46ms 0.96% [libstdc++.so.6.0.33] 0 0% 64.15% 46ms 0.96% std::_Destroy (inline) 0 0% 64.15% 46ms 0.96% std::_Destroy_aux::__destroy (inline) 7ms 0.15% 64.29% 46ms 0.96% std::_Rb_tree::_M_insert_ (inline) 45ms 0.94% 65.23% 46ms 0.96% vtkObject::~vtkObject 22ms 0.46% 65.69% 45ms 0.94% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.19% 65.88% 45ms 0.94% std::num_put::_M_insert_int 22ms 0.46% 66.33% 43ms 0.9% std::_Hashtable::clear 2ms 0.042% 66.38% 43ms 0.9% std::basic_filebuf::_M_convert_to_external 0 0% 66.38% 43ms 0.9% std::basic_filebuf::overflow 0 0% 66.38% 41ms 0.85% DistributedBoxCollection::SetupLocalBoxesHalfOnly 40ms 0.83% 67.21% 41ms 0.85% __GI___libc_write 0 0% 67.21% 41ms 0.85% std::__basic_file::xsputn 41ms 0.85% 68.06% 41ms 0.85% std::codecvt::do_always_noconv 41ms 0.85% 68.92% 41ms 0.85% std::ostream::sentry::sentry 0 0% 68.92% 40ms 0.83% _dl_init 0 0% 68.92% 40ms 0.83% call_init (inline) 7ms 0.15% 69.06% 40ms 0.83% vtkAOSDataArrayTemplate::InsertTuple 12ms 0.25% 69.31% 40ms 0.83% vtkDataArray::~vtkDataArray 0 0% 69.31% 39ms 0.81% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.31% 39ms 0.81% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 69.31% 39ms 0.81% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 69.31% 38ms 0.79% PottsMesh::GetVonNeumannNeighbouringNodeIndices 3ms 0.062% 69.37% 38ms 0.79% vtkDataArrayPrivate::DoComputeVectorRange 38ms 0.79% 70.16% 38ms 0.79% vtkObjectBase::Delete 3ms 0.062% 70.23% 37ms 0.77% 0 0% 70.23% 36ms 0.75% CxxTest::RealWorldDescription::setUp 23ms 0.48% 70.71% 36ms 0.75% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 70.71% 36ms 0.75% DistributedBoxCollection::IsOwned 0 0% 70.71% 36ms 0.75% PMPI_Init_thread 0 0% 70.71% 36ms 0.75% PetscInitialize 0 0% 70.71% 36ms 0.75% PetscSetup::setUpWorld 0 0% 70.71% 36ms 0.75% PetscSetupUtils::CommonSetup 0 0% 70.71% 36ms 0.75% PetscSetupUtils::InitialisePetsc 0 0% 70.71% 36ms 0.75% _dl_start_user 0 0% 70.71% 36ms 0.75% ompi_mpi_init 2ms 0.042% 70.75% 36ms 0.75% tbb::detail::r1::cancel_group_execution 9ms 0.19% 70.93% 35ms 0.73% std::__new_allocator::construct (inline) 0 0% 70.93% 35ms 0.73% std::allocator_traits::construct (inline) 0 0% 70.93% 35ms 0.73% std::make_unique (inline) 7ms 0.15% 71.08% 35ms 0.73% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 71.08% 34ms 0.71% std::__basic_file::xsputn_2 34ms 0.71% 71.79% 34ms 0.71% vtkObjectBase::~vtkObjectBase 33ms 0.69% 72.48% 33ms 0.69% __GI___writev 16ms 0.33% 72.81% 32ms 0.67% _int_free_merge_chunk 0 0% 72.81% 32ms 0.67% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.042% 72.85% 32ms 0.67% vtkDoubleArray::New 31ms 0.65% 73.50% 31ms 0.65% __mpn_divrem 4ms 0.083% 73.58% 31ms 0.65% vtkAOSDataArrayTemplate::AllocateTuples 5ms 0.1% 73.68% 31ms 0.65% vtkIdList::~vtkIdList 31ms 0.65% 74.33% 31ms 0.65% vtkObjectBase::vtkObjectBase 1ms 0.021% 74.35% 30ms 0.62% Cell::GetCellId 30ms 0.62% 74.97% 30ms 0.62% __memset_avx2_unaligned_erms 0 0% 74.97% 30ms 0.62% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.062% 75.04% 30ms 0.62% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.021% 75.06% 30ms 0.62% std::less::operator() (inline) 0 0% 75.06% 30ms 0.62% std::map::~map (inline) 0 0% 75.06% 30ms 0.62% std::unique_ptr::~unique_ptr (inline) 29ms 0.6% 75.66% 29ms 0.6% boost::numeric::ublas::c_vector::operator() 3ms 0.062% 75.72% 29ms 0.6% boost::serialization::singleton::get_instance 0 0% 75.72% 29ms 0.6% std::default_delete::operator() (inline) 29ms 0.6% 76.33% 29ms 0.6% std::operator< (inline) 1ms 0.021% 76.35% 28ms 0.58% CellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.042% 76.39% 28ms 0.58% Node::ConstructNodeAttributes (inline) 28ms 0.58% 76.97% 28ms 0.58% Node::GetIndex 0 0% 76.97% 28ms 0.58% Node::SetRadius 4ms 0.083% 77.06% 28ms 0.58% vtkAbstractArray::~vtkAbstractArray 1ms 0.021% 77.08% 27ms 0.56% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.08% 27ms 0.56% OutputFileHandler::OpenOutputFile 2ms 0.042% 77.12% 27ms 0.56% VertexMeshWriter::GetNextElement 0 0% 77.12% 27ms 0.56% VtkMeshWriter::MakeVtkMesh 0 0% 77.12% 27ms 0.56% __GI___get_nprocs 0 0% 77.12% 27ms 0.56% read_sysfs_file 27ms 0.56% 77.68% 27ms 0.56% std::_Rb_tree_increment 0 0% 77.68% 27ms 0.56% std::basic_filebuf::sync 21ms 0.44% 78.12% 27ms 0.56% std::num_put::do_put 0 0% 78.12% 27ms 0.56% std::ostream::flush 0 0% 78.12% 27ms 0.56% std::thread::hardware_concurrency 0 0% 78.12% 27ms 0.56% vtkDataArrayPrivate::DoComputeScalarRange 6ms 0.12% 78.24% 27ms 0.56% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 78.24% 26ms 0.54% CellIdWriter::GetCellDataForVtkOutput 0 0% 78.24% 26ms 0.54% Edge::Edge 0 0% 78.24% 26ms 0.54% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.24% 25ms 0.52% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.24% 25ms 0.52% std::basic_filebuf::open 0 0% 78.24% 25ms 0.52% vtkDataSet::GetCellTypes