File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3827ms, 76.89% of 4977ms total Dropped 782 nodes (cum <= 24.89ms) flat flat% sum% cum cum% 0 0% 0% 4740ms 95.24% __libc_start_call_main 0 0% 0% 4740ms 95.24% __libc_start_main_impl 0 0% 0% 4740ms 95.24% _start 0 0% 0% 4725ms 94.94% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4725ms 94.94% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4725ms 94.94% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4725ms 94.94% main 0 0% 0% 4686ms 94.15% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4686ms 94.15% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4686ms 94.15% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4675ms 93.93% AbstractCellBasedSimulation::Solve 0 0% 0% 4356ms 87.52% AbstractCellPopulation::WriteResultsToFiles 11ms 0.22% 0.22% 4115ms 82.68% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.22% 1977ms 39.72% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.08% 0.3% 1699ms 34.14% VertexMeshWriter::MakeVtkMesh 0 0% 0.3% 1274ms 25.60% vtkPolygon::New 1ms 0.02% 0.32% 1271ms 25.54% vtkPolygon::vtkPolygon 7ms 0.14% 0.46% 945ms 18.99% vtkCell::vtkCell 5ms 0.1% 0.56% 822ms 16.52% vtkPoints::New 1ms 0.02% 0.58% 799ms 16.05% VertexMeshWriter::WriteFiles 16ms 0.32% 0.9% 777ms 15.61% vtkPoints::vtkPoints 2ms 0.04% 0.94% 776ms 15.59% std::ostream::operator<< (inline) 55ms 1.11% 2.05% 774ms 15.55% std::ostream::_M_insert 3ms 0.06% 2.11% 656ms 13.18% vtkQuad::New 3ms 0.06% 2.17% 649ms 13.04% vtkQuad::vtkQuad 47ms 0.94% 3.11% 641ms 12.88% std::num_put::_M_insert_float 37ms 0.74% 3.86% 634ms 12.74% operator new 200ms 4.02% 7.88% 607ms 12.20% __GI___libc_malloc 1ms 0.02% 7.90% 597ms 12.00% vtkLine::New 0 0% 7.90% 585ms 11.75% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.90% 585ms 11.75% vtkXMLWriterBase::Write 0 0% 7.90% 582ms 11.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.90% 582ms 11.69% vtkExecutive::CallAlgorithm 9ms 0.18% 8.08% 582ms 11.69% vtkLine::vtkLine 0 0% 8.08% 582ms 11.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.08% 581ms 11.67% vtkCompositeDataPipeline::ExecuteData 0 0% 8.08% 581ms 11.67% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.08% 581ms 11.67% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.02% 8.10% 567ms 11.39% vtkTriangle::New 6ms 0.12% 8.22% 560ms 11.25% vtkTriangle::vtkTriangle 0 0% 8.22% 519ms 10.43% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.22% 519ms 10.43% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.1% 8.32% 497ms 9.99% std::__cxx11::collate::do_transform 146ms 2.93% 11.25% 490ms 9.85% __GI___libc_free 26ms 0.52% 11.77% 481ms 9.66% vtkPoints::SetDataType 9ms 0.18% 11.95% 476ms 9.56% ___vsnprintf 0 0% 11.95% 467ms 9.38% __vsnprintf_internal (inline) 63ms 1.27% 13.22% 456ms 9.16% __printf_buffer 0 0% 13.22% 453ms 9.10% vtkXMLWriter::WriteBinaryData 0 0% 13.22% 444ms 8.92% vtkXMLWriter::WriteBinaryDataBlock 0 0% 13.22% 444ms 8.92% vtkXMLWriter::WriteBinaryDataInternal 0 0% 13.22% 441ms 8.86% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 13.22% 375ms 7.53% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.02% 13.24% 373ms 7.49% vtkPolygon::~vtkPolygon 0 0% 13.24% 372ms 7.47% VtkMeshWriter::WriteFiles 2ms 0.04% 13.28% 356ms 7.15% __printf_fp_spec (inline) 20ms 0.4% 13.68% 354ms 7.11% __printf_fp_l_buffer 227ms 4.56% 18.24% 343ms 6.89% _int_free 232ms 4.66% 22.91% 335ms 6.73% _int_malloc 0 0% 22.91% 329ms 6.61% vtkXMLWriter::WritePointsAppendedData 155ms 3.11% 26.02% 317ms 6.37% __printf_fp_buffer_1 0 0% 26.02% 314ms 6.31% OnLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.18% 26.20% 314ms 6.31% PottsBasedCellPopulation::UpdateCellLocations 6ms 0.12% 26.32% 311ms 6.25% vtkCell::~vtkCell 54ms 1.08% 27.41% 303ms 6.09% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 46ms 0.92% 28.33% 280ms 5.63% std::__new_allocator::allocate (inline) 0 0% 28.33% 276ms 5.55% std::allocator_traits::allocate (inline) 6ms 0.12% 28.45% 252ms 5.06% std::__new_allocator::deallocate (inline) 0 0% 28.45% 246ms 4.94% std::allocator_traits::deallocate (inline) 0 0% 28.45% 229ms 4.60% vtkXMLWriter::WriteCompressionBlock 0 0% 28.45% 221ms 4.44% std::set::set (inline) 0 0% 28.45% 220ms 4.42% compress2 15ms 0.3% 28.75% 220ms 4.42% std::_Rb_tree::_Rb_tree 0 0% 28.75% 220ms 4.42% vtkDataCompressor::Compress 0 0% 28.75% 220ms 4.42% vtkZLibDataCompressor::CompressBuffer 57ms 1.15% 29.90% 217ms 4.36% crc32 0 0% 29.90% 217ms 4.36% deflate 6ms 0.12% 30.02% 217ms 4.36% vtkBase64OutputStream::Write 9ms 0.18% 30.20% 211ms 4.24% vtkBase64OutputStream::EncodeTriplet 2ms 0.04% 30.24% 210ms 4.22% vtkFloatArray::New 0 0% 30.24% 208ms 4.18% tbb::detail::r1::parallel_pipeline 11ms 0.22% 30.46% 202ms 4.06% vtkPoints::~vtkPoints 0 0% 30.46% 199ms 4.00% clone3 0 0% 30.46% 199ms 4.00% start_thread 1ms 0.02% 30.48% 192ms 3.86% tbb::detail::r1::reset 0 0% 30.48% 191ms 3.84% VertexMesh::~VertexMesh 1ms 0.02% 30.50% 191ms 3.84% vtkQuad::~vtkQuad 93ms 1.87% 32.37% 189ms 3.80% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.06% 32.43% 186ms 3.74% vtkFloatArray::vtkFloatArray 64ms 1.29% 33.72% 179ms 3.60% std::ostream::write 0 0% 33.72% 174ms 3.50% NodeLocationWriter::VisitAnyPopulation 63ms 1.27% 34.98% 170ms 3.42% std::_Rb_tree::_M_erase 0 0% 34.98% 166ms 3.34% std::_Rb_tree::_M_create_node (inline) 1ms 0.02% 35.00% 163ms 3.28% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.04% 35.04% 162ms 3.25% vtkLine::GetParametricCenter 1ms 0.02% 35.06% 159ms 3.19% vtkTriangle::~vtkTriangle 0 0% 35.06% 158ms 3.17% std::_Rb_tree::_M_get_node (inline) 6ms 0.12% 35.18% 157ms 3.15% NodesOnlyMesh::ConstructNodesWithoutMesh 18ms 0.36% 35.54% 157ms 3.15% std::_Rb_tree::_M_copy (inline) 8ms 0.16% 35.70% 157ms 3.15% vtkIdList::AllocateInternal 6ms 0.12% 35.82% 155ms 3.11% std::_Vector_base::_M_deallocate (inline) 0 0% 35.82% 153ms 3.07% VertexMesh::VertexMesh 6ms 0.12% 35.95% 152ms 3.05% vtkFloatArray::~vtkFloatArray 2ms 0.04% 35.99% 151ms 3.03% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.02% 36.01% 149ms 2.99% vtkDataArray::CreateDataArray 0 0% 36.01% 148ms 2.97% std::_Rb_tree::_Alloc_node::operator() (inline) 85ms 1.71% 37.71% 147ms 2.95% malloc_consolidate 0 0% 37.71% 145ms 2.91% std::vector::~vector (inline) 142ms 2.85% 40.57% 144ms 2.89% [libz.so.1.3] 2ms 0.04% 40.61% 143ms 2.87% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 40.61% 143ms 2.87% VertexMesh::GenerateEdgesFromElements (inline) 4ms 0.08% 40.69% 142ms 2.85% MutableElement::BuildEdges 5ms 0.1% 40.79% 139ms 2.79% vtkTypeFloat64Array::New 0 0% 40.79% 137ms 2.75% EdgeHelper::~EdgeHelper (inline) 16ms 0.32% 41.11% 131ms 2.63% std::_Rb_tree::_M_clone_node (inline) 8ms 0.16% 41.27% 131ms 2.63% std::vector::_M_default_append 6ms 0.12% 41.39% 125ms 2.51% EdgeHelper::GetEdgeFromNodes 4ms 0.08% 41.47% 125ms 2.51% vtkDoubleArray::vtkDoubleArray 123ms 2.47% 43.94% 123ms 2.47% __strcmp_avx2 62ms 1.25% 45.19% 123ms 2.47% std::basic_filebuf::xsputn 0 0% 45.19% 118ms 2.37% std::_Vector_base::_M_allocate (inline) 0 0% 45.19% 118ms 2.37% std::_Vector_base::~_Vector_base (inline) 24ms 0.48% 45.67% 118ms 2.37% vtkObject::vtkObject 5ms 0.1% 45.77% 115ms 2.31% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 45.77% 110ms 2.21% vtkXMLWriter::WritePointDataAppendedData 16ms 0.32% 46.09% 107ms 2.15% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 46.09% 102ms 2.05% std::_Rb_tree::_M_drop_node (inline) 45ms 0.9% 47.00% 100ms 2.01% std::__ostream_insert 0 0% 47.00% 100ms 2.01% std::set::~set (inline) 49ms 0.98% 47.98% 99ms 1.99% vtkTypeFloat64Array::PrintSelf 0 0% 47.98% 97ms 1.95% std::_Rb_tree::_M_put_node (inline) 2ms 0.04% 48.02% 97ms 1.95% std::operator<< (inline) 96ms 1.93% 49.95% 96ms 1.93% __GI_sched_yield 3ms 0.06% 50.01% 95ms 1.91% CellPropertyCollection::GetPropertiesType (inline) 64ms 1.29% 51.30% 94ms 1.89% std::basic_streambuf::xsputn 48ms 0.96% 52.26% 91ms 1.83% hack_digit 1ms 0.02% 52.28% 90ms 1.81% vtkIdList::Allocate 0 0% 52.28% 87ms 1.75% Cell::HasCellProperty (inline) 1ms 0.02% 52.30% 87ms 1.75% CellPropertyCollection::HasProperty 7ms 0.14% 52.44% 86ms 1.73% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 52.44% 85ms 1.71% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 5ms 0.1% 52.54% 83ms 1.67% AbstractCellProperty::IsType (inline) 2ms 0.04% 52.58% 83ms 1.67% std::map::operator[] (partial-inline) 2ms 0.04% 52.62% 82ms 1.65% std::vector::push_back (inline) 81ms 1.63% 54.25% 81ms 1.63% unlink_chunk 23ms 0.46% 54.71% 80ms 1.61% vtkObject::Modified 2ms 0.04% 54.75% 79ms 1.59% AbstractCellProperty::IsSubType (inline) 3ms 0.06% 54.81% 78ms 1.57% _int_free_maybe_consolidate 54ms 1.08% 55.90% 78ms 1.57% vtkObjectBase::UnRegisterInternal 19ms 0.38% 56.28% 77ms 1.55% __dynamic_cast 0 0% 56.28% 77ms 1.55% boost::numeric::ublas::vector_assign (inline) 0 0% 56.28% 74ms 1.49% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 7ms 0.14% 56.42% 71ms 1.43% AbstractCellProperty::IsSame 2ms 0.04% 56.46% 70ms 1.41% vtkDoubleArray::~vtkDoubleArray 2ms 0.04% 56.50% 68ms 1.37% AbstractCellPopulation::GetCellUsingLocationIndex 49ms 0.98% 57.48% 65ms 1.31% std::_Hashtable::clear 19ms 0.38% 57.87% 65ms 1.31% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.2% 58.07% 65ms 1.31% std::vector::_M_realloc_insert 7ms 0.14% 58.21% 64ms 1.29% std::type_info::operator== (inline) 0 0% 58.21% 64ms 1.29% tcache_get (inline) 64ms 1.29% 59.49% 64ms 1.29% tcache_get_n (inline) 0 0% 59.49% 63ms 1.27% std::map::~map (inline) 0 0% 59.49% 62ms 1.25% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.02% 59.51% 61ms 1.23% vtkIdList::New 18ms 0.36% 59.88% 60ms 1.21% boost::numeric::ublas::indexing_vector_assign 4ms 0.08% 59.96% 58ms 1.17% VertexMeshWriter::GetNextNode 0 0% 59.96% 57ms 1.15% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 59.96% 56ms 1.13% NodesOnlyMesh::SetUpBoxCollection 3ms 0.06% 60.02% 56ms 1.13% std::_Rb_tree::_M_insert_unique 0 0% 60.02% 56ms 1.13% std::set::insert (inline) 2ms 0.04% 60.06% 54ms 1.08% VertexMesh::Clear 53ms 1.06% 61.12% 53ms 1.06% vtkTimeStamp::Modified 9ms 0.18% 61.30% 51ms 1.02% vtkIdList::~vtkIdList 0 0% 61.30% 50ms 1.00% PottsMesh::GetMooreNeighbouringNodeIndices 5ms 0.1% 61.40% 50ms 1.00% vtkDataArray::vtkDataArray 11ms 0.22% 61.62% 49ms 0.98% std::num_put::_M_insert_int 0 0% 61.62% 48ms 0.96% Cell::GetCellProliferativeType 48ms 0.96% 62.59% 48ms 0.96% __memcpy_avx_unaligned_erms 0 0% 62.59% 48ms 0.96% vtkDataArray::ComputeRange 0 0% 62.59% 47ms 0.94% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 47ms 0.94% 63.53% 47ms 0.94% std::_Rb_tree_header::_M_reset (inline) 0 0% 63.53% 47ms 0.94% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 63.53% 47ms 0.94% vtk::detail::smp::vtkSMPToolsImplForTBB 46ms 0.92% 64.46% 46ms 0.92% [libvtkCommonCore-9.3.so.9.3] 4ms 0.08% 64.54% 46ms 0.92% tbb::detail::r1::cancel_group_execution 44ms 0.88% 65.42% 44ms 0.88% vtkObjectBase::~vtkObjectBase 0 0% 65.42% 43ms 0.86% std::_Rb_tree::lower_bound (inline) 0 0% 65.42% 43ms 0.86% std::map::lower_bound (inline) 5ms 0.1% 65.52% 43ms 0.86% vtkAOSDataArrayTemplate::InsertTuple 8ms 0.16% 65.68% 43ms 0.86% vtkAbstractArray::vtkAbstractArray 42ms 0.84% 66.53% 42ms 0.84% std::ostream::sentry::sentry 10ms 0.2% 66.73% 42ms 0.84% vtkDataArray::~vtkDataArray 8ms 0.16% 66.89% 42ms 0.84% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.02% 66.91% 41ms 0.82% DistributedBoxCollection::IsOwned 2ms 0.04% 66.95% 41ms 0.82% std::_Rb_tree::_M_insert_ (inline) 23ms 0.46% 67.41% 40ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 20ms 0.4% 67.81% 40ms 0.8% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 67.81% 39ms 0.78% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.14% 67.95% 39ms 0.78% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 67.95% 38ms 0.76% _dl_init 0 0% 67.95% 38ms 0.76% _dl_start_user 0 0% 67.95% 38ms 0.76% call_init (inline) 0 0% 67.95% 38ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 0 0% 67.95% 38ms 0.76% std::make_unique (inline) 37ms 0.74% 68.70% 38ms 0.76% vtkObjectBase::Delete 38ms 0.76% 69.46% 38ms 0.76% vtkObjectBase::vtkObjectBase 6ms 0.12% 69.58% 37ms 0.74% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 69.58% 36ms 0.72% PottsMesh::GetVonNeumannNeighbouringNodeIndices 35ms 0.7% 70.28% 36ms 0.72% vtkObject::~vtkObject 0 0% 70.28% 35ms 0.7% CxxTest::RealWorldDescription::setUp 2ms 0.04% 70.32% 35ms 0.7% Node::GetPoint 0 0% 70.32% 35ms 0.7% PMPI_Init_thread 0 0% 70.32% 35ms 0.7% PetscInitialize 0 0% 70.32% 35ms 0.7% PetscSetup::setUpWorld 0 0% 70.32% 35ms 0.7% PetscSetupUtils::CommonSetup 0 0% 70.32% 35ms 0.7% PetscSetupUtils::InitialisePetsc 2ms 0.04% 70.36% 35ms 0.7% boost::serialization::singleton::get_instance 0 0% 70.36% 35ms 0.7% ompi_mpi_init 0 0% 70.36% 34ms 0.68% std::_Destroy (inline) 0 0% 70.36% 34ms 0.68% std::_Destroy_aux::__destroy (inline) 1ms 0.02% 70.38% 33ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 1ms 0.02% 70.40% 33ms 0.66% VtkMeshWriter::MakeVtkMesh 0 0% 70.40% 33ms 0.66% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 70.40% 33ms 0.66% std::basic_filebuf::open 2ms 0.04% 70.44% 32ms 0.64% Cell::GetMutationState 32ms 0.64% 71.09% 32ms 0.64% __GI___writev 0 0% 71.09% 32ms 0.64% std::__basic_file::xsputn_2 0 0% 71.09% 32ms 0.64% std::less::operator() (inline) 32ms 0.64% 71.73% 32ms 0.64% std::operator< (inline) 0 0% 71.73% 31ms 0.62% DistributedBoxCollection::~DistributedBoxCollection 0 0% 71.73% 31ms 0.62% NodesOnlyMesh::Clear (inline) 0 0% 71.73% 31ms 0.62% NodesOnlyMesh::ClearBoxCollection (inline) 1ms 0.02% 71.75% 31ms 0.62% _IO_new_fopen 31ms 0.62% 72.37% 31ms 0.62% boost::numeric::ublas::same_impl_ex 0 0% 72.37% 31ms 0.62% std::__basic_file::open 0 0% 72.37% 31ms 0.62% vtkDataArrayPrivate::DoComputeScalarRange 2ms 0.04% 72.41% 30ms 0.6% 1ms 0.02% 72.43% 30ms 0.6% _IO_new_file_fopen 0 0% 72.43% 30ms 0.6% __fopen_internal (inline) 2ms 0.04% 72.47% 30ms 0.6% std::basic_filebuf::overflow 0 0% 72.47% 29ms 0.58% OutputFileHandler::OpenOutputFile 0 0% 72.47% 29ms 0.58% __GI__IO_file_open 29ms 0.58% 73.06% 29ms 0.58% __mpn_divrem 29ms 0.58% 73.64% 29ms 0.58% std::_Rb_tree_increment 29ms 0.58% 74.22% 29ms 0.58% std::codecvt::do_always_noconv 0 0% 74.22% 28ms 0.56% Cell::GetCellId 5ms 0.1% 74.32% 28ms 0.56% __find_specmb (inline) 28ms 0.56% 74.88% 28ms 0.56% __libc_open64 1ms 0.02% 74.90% 28ms 0.56% std::__basic_file::xsputn 0 0% 74.90% 28ms 0.56% std::basic_filebuf::_M_convert_to_external 0 0% 74.90% 27ms 0.54% Edge::Edge 0 0% 74.90% 27ms 0.54% Edge::SetNodes (inline) 1ms 0.02% 74.92% 27ms 0.54% VertexElement::~VertexElement 27ms 0.54% 75.47% 27ms 0.54% __GI___libc_write 13ms 0.26% 75.73% 27ms 0.54% _int_free_merge_chunk 3ms 0.06% 75.79% 27ms 0.54% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 75.79% 27ms 0.54% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 75.79% 27ms 0.54% vtkDoubleArray::New 0 0% 75.79% 25ms 0.5% CellIdWriter::GetCellDataForVtkOutput 25ms 0.5% 76.29% 25ms 0.5% std::_Rb_tree_insert_and_rebalance 5ms 0.1% 76.39% 25ms 0.5% vtkAOSDataArrayTemplate::AllocateTuples 25ms 0.5% 76.89% 25ms 0.5% vtkDataArray::Modified