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At least 1,423 records · Page 79

Collaborative Project: Building improved optimized parameter estimation algorithms to improve methane and nitrogen fluxes in a climate model

Soils in natural and managed ecosystems and wetlands are well known sources of methane, nitrous oxides, and reactive nitrogen gases, but the magnitudes of gas flux to the atmosphere are still poorly constrained. Thus, the reasons for the large increases in atmospheric concentrations of methane and nitrous oxide since the preindustrial time period are not well understood. The low atmospheric concentrations of methane and nitrous oxide, despite being more potent greenhouse gases than carbon dioxide, complicate empirical studies to provide explanations. In addition to climate concerns, the emissions of reactive nitrogen gases from soils are important to the changing nitrogen balance in the earth system, subject to human management, and may change substantially in the future. Thus improved modeling of the emission fluxes of these species from the land surface is important. Currently, there are emission modules for methane and some nitrogen species in the Community Earth System Model’s Community Land Model (CLM-ME/N); however, there are large uncertainties and problems in the simulations, resulting in coarse estimates. In this proposal, we seek to improve these emission modules by combining state-of-the-art process modules for emissions, available data, and new optimization methods. In earth science problems, we often have substantial data and knowledge of processes in disparate systems, and thus we need to combine data and a general process level understanding into a model for projections of future climate that are as accurate as possible. The best methodologies for optimization of parameters in earth system models are still being developed. In this proposal we will develop and apply surrogate algorithms that a) were especially developed for computationally expensive simulations like CLM-ME/N models; b) were (in the earlier surrogate optimization Stochastic RBF) demonstrated to perform very well on computationally expensive complex partial differential equations in earth science with limited numbers of simulations; and, c) will be (as part of the proposed research) significantly improved both by adding asynchronous parallelism, early truncation of unsuccessful simulations, and the improvement of both serial and parallel performance by the use of derivative and sensitivity information from global and local surrogate approximations S(x) . The algorithm development and testing will be focused on the CLM-ME/N model application, but the methods are general and are expected to also perform well on optimization for parameter estimation of other climate models and other classes of continuous multimodal optimization problems arising from complex simulation models. In addition, this proposal will compile available datasets of emissions of methane, nitrous oxides and reactive nitrogen species and develop protocols for site level comparisons with the CLM-ME/N. Once the model parameters are optimized against site level data, the model will be simulated at the global level and compared to atmospheric concentration measurements for the current climate, and future emissions will be estimated using climate change as simulated by the CESM. This proposal combines experts in earth system modeling, optimization, computer science, and process level understanding of soil gas emissions in an interdisciplinary team in order to improve the modeling of methane and nitrogen gas emissions. This proposal thus meets the requirements of the SciDAC RFP, by integrating state-of-the-art computer science and earth system to build an improved earth system model.

54 ENVIRONMENTAL SCIENCES↗

Summary of Documentation for DYNA3D-ParaDyn's Software Quality Assurance Regression Test Problems

The Software Quality Assurance (SQA) regression test suite for DYNA3D (Zywicz and Lin, 2015) and ParaDyn (DeGroot, et al., 2015) currently contains approximately 600 problems divided into 21 suites, and is a required component of ParaDyn’s SQA plan (Ferencz and Oliver, 2013). The regression suite allows developers to ensure that software modifications do not unintentionally alter the code response. The entire regression suite is run prior to permanently incorporating any software modification or addition. When code modifications alter test problem results, the specific cause must be determined and fully understood before the software changes and revised test answers can be incorporated. The regression suite is executed on LLNL platforms using a Python script and an associated data file. The user specifies the DYNA3D or ParaDyn executable, number of processors to use, test problems to run, and other options to the script. The data file details how each problem and its answer extraction scripts are executed. For each problem in the regression suite there exists an input deck, an eight-processor partition file, an answer file, and various extraction scripts. These scripts assemble a temporary answer file in a specific format from the simulation results. The temporary and stored answer files are compared to a specific level of numerical precision, and when differences are detected the test problem is flagged as failed. Presently, numerical results are stored and compared to 16 digits. At this accuracy level different processor types, compilers, number of partitions, etc. impact the results to various degrees. Thus, for consistency purposes the regression suite is run with ParaDyn using 8 processors on machines with a specific processor type (currently the Intel Xeon E5530 processor). For non-parallel regression problems, i.e., the two XFEM problems, DYNA3D is used instead. When environments or platforms change, executables using the current source code and the new resource are created and the regression suite is run. If differences in answers arise, the new answers are retained provided that the differences are inconsequential. This bootstrap approach allows the test suite answers to evolve in a controlled manner with a high level of confidence. Developers also run the entire regression suite with (serial) DYNA3D. While these results normally differ from the stored (parallel) answers, abnormal termination or wildly different values are strong indicators of potential issues.

42 ENGINEERING↗

FY16 Status of Immersion Phased Array Ultrasonic Probe Development and Performance Demonstration Results for Under Sodium Viewing

This section of the Joint summary technical letter report (TLR) describes work conducted at the Pacific Northwest National Laboratory (PNNL) during FY 2016 (FY16) on the under-sodium viewing (USV) PNNL project 58745, work package AT-16PN230102. This section of the TLR satisfies PNNL’s M3AT-16PN2301025 milestone and is focused on summarizing the design, development, and evaluation of two different phased-array ultrasonic testing (PA-UT) probe designs—a two-dimensional (2D) matrix phased-array probe, and two one-dimensional (1D) linear array probes, referred to as serial number 4 (SN4) engineering test units (ETUs). The 2D probe is a pulse-echo (PE), 32×2, 64-element matrix phased-array ETU. The 1D probes are 32×1 element linear array ETUs. This TLR also provides the results from a performance demonstration (PD) of in-sodium target detection trials at 260°C using both probe designs. This effort continues the iterative evolution supporting the longer term goal of producing and demonstrating a pre-manufacturing prototype ultrasonic probe that possesses the fundamental performance characteristics necessary to enable the development of a high-temperature sodium-cooled fast reactor (SFR) inspection system for in-sodium detection and imaging.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

PaRSEC: A Software Framework for Performance and Productivity on Hybrid, Manycore Platforms

As the era of computer architectures dominated by serial processors ends, the convergence of several unprecedented challenges suggests that closing the longstanding "application–architecture performance gap" will become more challenging than ever. To address this problem, the Parallel Runtime Scheduling and Execution Control (PaRSEC) project created a modular software framework that achieved two major objectives: first, it built a task-based runtime capable of delivering portable performance to a wide range of science and engineering applications at all levels of the platform pyramid, including the upcoming 100 Pflop/s systems and then exascale; and second, it supported and facilitated the work of developers in migrating their legacy codes and writing entirely new ones for the emerging hybrid and massively parallel manycore processor system designs. PaRSEC will support multiple domain-specific languages capable of increasing the developers' productivity while also providing the runtime with the constructs and flexibility necessary to exploit the maximal parallelism from parallel applications. Extensive preliminary research in dense linear algebra showed convincingly that a parameterized task graph representation that symbolically describes the algorithm content can achieve the project's twofold objective within that domain. The research also strongly suggested that this powerful method could be generalized to a far-wider variety of applications.

97 MATHEMATICS AND COMPUTING↗

Block-Parallel Data Analysis with DIY2

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial, parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.

97 MATHEMATICS AND COMPUTING↗

Portable Radiation Package (PRP) Instrument Handbook

The Portable Radiation Package (PRP) was developed to provide basic radiation information in locations such as ships at sea where proper exposure is remote and difficult, the platform is in motion, and azimuth alignment is not fixed. Development of the PRP began at Brookhaven National Laboratory (BNL) in the mid-1990s and versions of it were deployed on ships in the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Nauru-99 project. The PRP was deployed on ships in support of the National Aeronautics and Space Administration (NASA) Sensor Intercomparison for Marine Biological and Interdisciplinary Ocean Studies (SIMBIOS) program. Over the years the measurements have remained the same while the post-processing data analysis, especially for the FRSR, has evolved. This document describes the next-generation Portable Radiation Package (PRP2) that was developed for the DOE ARM Facility, under contract no. 9F-31462 from Argonne National Laboratory (ANL). The PRP2 has the same scientific principles that were well validated in prior studies, but has upgraded electronic hardware. The PRP2 approach is completely modular, both in hardware and software. Each sensor input is treated as a separate serial stream into the data collection computer. In this way the operator has complete access to each component of the system for purposes of error checking, calibration, and maintenance. The resulting system is more reliable, easier to install in complex situations, and more amenable to upgrade.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

3D Microstructural Characterization of Uranium Oxide as a Surrogate Nuclear Fuel: Effect of Oxygen Stoichiometry on Grain Boundary Distributions

The initial microstructure of an oxide fuel can play a key role in its performance. At low burn-ups, the diffusion of fission products can depend strongly on grain size and grain boundary (GB) characteristics, which in turn depend on processing conditions and oxygen stoichiometry. Serial sectioning techniques using Focused Ion Beam were developed to obtain Electron Backscatter Diffraction (EBSD) data for depleted UO2 pellets that were processed to obtain 3 different oxygen stoichiometries. The EBSD data were used to create 3D microstructure reconstructions and to gather statistical information on the grain and GB crystallography, with emphasis on identifying the character (twist, tilt, mixed) for GBs that meet the Coincident Site Lattice (CSL) criterion as well as GBs with the most common misorientation angles. Data on dihedral angles at triple points were also collected. The results were compared across different samples to understand effects of oxygen content on microstructure evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Note on Compiling Fortran

Fortran modules tend to serialize compilation of large Fortran projects, by introducing dependencies among the source files. If file A depends on file B, (A uses a module defined by B), you must finish compiling B before you can begin compiling A. Some Fortran compilers (Intel ifort, GNU gfortran and IBM xlf, at least) offer an option to ‘‘verify syntax’’, with the side effect of also producing any associated Fortran module files. As it happens, this option usually runs much faster than the object code generation and optimization phases. For some projects on some machines, it can be advantageous to compile in two passes: The first pass generates the module files, quickly; the second pass produces the object files, in parallel. We achieve a 3.8× speedup in the case study below.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual Revision 3.8

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

97 MATHEMATICS AND COMPUTING↗

Revised SNAP III Training Manual

The Shielded Neutron Assay Probe (SNAP) technique was developed to determine the leakage neutron source strength of a radioactive object. The original system consisted of an Eberline TM Mini-scaler and discrete neutron detector. The system was operated by obtaining the count rate with the Eberline TM instrument, determining the absolute efficiency from a graph, and calculating the neutron source strength by hand. In 2003 the SNAP III, shown in Figure 1, was designed and built. It required the operator to position the SNAP, and then measure the source-to-detector and detectorto- reflector distances. Next the operator entered the distance measurements and started the data acquisition. The SNAP acquired the required count rate and then calculated and displayed the leakage neutron source strength (NSS). The original design of the SNAP III is described in SNAP III Training Manual (ER-TRN-PLN-0258, Rev. 0, January 2004, prepared by William Baird) This report describes some changes that have been made to the SNAP III. One important change is the addition of a LEMO connector to provide neutron detection output pulses for input to the MC-15. This feature is useful in active interrogation with a neutron generator because the MC-15 has the capability to only record data when it is not gated off by a pulse from the neutron generator. This avoids recording of a lot of data during the generator pulses that are not useful. Another change was the replacement of the infrared RS-232 serial communication output by a similar output via a 4-pin LEMO connector. The current document includes a more complete explanation of how to estimate the amount of moderation around a neutron-emitting source.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Test Problems for Programmed Burn [Slides]

This document presents updated FLAG results for the Kenamond programmed burn test problems. Problem definition, exact solutions for constant detonation velocity, and FLAG results using a Huygens solution are provided in Kenamond’s “Lund High Explosive Programmed Burn Model in the FLAG Code” LA-UR-09-08297. FLAG results using Line-of-Sight (LOS) preconditioning of the Huygens solution are presented in Kenamond’s “Line-of-Sight (LOS) High Explosive Programmed Burn Model in the FLAG Code” LA-UR-09-08296. FLAG has an old, serial, uniform-grid “mapped” 2D DSD solver and a new, inline, parallel, conformal mesh 2D/3D DSD solver. These solvers will be exercised with flat Dn-Kappa relations to facilitate comparison with analytic solutions. The remaining slides document FLAG results with 1) Huygens, 2) Huygens with LOS, 3) old DSD, and 4) new DSD. By design, these geometries are coarsely meshed. Plotting error with respect to the analytic solutions reveals sensitivities to element type, element aspect ratio, boundary conditions, detonator timing, and discontinuous detonation velocity. In all plots of this document, color is absolute error relative to the exact solution. In all plots of this document, contours are burntime isochrones of the numerical solution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High Gradient High Shunt Impedance Accelerating Structure

develop an inexpensive accelerating structure with a high gradient and high shunt impedance. Euclid Techlabs proposes to optimize this technology (based on a successful accelerating structure with distributed coupling developed at SLAC) for industrial applications and serial production. Future colliders require high gradient and high efficiency accelerating structures (high shunt impedance). The SLAC accelerator laboratory recently developed a series of accelerating structures with distributed coupling. Such a structure includes one or more parallel waveguides which are loaded by accelerating cavities. This approach allows configurations where no RF power is flowing axially through the accelerating cavity while maintaining a traveling RF wave through the cross-section of the accelerating structure. In this case the accelerating cavities are isolated at the beam pipe. Conventional traveling wave structures typically couple the RF power through the beam pipe. This feature constrains the cavity shunt impedance to relatively small values. For this reason, the distributed coupling design improves efficiency while reducing cost and improving the operational flexibility of particle accelerators. High gradient operation poses the risk of having a high breakdown rates. In traditional standing and traveling wave structures, RF power flows through the accelerating cells. For distributed coupling structures, this risk is reduced because the absence of power flow through the accelerating cavity allows configurations where no power flows through the beam pipe. Finally, the distributed coupling accelerating structure design allows fabricating structures in two halves. This significantly reduces the complexity of machining, brazing and tuning.

43 PARTICLE ACCELERATORS↗

DARMA-MPI Interoperability WBS 2.3.1.04 Milestone 15 (ECP Milestone Report)

DARMA (Distributed Asynchronous Resilient Models for Applications) is a runtime library developed as part of the the Sandia ATDM (Advanced Technology Development and Mitigation) program. DARMA supports applications within 2.2.5.03 ADNN03-ASC ATDM SNL Application, which includes a number of applications featuring dynamic physics which requires load balancing and asynchronous communication for high performance. We have implemented a modern C++ programming model that can enable dynamic, asynchronous communication on top of existing data structures from a serial or MPI code. DARMA development has occurred in parallel with a verification milestone for ATDM in FY18. For FY19, DARMA will impact ATDM by enabling the performance benefits of a dynamic runtime through only incremental changes to existing verified MPI codes. The results presented here demonstrate the DARMA development process for an MPI mini-app, showing a 3-4x improvement in performance for a challenging problem relative to the parent MPI code and coming within 25 percent of the theoretically optimal performance achievable from a perfect, fine-grained load balancer for most cases.

97 MATHEMATICS AND COMPUTING↗

Next Generation Qualification: Geotech Instruments SMART24B Digitizer Evaluation

Sandia National Laboratories has tested and evaluated a digitizer, the SMART24B, manufactured by Geotech Instruments, LLC. These digitizers are used to record sensor output for seismic and infrasound monitoring applications. The purpose of the digitizer evaluation was to measure the performance characteristics in such areas as power consumption, input impedance, sensitivity, full scale, self-noise, dynamic range, system noise, response, passband, and timing. The SMART24B is Geotech's datalogger intended for borehole deployment in their digitizer product line. The SMART24B is available with either 3 or 6 channels at 24 bit resolution. The digitizer is to be deployed in boreholes, therefore are a minimum number of connections required on the digitizer case as datalogger utilizes a distribution panel, mounted up-hole, serving to breakout power, GPS, serial communications and ethernet connections.

47 OTHER INSTRUMENTATION↗

Deploy threading in Nalu solver stack

The goal of the ExaWind project is to enable predictive simulations of wind farms composed of many MW-scale turbines situated in complex terrain. Predictive simulations will require computational fluid dynamics (CFD) simulations for which the mesh resolves the geometry of the turbines, and captures the rotation and large deflections of blades. Whereas such simulations for a single turbine are arguably petascale class, multi-turbine wind farm simulations will require exascale-class resources. The primary code in the ExaWind project is Nalu, which is an unstructured-grid solver for the acousticallyincompressible Navier-Stokes equations, and mass continuity is maintained through pressure projection. The model consists of the mass-continuity Poisson-type equation for pressure and a momentum equation for the velocity. For such modeling approaches, simulation times are dominated by linear-system setup and solution for the continuity and momentum systems. For the ExaWind challenge problem, the moving meshes greatly affect overall solver costs as re-initialization of matrices and re-computation of preconditioners is required at every time step In this Milestone, we examine the effect of threading on the solver stack performance against flat-MPI results obtained from previous milestones using Haswell performance data full-turbine simulations. Whereas the momentum equations are solved only with the Trilinos solvers, we investigate two algebraic-multigrid preconditioners for the continuity equations: Trilinos/Muelu and HYPRE/BoomerAMG. These two packages embody smoothed-aggregation and classical Ruge-Stiiben AMG methods, respectively. In our FY18 Q2 report, we described our efforts to improve setup and solve of the continuity equations under flat-MPI parallelism. While significant improvement was demonstrated in the solve phase, setup times remained larger than expected. Starting with the optimized settings described in the Q2 report, we explore here simulation performance where OpenMP threading is employed in the solver stack. For Trilinos, threading is acheived through the Kokkos abstraction where, whereas HYPRE/BoomerAMG employs straight OpenMP. We examined results for our mid-resolution baseline turbine simulation configuration (229M DOF). Simulations on 2048 Haswell cores explored the effect of decreasing the number of MPI ranks while increasing the number of threads. Both HYPRE and Trilinos exhibited similar overal solution times, and both showed dramatic increases in simulation time in the shift from MPI ranks to OpenMP threads. This increase is attributed to the large amount of work per MPI rank starting at the single-thread configuration. Decreasing MPI ranks, while increasing threads, may be increasing simulation time due to thread synchronization and start-up overhead contributing to the latency and serial time in the model. These result showed that an MPI+OpenMP parallel decomposition will be more effective as the amount per MPI rank computation per MPI rank decreases and the communication latency increases. This idea was demonstrated in a strong scaling study of our low-resolution baseline model (29M DOF) with the Trilinos-HYPRE configuration. While MPI-only results showed scaling improvement out to about 1536 cores, engaging threading carried scaling improvements out to 4128 cores — roughly 7000 DOF per core. This is an important result as improved strong scaling is needed for simulations to be executed over sufficiently long simulated durations (i.e., for many timesteps). In addition to threading work described above, the team examined solver-performance improvements by exploring communication-overhead in the HYPRE-GMRES implementation through a communicationoptimal- GMRE algorithm (CO-GMRES), and offloading compute-intensive solver actions to GPUs. To those ends, a HYPRE mini-app was allow us to easily test different solver approaches and HYPRE parameter settings without running the entire Nalu code. With GPU acceleration on the Summitdev supercomputer, a 20x speedup was achieved for the overall preconditioner and solver execution time for the mini-app. A study on Haswell processors showed that CO-GMRES provides benefits as one increases MPI ranks.

17 WIND ENERGY↗

PETSc Users Manual: Revision 3.10

This manual describes the use of PETSc for the numerical solution of partial differential equa-tions and related problems on high-performance computers. The Portable, Extensible Toolkit forScientific Computation (PETSc) is a suite of data structures and routines that provide the buildingblocks for the implementation of large-scale application codes on parallel (and serial) computers.PETSc uses the MPI standard for all message-passing communication.

97 MATHEMATICS AND COMPUTING↗

SCEPTRE 2.0 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general purpose C++ code for solving the Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL's are provided. The TPL's needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autoconf build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

ECP Milestone Memo WBS 2.3.4.13 ECP/VTK-m FY18Q4 [MS-18/09-10] Dynamic Types / Rendering Topologies STDA05-16

The STDA05-16 milestone comprises the following 3 distinct deliverables. OpenMP VTK-m currently supports three types of devices: serial CPU, TBB, and CUDA. To run algorithms on multicore CPU-type devices (such as Xeon and Xeon Phi), TBB is required. However, there are known issues with integrating a software product using TBB with another one using OpenMP. Therefore, we will add an OpenMP device to the VTK-m software. When engaged, this device will run parallel algorithms using OpenMP directives. This will mesh more nicely with other code also using OpenMP. Rendering Topological Entities VTK-m currently supports surface rendering by tessellation of data structures,and rendering the resulting triangles. We will extend current functionality to include face, edge, and point rendering. Better Dynamic Types Impl For the best efficiency across all platforms, VTK-m algorithms use static typing with C++ templates. However, many libraries like VTK, ParaView, and Visit use dynamic types with virtual functions because data types often cannot be determined at compile time. We have an interface in VTK-m to merge these two typing mechanisms by generating all possible combinations of static types when faced with a dynamic type. Although this mechanism works, it generates very large executables and takes a very long time to compile. As we move forward, it is clear that these problems will get worse and become infeasible at exascale. We will rectify the problem by introducing some level of virtual methods, which require only a single code path, within VTK-m algorithms. This first milestone produces a design document to propose an approach to the new system.

97 MATHEMATICS AND COMPUTING↗