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At least 1,387 records · Page 77

Reductive Analysis with Compiler-Guided Large Language Models for Input-Centric Code Optimizations

Input-centric program optimization aims to optimize code by considering the relations between program inputs and program behaviors. Despite its promise, a long-standing barrier for its adoption is the difficulty of automatically identifying critical features of complex inputs. This paper introduces a novel technique, reductive analysis through compiler-guided Large Language Models (LLMs), to solve the problem through a synergy between compilers and LLMs. It uses a reductive approach to overcome the scalability and other limitations of LLMs in program code analysis. The solution, for the first time, automates the identification of critical input features without heavy instrumentation or profiling, cutting the time needed for input identification by 44× (or 450× for local LLMs), reduced from 9.6 hours to 13 minutes (with remote LLMs) or 77 seconds (with local LLMs) on average, making input characterization possible to be integrated into the workflow of program compilations. Optimizations on those identified input features show similar or even better results than those identified by previous profiling-based methods, leading to optimizations that yield 92.6% accuracy in selecting the appropriate adaptive OpenMP parallelization decisions, and 20-30% performance improvement of serverless computing while reducing resource usage by 50-60%.

Input-Centric Optimization↗

Using modularity to segment binary code

We consider the problem of recovering program structure from compiled binary code. We first extract the call graph and layout of functions in memory from the compiled code and represent this information in a graphical format. We then employ Louvain's modularity algorithm to identify clusters of functions that are considered to be related. We find that the quality and properties of clusters extracted by our technique are greatly impacted by the relative importance we assign to the call graph and the ordering of functions in memory.

97 MATHEMATICS AND COMPUTING↗

Joint Analysis of Program Data Representations using Machine Learning for Improved Software Assurance and Development Capabilities

We explore the use of multiple deep learning models for detecting flaws in software programs. Current, standard approaches for flaw detection rely on a single representation of a software program (e.g., source code or a program binary). We illustrate that, by using techniques from multimodal deep learning, we can simultaneously leverage multiple representations of software programs to improve flaw detection over single representation analyses. Specifically, we adapt three deep learning models from the multimodal learning literature for use in flaw detection and demonstrate how these models outperform traditional deep learning models. We present results on detecting software flaws using the Juliet Test Suite and Linux Kernel.

97 MATHEMATICS AND COMPUTING↗

Large Program Design [Slides]

A slideshow presentation describing how different writing small software coding projects is from writing large software coding projects. It can be OK to just throw together code that is small, single-purpose, and short-lived, but there's more need for good design if the code has to live longer, give highly reliable results, be easy to use, get bigger/cover more physics, cover more application domains. Larger projects also need good code if they are to have more widely-distributed users, have more developers work on it, run larger problems, or run on new architectures.

97 MATHEMATICS AND COMPUTING↗

Evaluating the networking characteristics of the Cray XC-40 Intel Knights Landing-based Cori supercomputer at NERSC

There are many potential issues associated with deploying the Intel Xeon Phi™ (code named Knights Landing [KNL]) manycore processor in a large-scale supercomputer. One in particular is the ability to fully utilize the high-speed communications network, given that the serial performance of a Xeon Phi TM core is a fraction of a Xeon®core. In this paper, we take a look at the trade-offs associated with allocating enough cores to fully utilize the Aries high-speed network versus cores dedicated to computation, e.g., the trade-off between MPI and OpenMP. In addition, we evaluate new features of Cray MPI in support of KNL, such as internode optimizations. We also evaluate one-sided programming models such as Unified Parallel C. We quantify the impact of the above trade-offs and features using a suite of National Energy Research Scientific Computing Center applications.

97 MATHEMATICS AND COMPUTING↗

The Development of Kinetic and Radiation Hydrodynamics Modeling of Thermonuclear Burn Propagation in Isochoric p - 11 B Through the Support of the INFUSE Program

The report summarizes DOE INFUSE-supported work between HB11 Energy and the University of Rochester’s TriForce Institute to improve computational modeling of advanced fusion fuels, especially proton–boron-11 (p- 11 B). The project extended the TriForce particle-in-cell/Monte Carlo collision code to include physics needed for dense, high-temperature p- 11 B burn studies, including p- 11 B fusion reactions, three-alpha-particle reaction products, relativistic Coulomb collisions, large-angle nuclear scattering, bremsstrahlung radiation, inverse bremsstrahlung absorption, and photon transport. The upgraded models were verified against focused physics tests and against known deuterium–tritium burn behavior. The study then used one-dimensional spherical simulations to estimate the conditions required for thermonuclear burn propagation in isochoric p- 11 B fuel. The calculations found that burn propagation is possible in the model, but only under very extreme hot-spot conditions, such as about 7000 g/cm 3 at 500 keV or 9000 g/cm 3 at 300 keV for a 20-micron hot spot. These conditions are much more demanding than current demonstrated inertial confinement fusion hot spots. The report concludes that the INFUSE collaboration successfully advanced kinetic and radiation modeling capabilities for p- 11 B fusion and provided useful estimates of ignition requirements. However, the simulated fuel gains remain below what would be needed for practical inertial fusion energy, and further work is needed to reconcile differences among kinetic, radiation-hydrodynamic, and analytic models and to identify more achievable target designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FEHM V3.0 - V3.X

The numerical background of the FEHM computer code can be traced to the early 1970s when it was used to simulate geothermal and hot dry rock reservoirs. The primary use over a number of years was to assist in the understanding of flow fields and mass transport in the saturated and unsaturated zones below the potential Yucca Mountain repository. Today FEHM is used to simulate groundwater and contaminant flow and transport in deep and shallow, fractured and un-fractured porous media throughout the US DOE complex. FEHM has proved to be a valuable asset on a variety of projects of national interest including Environmental Remediation of the Nevada Test Site, the LANL Groundwater Protection Program, geologic CO2 sequestration, Enhanced Geothermal Energy (EGS) programs, Oil and Gas production, Nuclear Waste Isolation, and Arctic Permafrost. Subsurface physics has ranged from single fluid/single phase fluid flow when simulating basin scale groundwater aquifers to complex multifluid/ multi-phase fluid flow that includes phase change with boiling and condensing in applications such as unsaturated zone surrounding nuclear waste storage facility or leakage of CO2/brine through faults or wellbores. The numerical method used in FEHM is the control volume method (CV) for fluid flow and heat transfer equations which allows FEHM to exactly enforce energy/mass conservation; while an option is available to use the finite element (FE) method for displacement equations to obtain more accurate stress calculations. In addition to these standard methods, an option to use FE for flow is available, as well as a simple Finite Difference scheme.

Pawar, Rajesh↗

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis version 6.0 theory manual

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quanti cation, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis :

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

97 MATHEMATICS AND COMPUTING↗

FY17 Status Report on NEAMS Neutronics Activities

Under the U.S. DOE NEAMS program, the high-fidelity neutronics code system has been developed to support the multiphysics modeling and simulation capability named SHARP. The neutronics code system includes the high-fidelity neutronics code PROTEUS, the cross section library and preprocessing tools, the multigroup cross section generation code MC2-3, the in-house meshing generation tool, the perturbation and sensitivity analysis code PERSENT, and post-processing tools. The main objectives of the NEAMS neutronics activities in FY17 are to continue development of an advanced nodal solver in PROTEUS for use in nuclear reactor design and analysis projects, implement a simplified sub-channel based thermal-hydraulic (T/H) capability into PROTEUS to efficiently compute the thermal feedback, improve the performance of PROTEUS-MOCEX using numerical acceleration and code optimization, improve the cross section generation tools including MC2-3, and continue to perform verification and validation tests for PROTEUS.

47 OTHER INSTRUMENTATION↗

Upcoming MCNP6.3 ® Release: New Features and Improvements [Slides]

The latest version of the MCNP6.3 code will be done and released this year. Many new features, substantial improvements, and bugfixes have made their way into the code. Improved documentation, testing, and peripheral tools will also be delivered.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Optimizing fusion PIC code performance at scale on Cori Phase 2

In this paper we present the results of optimizing the performance of the gyrokinetic full-f fusion PIC code XGC1 on the Cori Phase Two Knights Landing system. The code has undergone substantial development to enable the use of vector instructions in its most expensive kernels within the NERSC Exascale Science Applications Program. We study the single-node performance of the code on an absolute scale using the roofline methodology to guide optimization efforts. We have obtained 2x speedups in single node performance due to enabling vectorization and performing memory layout optimizations. On multiple nodes, the code is shown to scale well up to 4000 nodes, near half the size of the machine. We discuss some communication bottlenecks that were identified and resolved during the work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis of xRAGE and flag high explosive burn models with PBX 9404 cylinder tests

High explosives are energetic materials that release their chemical energy in a short interval of time. They are able to generate extreme heat and pressure by a shock driven chemical decomposition reaction, which makes them valuable tools that must be understood. This study investigated the accuracy and performance of two Los Alamos National Laboratory hydrodynamic codes, which are used to determine the behavior of explosives within a variety of systems: xRAGE which utilizes an Eulerian mesh, and FLAG with utilizes a Lagrangian mesh. Various programmed and reactive burn models within both codes were tested using a copper cylinder expansion test. The test was based on a recent experimental setup which contained the plastic bonded explosive PBX 9404. Detonation velocity versus time curves for this explosive were obtained using Photon Doppler Velocimetry (PDV). The modeled results from each of the burn models tested were then compared to one another and to the experimental results. This study validate

36 MATERIALS SCIENCE↗

SAS4A/SASSYS-1 Code Improvements for FY2016

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced reactors. This report summarizes ongoing tasks to modernize the SAS4A/SASSYS-1 code system to improve internal data management, update several other code modules, and add new features. Code modernization activities focused on eliminating legacy data management in the balance-of-plant module, which was the only module that still used non-portable data allocation. Code extensions include the development of a new axial expansion model that can accurately account for non-uniform or heterogeneous fuel compositions. The most significant accomplishment is the addition of uncertainty quantification capabilities for transient simulations using the Dakota toolkit from Sandia National Laboratory. The motivation for performing these updates stems from the relevance of SAS4A/SASSYS-1 to a number of U.S. Department of Energy programs as well as domestic and international collaborations. External collaborations have also produced improvements in the SAS4A/SASSYS-1 code, and these are summarized in this report. SAS4A/SASSYS-1 has a growing user base that continues to strengthen the promotion of advanced reactor concepts such as sodium cooled fast reactors. Additional users will help solidify DOE’s leadership role in fast reactor safety both domestically and in international collaborations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

SU-E-T-455: Impact of Different Independent Dose Verification Software Programs for Secondary Check

Purpose: There have been many reports for different dose calculation algorithms for treatment planning system (TPS). Independent dose verification program (IndpPro) is essential to verify clinical plans from the TPS. However, the accuracy of different independent dose verification programs was not evident. We conducted a multi-institutional study to reveal the impact of different IndpPros using different TPSs. Methods: Three institutes participated in this study. They used two different IndpPros (RADCALC and Simple MU Analysis (SMU), which implemented the Clarkson algorithm. RADCALC needed the input of radiological path length (RPL) computed by the TPSs (Eclipse or Pinnacle3). SMU used CT images to compute the RPL independently from TPS). An ion-chamber measurement in water-equivalent phantom was performed to evaluate the accuracy of two IndpPros and the TPS in each institute. Next, the accuracy of dose calculation using the two IndpPros compared to TPS was assessed in clinical plan. Results: The accuracy of IndpPros and the TPSs in the homogenous phantom was +/−1% variation to the measurement. 1543 treatment fields were collected from the patients treated in the institutes. The RADCALC showed better accuracy (0.9 ± 2.2 %) than the SMU (1.7 ± 2.1 %). However, the accuracy was dependent on the TPS (Eclipse: 0.5%, Pinnacle3: 1.0%). The accuracy of RADCALC with Eclipse was similar to that of SMU in one of the institute. Conclusion: Depending on independent dose verification program, the accuracy shows systematic dose accuracy variation even though the measurement comparison showed a similar variation. The variation was affected by radiological path length calculation. IndpPro with Pinnacle3 has different variation because Pinnacle3 computed the RPL using physical density. Eclipse and SMU uses electron density, though.

60 APPLIED LIFE SCIENCES↗

Radiation shielding properties of barite coated fabric by computer programme

With the development of technology radiation started to be used in variety of different fields. As the radiation is hazardous for human health, it is important to keep radiation dose as low as possible. This is done mainly using shielding materials. Barite is one of the important materials in this purpose. As the barite is not used directly it can be used in some other materials such as fabric. For this purposes barite has been coated on fabric in order to improve radiation shielding properties of fabric. Determination of radiation shielding properties of coated fabric has been done by using computer program written C# language. With this program the images obtained from digital Rontgen films is used to determine radiation shielding properties in terms of image processing numerical values. Those values define radiation shielding and in this way the coated barite effect on radiation shielding properties of fabric has been obtained.

07 ISOTOPE AND RADIATION SOURCES↗

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗