A language to simplify computation of differential mobility analyzer response functions
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Engineering↗
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QCOR; A Language Extension Specification for the Heterogeneous Quantum-Classical Model of Computation
Quantum computing (QC) is an emerging computational paradigm that leverages the laws of quantum mechanics to perform elementary logic operations. Existing programming models for QC were designed with fault-tolerant hardware in mind, envisioning stand-alone applications. However, the susceptibility of near-term quantum computers to noise limits their stand-alone utility. To better leverage limited computational strengths of noisy quantum devices, hybrid algorithms have been suggested whereby quantum computers are used in tandem with their classical counterparts in a heterogeneous fashion. This modus operandi calls out for a programming model and a high-level programming language that natively and seamlessly supports heterogeneous quantum-classical hardware architectures in a single-source-code paradigm. Motivated by the lack of such a model, we introduce a language extension specification, called QCOR, which enables single-source quantum-classical programming. Programs written using the QCOR library–based language extensions can be compiled to produce functional hybrid binary executables. After defining QCOR’s programming model, memory model, and execution model, we discuss how QCOR enables variational, iterative, and feed-forward QC. Additionally, QCOR approaches quantum-classical computation in a hardware-agnostic heterogeneous fashion and strives to build on best practices of high-performance computing. The high level of abstraction in the language extension is intended to accelerate the adoption of QC by researchers familiar with classical high-performance computing.
97 MATHEMATICS AND COMPUTING↗
Library for Evolutionary Algorithms in Python (LEAP)
There are generally three types of scientific software users: users that solve problems using existing science software tools, researchers that explore new approaches by extending existing code, and educators that teach students scientific concepts. Python is a general-purpose programming language that is accessible to beginners, such as students, but also as a language that has a rich scientific programming ecosystem that facilitates writing research software. Additionally, as high-performance computing (HPC) resources become more readily available, software support for parallel processing becomes more relevant to scientific software.There currently are no Python-based evolutionary computation frameworks that support all three types of scientific software users. Moreover, some support synchronous concurrent fitness evaluation that do not efficiently use HPC resources. We pose here a new Python-based EC framework that uses an established generalized unified approach to EA concepts to provide an easy to use toolkit for users wishing to use an EA to solve a problem, for researchers to implement novel approaches, and for providing a low-bar to entry to EA concepts for students. Additionally, this toolkit provides a scalable asynchronous fitness evaluation implementation friendly to HPC that has been vetted on hardware ranging from laptops to the world’s fastest supercomputer, Summit.
Coletti, Mark↗
Tough Errors are no Match (TEAM): Optimizing the Quantum Compiler for Noise Resilience
This project builds toward a comprehensive error-mitigating toolkit that makes quantum programming more robust and adaptive to the noisy, resource-limited nature of today’s quantum hardware. To that end, it integrates established error-mitigation methods — such as zero-noise extrapolation and dynamical decoupling — directly into compiler infrastructures. These techniques will be packaged as modules that can automatically adjust and combine based on performance analysis, enabling compilers to explore large design spaces and produce optimized, low-noise quantum programs with minimal manual intervention. In parallel, this project also explores new approaches to analog quantum programming or quantum simulation, and has developed the programming language SimuQ which treats quantum Hamiltonian evolution as the central object.
97 MATHEMATICS AND COMPUTING↗
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
This paper assesses and reports the experience of ten teams working to port, validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC Developer Kit systems, each one equipped with a server-class Arm CPU from Ampere Computing and two data center GPUs from NVIDIA Corp. The systems are connected together using InfiniBand interconnect. The selected applications and mini-apps are written using several programming languages and use multiple accelerator-based programming models for GPUs such as CUDA, OpenACC, and OpenMP offloading. Working on application porting requires a robust and easy-to-access programming environment, including a variety of compilers and optimized scientific libraries. The goal of this work is to evaluate platform readiness and assess the effort required from developers to deploy well-established scientific workloads on current and future generation Arm-based GPU-accelerated HPC systems. The reported case studies demonstrate that the current level of maturity and diversity of software and tools is already adequate for large-scale production deployments.
Elwasif, Wael↗
eCC++ : A Compiler Construction Framework for Embedded Domain-Specific Languages
eCC++ is a new compiler construction framework for embedding domain-specific programming languages within C++. That is, the host language is C++, the guest language is the DSL to be embedded in C++, and eCC++ is the tool that enables the embedding. The eCC++ framework is composed of three main components: a front-end, an API for program verification based on a functional and declarative intermediate representation (IR), and a Multi-Level Intermediate Representation (MLIR) code generator. The eCC++ front-end consists of a library of C++ classes and operators that can be used to define the guest language. Guest sources are compiled with any standard C++ compiler, and when run, the resulting executable generates an eCC++ IR representation of the program, which can be verified within the eCC++ framework. Finally, eCC++ allows for high-level and domain-specific optimizations before generating MLIR. In summary, eCC++ aims to act as a generic front-end that enables embedding guest languages into C++, and provides necessary compiler technology for program verification, targeting the existing capabilities in the MLIR infrastructure. The paper evaluates the eCC++ expressiveness and usability describing the process of embedding GraphIt, a high-performance graph language in C++.
Gonzalez Tallada, Marc↗
JaqalPaq v.1.1
Jaqal-pup (Jaqal Programming Utilities Project) is a high-level Python metaprogramming interface for Jaqal, a quantum programming language for near-term quantum hardware (see https://arxiv.org/abs/2003.09382 for a description of Jaqal). In addition to parsing and writing out Jaqal programs, it includes the ability to read in and write out quantum programs in other languages and frameworks, e.g. Qiskit (IBM), Quil (Rigetti), Cirq (Google), Q# (Microsoft), ProjectQ (ETH Zurich), and tket (Cambridge Quantum Computing). It implements a gate scheduler, an emulator of a small-scale quantum computer programmed using Jaqal, and tie-ins for other simulation back-ends. SAND2020-12710 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Russo, Antonio↗
Performance of Julia for High Energy Physics Analyses
We argue that the Julia programming language is a compelling alternative to currently more common implementations in Python and C++ for common data analysis workflows in high energy physics. We compare the speed of implementations of different workflows in Julia with those in Python and C++. Furthermore, our studies show that the Julia implementations are competitive for tasks that are dominated by computational load rather than data access. For work that is dominated by data access, we demonstrate an application with concurrent file reading and parallel data processing.
97 MATHEMATICS AND COMPUTING↗
pnnl/mcl-runtime
The Minos Computing Library (MCL) is a task-based programming language and runtime for extremely heterogeneous systems. MCL facilitates writing program for heterogeneous devices and porting applications across different systems and devices. MCL supports asynchronous execution of computing tasks on all available heterogeneous devices, including GPUs, FGPAs, fixed-point accelerators, and AI accelerators. MCL provides a high-level programming interface and automatically and autonomously performs resource management, load balancing, and locality-aware scheduling.
Central, PNNL Developer↗
OpenACC unified programming environment for GPU and FPGA multi-hybrid acceleration
Attached accelerators have been frequently used in recent High Per- formance Computing (HPC) systems because of their high performance/power ratio. In particular, the Graphics Processing Unit (GPU) is the most popu- lar accelerator owing to its high peak FLOPS performance and high memory bandwidth supported by HBM2, etc. However, the performance of GPU depends highly on a large degree of SIMD parallelism and has difficulty sustaining a high performance on programs with frequent branch operations or a partially low degree of parallelism.By contrast, a Field Programmable Gate Array (FPGA) has received attention as a different type of accelerator than GPU as a fully reconfigurable processor fitting the target applications. The high performance of FPGA is mainly provided by a pipelined operation and optimized circuit suitable for any operation even with frequent conditional branches. We have been focusing on the flexibility of FPGA to compensate for the weakness of GPU. We believe that the coupling of GPU with FPGA can result in one of the most powerful accelerating platforms available.However, the program coding of GPU and FPGA coupling can be quite difficult for application users. Traditionally, CUDA by NVIDIA has been the most popular programming language with the largest share of GPUs used in HPC, whereas a hardware description language such as Verilog HDL has been used in FPGA programming. OpenCL coding has recently become available even on high-end FPGAs. Moreover, several recent studies have also enabled the OpenACC coding for use in FPGA. In this study, we provide a unified programming system based on OpenACC for a platform equipped with both GPU and FPGA aiming at the next-generation accelerated supercomputer framework. Our programming environment is called Multi-Hybrid OpenACC Translator (MHOAT), and in this paper, we describe the basic concept and prototype system of MHOAT based on an evaluation on the amount of coding required and the performance of a hybrid multi-device accelerated system.
Tsunashima, Ryuta↗
App2Net: Moving App Functions to Network & a Case Study on Low-latency Feedback
Recent advances in programmable networks enable custom processing of data at hundreds of gigabits per second. These advances can boost the performance of many distributed applications. Yet the high-level languages used by application developers are different from the data plane programming languages (such as P4 and NPL) used by network equipment. This language barrier slows innovation. Our hourglass-shaped architectural solution aims to lower this language barrier. This enables the application developer community to leverage programmable networks for achieving better performance. In this paper we propose a JSON-based intermediate representation to bridge the gap between applications and in-network computing. We demonstrate an instance of the solution in the context of a low-latency feedback application that enables SQL-based data filtering in a P4-based programmable environment. We also present a prototype compiler to convert an intermediate representation in JSON to P4 source.
Sankaran, Ganesh↗
DaCe - Data Centric Parallel Programming
DaCe is a parallel programming framework that takes code in Python/NumPy and other programming languages, and maps it to high-performance CPU, GPU, and FPGA programs, which can be optimized to achieve state-of-the-art. Internally, DaCe uses the Stateful DataFlow multiGraph (SDFG) data-centric intermediate representation: A transformable, interactive representation of code based on data movement. Since the input code and the SDFG are separate, it is possible to optimize a program without changing its source, so that it stays readable. On the other hand, transformations are customizable and user-extensible, so they can be written once and reused in many applications. With data-centric parallel programming, we enable direct knowledge transfer of performance optimization, regardless of the application or the target processor.
Ben-Nun, Tal↗
Inference-Engine v0.1.0
Given a pre-trained neural network, Inference-Engine performs maps network inputs to outputs by executing the forward pass through the provided network. Although the predominant programming language for machine-learning is Python, most high-performance computing (HPC) applications are written in Fortran, C, or C++. Inference-Engine aims to support HPC programs and is written in Fortran, a language with a large feature set supporting interoperability with C. This software exposes concurrency in a portable way by using standard language features that some modern Fortran compilers can exploit with various optimizations, including offloading computation to a Graphics Processing Unit (GPU). In particular, this software makes extensive use of Fortran's "do concurrent" parallel loop construct, implicitly parallel array statements, and pure procedures that can be invoked inside "do concurrent" blocks. Inference-Engine also supports dynamic choice of inference methods at runtime. Two current options include one method that uses Fortran's "dot_product" intrinsic function inside "do concurrent" blocks and another method that instead uses Fortran' "matmul" array intrinsic function. We plan to investigate automatic compiler offloading of "do concurrent" calculations to GPUs and compile-time substitution of optimized libraries such as the Basic Linear Algebra Library (BLAS) for "matmul" invocations. We also envision the potential for the choice of which method to use could happen at program launch based on in situ performance measurements on any given platform.
Rouson, Damian↗
Mini Report: LLMs on Code Translation
The goal of this mini report is to give opinions on the current state of the art in large language model (LLM) assisted code translation, which aims to replicate the behavior of a program written in one programming language to another. The first section provides our overall sense of literature and suggested directions of research, and the second section summarizes a few of the most relevant papers in greater depth.
97 MATHEMATICS AND COMPUTING↗
TeraChem protocol buffers ( TCPB ): Accelerating QM and QM/MM simulations with a client–server model
The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. Here, we describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI - )—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Do Programmers Prefer Predictable Expressions in Code?
Source code is a form of human communication, albeit one where the information shared between the programmers reading and writing the code is constrained by the requirement that the code executes correctly. Programming languages are more syntactically constrained than natural languages, but they are also very expressive, allowing a great many different ways to express even very simple computations. Still, code written by developers is highly predictable, and many programming tools have taken advantage of this phenomenon, relying on language model surprisal as a guiding mechanism. Additionally, while surprisal has been validated as a measure of cognitive load in natural language, its relation to human cognitive processes in code is still poorly understood. In this paper, we explore the relationship between surprisal and programmer preference at a small granularity—do programmers prefer more predictable expressions in code? Using meaning-preserving transformations, we produce equivalent alternatives to developer-written code expressions and run a corpus study on Java and Python projects. In general, language models rate the code expressions developers choose to write as more predictable than these transformed alternatives. Then, we perform two human subject studies asking participants to choose between two equivalent snippets of Java code with different surprisal scores (one original and transformed). We find that programmers do prefer more predictable variants, and that stronger language models like the transformer align more often and more consistently with these preferences.
97 MATHEMATICS AND COMPUTING↗
Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)
Not Available
Schneider, L. (ORCID:0000000239108217)↗
R “SHINY” GUI DEVELOPMENT FOR URANIUM ISOTOPIC ANALYSIS WITH MATRIX-ASSISTED IONIZATION MASS SPECTROMETRY
The international nuclear safeguards community continues to seek rapid, accurate, and precise characterization capabilities for the in-field measurement of uranium isotopic compositions in nuclear facilities. Mass spectrometry (MS) is considered the “gold standard” for analysis of relatively long-lived actinides such as uranium (U) and plutonium; however, conventional MS analysis often requires time consuming sample preparation and complex analytical methodologies that are difficult to perform in-field or in-facility. Matrix assisted ionization (MAI) is a novel ambient ionization MS technique (i.e., MAI-MS) that potentially addresses these challenges due to the relative simplicity of the ionization phenomenon and ruggedness of ambient MS instrumentation. Savannah River National Laboratory (SRNL, USA) has demonstrated this technique for nanogram-level 235U/238U isotope ratio measurements within seconds, with percent-level analytical uncertainties capable of discriminating depleted, natural, and low-enriched uranium. Current experimental work on developing MAI methods for uranium isotopic analysis has been enabled by parallel development of a comprehensive MAI-MS data analysis suite at SRNL. Development of this bespoke data analysis software was necessary because commercially available ambient MS software is poorly suited for uranium isotope ratio measurement. The effort leverages the power of R, a popular open-source programming language, and Shiny, an R package providing tools for graphical user interface (GUI) and web interface coding. This software allows researchers without any programming experience to harness and utilize R’s considerable data analysis/visualization power.
LaBone, Elizabeth D.↗