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At least 1,423 records · Page 79

Machine Learning-enabled Scalable Performance Prediction of Scientific Codes

Hardware architectures become increasingly complex as the compute capabilities grow to exascale. Here, we present the Analytical Memory Model with Pipelines (AMMP) of the Performance Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware architecture parameters as input and predicts runtime of that code on the target hardware platform, which is defined in the input parameters. PPT-AMMP transforms the code to an (architecture-independent) intermediate representation, then (i) analyzes the basic block structure of the code, (ii) processes architecture-independent virtual memory access patterns that it uses to build memory reuse distance distribution models for each basic block, and (iii) runs detailed basic-block level simulations to determine hardware pipeline usage. PPT-AMMP uses machine learning and regression techniques to build the prediction models based on small instances of the input code, then integrates into a higher-order discrete-event simulation model of PPT running on Simian PDES engine. We validate PPT-AMMP on four standard computational physics benchmarks and present a use case of hardware parameter sensitivity analysis to identify bottleneck hardware resources on different code inputs. We further extend PPT-AMMP to predict the performance of a scientific application code, namely, the radiation transport mini-app SNAP. To this end, we analyze multi-variate regression models that accurately predict the reuse profiles and the basic block counts. We validate predicted SNAP runtimes against actual measured times.

97 MATHEMATICS AND COMPUTING↗

Giallar: push-button verification for the qiskit Quantum compiler

This paper presents Giallar, a fully-automated verification toolkit for quantum compilers. Giallar requires no manual specifications, invariants, or proofs, and can automatically verify that a compiler pass preserves the semantics of quantum circuits. To deal with unbounded loops in quantum compilers, Giallar abstracts three loop templates, whose loop invariants can be automatically inferred. To efficiently check the equivalence of arbitrary input and output circuits that have complicated matrix semantics representation, Giallar introduces a symbolic representation for quantum circuits and a set of rewrite rules for showing the equivalence of symbolic quantum circuits. With Giallar, we implemented and verified 44 (out of 56) compiler passes in 13 versions of the Qiskit compiler, the open-source quantum compiler standard, during which three bugs were detected in and confirmed by Qiskit. Furthermore, our evaluation shows that most of Qiskit compiler passes can be automatically verified in seconds and verification imposes only a modest overhead to compilation performance.

automated verification↗

VTK-m: Visualization for the Exascale Era and Beyond

A recent trend in modern high-performance computing is the increasing use of hybrid architectures, where the vast majority of performance comes from accelerators. Modern accelerators are based on Graphics Processing Units (GPU) that contain many low power cores that in their aggregate provides an extremely high computation rate. Current and future CPU processors are requiring more explicit parallelism as each successive version of the hardware packs in more cores, and technologies like hyperthreading and vector operations require even more parallel processing to leverage each core’s full potential. As an example, the Frontier supercomputer installed at Oak Ridge National Laboratories recently hit a record breaking 1.1 exaflops1 on the LINPACK HPC benchmark [Shoemaker 2022]. The system contains 37632 AMD MI250x GPUs which requires more than half a billion threads to keep the system fully utilized [Khizeran 2022].VTK-m is a toolkit of scientific visualization algorithms for these emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

Bolstad, Mark↗

PyOED: An Extensible Suite for Data Assimilation and Model-Constrained Optimal Design of Experiments

This article describes PyOED, a highly extensible scientific package that enables developing and testing model-constrained optimal experimental design (OED) for inverse problems. Specifically, PyOED aims to be a comprehensive Python toolkit for model-constrained OED. The package targets scientists and researchers interested in understanding the details of OED formulations and approaches. It is also meant to enable researchers to experiment with standard and innovative OED technologies with a wide range of test problems (e.g., simulation models). OED, inverse problems (e.g., Bayesian inversion), and data assimilation (DA) are closely related research fields, and their formulations overlap significantly. Thus, PyOED is continuously being expanded with a plethora of Bayesian inversion, DA, and OED methods as well as new scientific simulation models, observation error models, and observation operators. These pieces are added such that they can be permuted to enable testing OED methods in various settings of varying complexities. The PyOED core is completely written in Python and utilizes the inherent object-oriented capabilities; however, the current version of PyOED is meant to be extensible rather than scalable. Specifically, PyOED is developed to “enable rapid development and benchmarking of OED methods with minimal coding effort and to maximize code reutilization.” This article provides a brief description of the PyOED layout and philosophy and provides a set of exemplary test cases and tutorials to demonstrate the potential of the package.

97 MATHEMATICS AND COMPUTING↗

From Edge to HPC: Investigating Cross-Facility Data Streaming Architectures

In this paper, we investigate three cross-facility data streaming architectures, Direct Streaming (DTS), Proxied Streaming (PRS), and Managed Service Streaming (MSS). We examine their architectural variations in data flow paths and deployment feasibility, and detail their implementation using the Data Streaming to HPC (DS2HPC) architectural framework and the SciStream memory-to-memory streaming toolkit on the production-grade Advanced Computing Ecosystem (ACE) infrastructure at Oak Ridge Leadership Computing Facility (OLCF). We present a workflow-specific evaluation of these architectures using three synthetic workloads derived from the streaming characteristics of scientific workflows. Through simulated experiments, we measure streaming throughput, round-trip time, and overhead under work sharing, work sharing with feedback, and broadcast and gather messaging patterns commonly found in AI-HPC communication motifs. Our study shows that DTS offers a minimal-hop path, resulting in higher throughput and lower latency, whereas MSS provides greater deployment feasibility and scalability across multiple users but incurs significant overhead. PRS lies in between, offering a scalable architecture whose performance matches DTS in most cases.

George, Anjus [ORNL] (ORCID:0000000179737061)↗

SetGo: Metadata Readiness for Scientific AI Datasets

Scientific datasets intended for AI use require both computational readiness for model training and metadata readiness for discovery, sharing, and reuse. The Readiness Engine for Data Integration (REDI) addresses computational readiness, but no corresponding tool evaluates whether a dataset’s metadata are sufficiently complete, governed, and standards-compliant for publication and agent-based consumption. Existing FAIR assessors operate only on published repository records, and no single system covers FAIR compliance, licensing, provenance, governance, reproducibility, and catalog readiness together. We present SetGo, an open-source Python toolkit that assesses and repairs metadata readiness across these six dimensions before a dataset is published or archived. Applied to four scientific corpora, SetGo surfaces deficiencies that general-purpose tools do not detect: ERA5 climate metadata scores 4% on ACDD 1.3 compliance; materials datasets fail OPTIMADE species-definition requirements; and PDB-derived proteomics data carries licensing terms incompatible with standard SPDX identifiers. Guided enrichment raises overall FAIR scores from 52–57% to 81–91%, and a single setgo publish command pushes to Hugging Face Hub, CKAN, or OpenMetadata with ML Commons Croissant 1.0 metadata sidecars. To support interactive and automated workflows, SetGo integrates with coding agents powered by large language models (LLMs) through a /setgo skill that enables natural-language execution of the full assess–enrich–publish loop, with user involvement limited to supplying missing metadata values.

Wilkinson, Sean [ORNL] (ORCID:0000000214437479)↗

Direct-Write Ion Beam Lithography

Patterning with a focused ion beam (FIB) is an extremely versatile fabrication process that can be used to create microscale and nanoscale designs on the surface of practically any solid sample material. Based on the type of ion-sample interaction utilized, FIB-based manufacturing can be both subtractive and additive, even in the same processing step. Indeed, the capability of easily creating three-dimensional patterns and shaping objects by milling and deposition is probably the most recognized feature of ion beam lithography (IBL) and micromachining. However, there exist several other techniques, such as ion implantation- and ion damage-based patterning and surface functionalization types of processes that have emerged as valuable additions to the nanofabrication toolkit and that are less widely known. While fabrication throughput, in general, is arguably low due to the serial nature of the direct-writing process, speed is not necessarily a problem in these IBL applications that work with small ion doses. Here we provide a comprehensive review of ion beam lithography in general and a practical guide to the individual IBL techniques developed to date. Special attention is given to applications in nanofabrication.

Joshi-Imre, Alexandra↗

Dax v. 1.0

The Dax Toolkit enables the fine-grained concurrency for data analysis and visualization required to drive multi-core processors, many-core GPU accelerators, and emerging architectures for exascale computing. Dax simplifies the design of finely threaded algorithms by characterizing them in per element operations, which we call worklets. Worklets simplify design because they can behave as serial processes without the complications of memory clashes or other race conditions. Yet worklets can be scheduled on a practically unlimited number of threads, thereby making effective utilization of many processing cores. Operations coordinated across elements are encapsulated in a few versatile communicative operations that are adapted to the specifics of computing devices.

SciDAC↗

Nalu

Nalu is a Sierra ToolKit (STK) based application module, and it has provided a set of "lessons learned" for the STK transition effort through its early adoption of STK. It makes use of the open-sourced Trilinos/ Tpetra library. Through the investment of LORD and ASCR projects, the Nalu code module has been extended beyond prototype status. Physics capability includes low Mach, variable density turbulent flow. The ongoing objective for Nalu is to facilitate partnerships with external organizations in order to extend code capability and knowledge; however, it is not intended to support routine CFD analysis. The targeted usage of this module is for non-NW applications that support work-for-others in the multiphysics energy sector.

Source record↗

Land Ice Verification and Validation Kit

To address a pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice-sheet models is underway. The associated verification and validation process of these models is being coordinated through a new, robust, python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVV). This release provides robust and automated verification and a performance evaluation on LCF platforms. The performance V&V involves a comprehensive comparison of model performance relative to expected behavior on a given computing platform. LIVV operates on a set of benchmark and test data, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-4-bit evaluation, and plots of tests where differences occur.

Source record↗

VTK-m

VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

ECP↗

Dynamic Power Grid Simulation

GridDyn is a part of power grid simulation toolkit. The code is designed using modern object oriented C++ methods utilizing C++11 and recent Boost libraries to ensure compatibility with multiple operating systems and environments.

Top, Philip↗

Albany v. 3.0

The Albany code is a general-purpose finite element code for solving partial differential equations (PDEs). Albany is a research code that demonstrates how a PDE code can be built by interfacing many of the open-source software libraries that are released under Sandia's Trilinos project. Part of the mission of Albany is to be a testbed for new Trilinos libraries, to refine their methods, usability, and interfaces. Albany includes hooks to optimization and uncertainty quantification algorithms, including those in Trilinos as well as those in the Dakota toolkit. Because of this, Albany is a desirable starting point for new code development efforts that wish to make heavy use of Trilinos. Albany is both a framework and the host for specific finite element applications. These applications have project names, and can be controlled by configuration option when the code is compiled, but are all developed and released as part of the single Albany code base, These include LCM, QCAD, FELIX, Aeras, and ATO applications.

SciDAC↗

VTK-m v. 1.0

VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

Moreland, Kenneth↗

Sirepo - Warp

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.

Nagler, Robert↗

Visualization Software for VisIT Java Client

The VisIT Java Client (JVC) library is a lightweight thin client that is designed and written purely in the native language of Java (the Python & JavaScript versions of the library use the same concept) and communicates with any new unmodified standalone version of VisIT, a high performance computing parallel visualization toolkit, over traditional or web sockets and dynamically determines capabilities of the running VisIT instance whether local or remote.

Billings, JayJay↗

LK Scripting Language [SWR-16-07]

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Version 3.0+ toolkit.

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G4beamline

G4beamline is a single-particle-tracking simulation code based on the Geant4 toolkit. It is specifically optimized for the realistic evaluation of beam lines. It is especially useful for evaluating future muon facilities.

Source record↗