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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Applying Machine Learning to Understand Write Performance of Large-scale Parallel Filesystems

In high-performance computing (HPC), I/O performance prediction offers the potential to improve the efficiency of scientific computing. In particular, accurate prediction can make runtime estimates more precise, guide users toward optimal checkpoint strategies, and better inform facility provisioning and scheduling policies. HPC I/O performance is notoriously difficult to predict and model, however, in large part because of inherent variability and a lack of transparency in the behaviors of constituent storage system components. In this work we seek to advance the state of the art in HPC I/O performance prediction by (1) modeling the mean performance to address high variability, (2) deriving model features from write patterns, system architecture and system configurations, and (3) employing Lasso regression model to improve model accuracy. We demonstrate the efficacy of our approach by applying it to a crucial subset of common HPC I/O motifs, namely, file-per-process checkpoint write workloads. We conduct experiments on two distinct production HPC platforms—Titan at the Oak Ridge Leadership Computing Facility and Cetus at the Argonne Leadership Computing Facility—to train and evaluate our models. We find that we can attain ≤ 30% relative error for 92.79% and 99.64% of the samples in our test set on these platforms, respectively.

Xie, Bing↗
DOE OSTI2023

LCIO

Performance of file systems shift during their life cycles. Evaluating this performance change over time is not trivial. Complexity arises in the interplay between external (i.e. application I/O workloads) and internal (i.e. the filesystem state) factors. Many benchmarks can test how a filesystem performs at the current snapshot state, but to observe the change over time necessitates that the filesystem state mutate (age) between benchmark runs. For a large-scale HPC parallel filesystem, the sheer scale and amount of interacting components during I/O operations magnify these challenges. LCIO addresses the question - how will the filesystem perform at different stages of its life cycle? LCIO is a synthetic benchmark, which provides the file system aging process to increase the amount of information that existing benchmarks like IOR and MDTest yield, as well as provide additional points of data that will be useful to system architects and engineers.

Bachstein, Matthew↗
DOE OSTI2022

Accelerating Scientific Workflows on HPC Platforms with In Situ Processing

Scientific workflows drive most modern large-scale science breakthroughs by allowing scientists to define their computations as a set of jobs executed in a given order based on their data dependencies. Workflow management systems (WMSs) have become key to automating scientific workflows-executing computational jobs and orchestrating data transfers between those jobs running on complex high-performance computing (HPC) platforms. Traditionally, WMSs use files to communicate between jobs: a job writes out files that are read by other jobs. However, HPC machines face a growing gap between their storage and compute capabilities. To address that concern, the scientific community has adopted a new approach called in situ, which bypasses costly parallel filesystem I/O operations with faster in-memory or in-network communications. When using in situ approaches, communication and computations can be interleaved. In this work, we leverage the Decaf in situ dataflow framework to accelerate task-based scientific workflows managed by the Pegasus WMS, by replacing file communications with faster MPI messaging. We propose a new execution engine that uses Decaf to manage communications within a sub-workflow (i.e., set of jobs) to optimize inter-job communications. We consider two workflows in this study: (i) a synthetic workflow that benchmarks and compares file- and MPI-based communication; and (ii) a realistic bioinformatics workflow that computes mu-tational overlaps in the human genome. Experiments show that in situ communication can improve the bioinformatics workflow execution time by 22% to 30% compared with file communication. Our results motivate further opportunities and challenges for bridging traditional WMSs with in situ frameworks.

Decaf↗
DOE OSTI2020

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory's (ORNL's) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high performance computing (HPC) needs; and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2019 was a big year as OLCF staff ran five world-class resources (the leadershipclass computers Titan and Summit, the large analysis cluster called Eos, and the massive parallel filesystems called Atlas and Alpine)) and also began power and cooling upgrades for a 2021 exascale system called Frontier. While continuing exceptional operation of Titan, Eos, and Rhea, the OLCF released the Summit supercomputer for production on January 1, 2019. Summit debuted as the most capable and efficient system in its class and has been recognized as the most powerful system in the world for its performance on both the high performance linpack (HPL) and conjugate gradient (HPCG) benchmark applications since June 2018 according to TOP500. Summit represents the culmination of a multiyear effort between the OLCF, IBM, NVIDIA, and Mellanox to deliver a system that is unmatched for modeling, simulation, data analysis, and learning. To hit the ground running with science-ready applications on day one, application teams worked closely with the OLCF through the Center for Accelerated Application Readiness (CAAR) program for years in advance of the Summit deployment. CY 2019 was filled with outstanding results and accomplishments: a very high rating from users on overall satisfaction for the sixth year in a row; a tremendous amount of core-hours delivered to researchers from two leadership-class systems; and success in delivering on the allocation split of roughly 60%, 30%, and 10% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director's Discretionary (DD) programs, respectively (see Operational Performance section). These accomplishments, coupled with the high utilization rates (overall and capability usage), represent the fulfillment of the promise of both leadership-class machines: efficient facilitation of leadership-class computational applications. Table ES.1 presents a summary of the 2019 OLCF metric targets and the associated results. More information can be found in the Operational Performance section for each OLCF resource. The scientific accomplishments of OLCF users are a strong indication of long-term operational success, with publications this year in such notable journals and publications as Nature, Nature Physics, Nature Plants, Physical Review X, Journal of the American Physical Society, Cell, Nano Letters, and Trends in Biotechnology. Crucial domain-specific discoveries facilitated by resources at the OLCF are described in the High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility (OAR) Strategic Results section. For example, researchers used Summit to pinpoint and understand the production of proteins from genetic information, including mutations and the functional expression of disease (Section 8.2).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Modeling I/O Performance Variability Using Conditional Variational Auto Encoders

Storage system performance modeling is crucial for efficient use of heterogeneous shared resources on leadership class computers. Variability in application performance, particularly variability arising from concurrent applications sharing I/O resources, is a major hurdle in the development of accurate performance models. We adopt a deep learning approach based on conditional variational auto encoders (CVAE) for I/O performance modeling, and use it to quantify performance variability. We illustrate our approach using the data collected on Edison, a production supercomputing system at the National Energy Research Scientific Computing Center (NERSC). The CVAE approach is investigated by comparing it to a previously proposed sensitivity-based Gaussian process (GP) model. We find that the CVAE model performs slightly better than the GP model in cases where training and testing data come from different applications, since CVAE can inherently leverage the whole data from multiple applications whereas GP partitions the data and builds separate models for each partition. Hence, the CVAE offers an alternative modeling approach that does not need preprocessing; it has enough flexibility to handle data from a wide variety of applications without changing the inference approach.

I/O perfornance variability↗
DOE OSTI2018

In‐memory integration of existing software components for parallel adaptive unstructured mesh workflows

Summary Reliable mesh‐based simulations are needed to solve complex engineering problems. Mesh adaptivity can increase reliability by reducing discretization errors but requires multiple software components to exchange information. Often, components exchange information by reading and writing a common file format. This file‐based approach becomes a problem on massively parallel computers where filesystem bandwidth is a critical performance bottleneck. Our approach using data streams and component interfaces avoids the filesystem bottleneck. In this paper, we present these techniques and their use for coupling mesh adaptivity to the PHASTA computational fluid dynamics solver, the Albany multi‐physics framework, and the Omega3P linear accelerator frequency analysis applications. Performance results are reported on up to 16,384 cores of an Intel Knights Landing‐based system.

Smith, Cameron W.↗
DOE OSTI2025

Lustre Unveiled: Evolution, Design, Advancements, and Current Trends

The Lustre filesystem serves as a vital element in high-performance parallel storage, meeting the rising demands of scientific, research, and enterprise environments. Widely deployed across HPC environments, ranging from small-scale applications in AI/ML, to domains like oil and gas, drug discovery, and meteorology, and manufacturing, Lustre addresses the universal challenge of efficiently accessing vast and ever-increasing volumes of data. Lustre is the filesystem of choice on six out of the top 10 fastest supercomputers in the world today, over 65% of the top 100, and also for over 60% of the top 500. Despite its widespread popularity, there is a lack of a complete and up-to-date reference, covering Lustre’s evolution, design, and various advancements made over the years. In this journal, we aim to fill this gap by providing a comprehensive journey of Lustre, including its history with significant contributions to HPC, detailed architecture and design elements, exploration of advancements added through its evolution, and future directions. Additionally, we present a comparison of Lustre with other prominent storage technologies of the era. To illustrate the current state of Lustre, we analyze several filesystem trends, including utilization, performance, and usage patterns on Orion, the Lustre filesystem on the first exascale supercomputer Frontier. We hope that this journal serves as a comprehensive educational reference for the current and future generations interested in HPC filesystem storage aspects.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2022

Automatic variable selection in ecological niche modeling: A case study using Cassin’s Sparrow (Peucaea cassinii)

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max’s Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin’s Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim’s Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species’ bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA’s Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.

John L. Schnase↗
NASA NTRS2019

Analysis Ready Data in Analytics Optimized Data Stores for Analysis of Big Earth Data in the Cloud

Cloud computing offers the possibility of making the analysis of Big Data approachable for a wider community due to affordable access to computing power, an ecosystem of usable tools for parallel processing, and migration of many large datasets to archives in the cloud, allowing data-proximal computing. Generally, data analysis acceleration in the cloud comes from running multiple nodes in a split-combine-apply strategy. Data systems such as the Earth Observing System Data and Information System are in a position to "pre-split" the data by storing them in a data store that is optimized for data parallel computing, i.e., an Analytics-Optimized Data Store (AODS). A variety of approaches to AODS are possible, from highly scalable databases to scalable filesystems to data formats optimized for cloud access (e.g., zarr and cloud-optimized datasets), with the optimal choice dependent on both the types of analysis and the geospatial structure of the data. A key question is how much preprocessing of the data to do, both before splitting and as the first part of the apply step. Again, the geospatial structure of the data and the analysis type influence the decision, with the added complexity of the user type. Trans-disciplinary users who are not well-versed in the nuances of quality-filtering and georeferencing of remote sensing orbit/swath/scene data tend to ask for more highly processed data, relying on the data provider to make sensible decisions on preprocessing parameters. (This accounts for the popularity of "Level 3" gridded data, despite the lower spatial resolution it provides.) In this case, data can be preprocessed before the split, resulting in higher performance in the rest of the "apply" step, which can be transformative for use cases such as interactive data exploration at scale. Discipline researchers who are experienced with remote sensing data often prefer more flexibility in customizing the preprocessing data into Analysis Ready Data, resulting in more need for on-the-fly preprocessing.

Lynnes, Christopher↗
DOE OSTI2021

Scalable augmented enumeration and metadata operations for large filesystems

Systems, apparatus, and methods are disclosed for performing scalable operations in a file system. Metadata entries in a namespace or directory tree are sharded across multiple file metadata servers. An augmented enumeration operation, such as listing a directory, is parallelized across the multiple file metadata servers, transparently to clients. Exemplary augmentation features can include filtering and sorting. Augmentation features can be executed concurrently with enumeration, prior to enumeration, after enumeration, or as a combination of these, and can utilize pre-built index structures or holding structures for intermediate results. Augmented enumeration operations can also include no-output operations such as changing file attributes or deleting a file, and cumulative operations such as counting total disk space usage. The parallelization is compatible with tree-level parallelization and storage-level parallelization. Disclosed technologies can be applied to other fields requiring scalable enumeration, such as database and network applications.

Grider, Gary A.↗
DOE OSTI2021

Scalable filesystem enumeration and metadata operations

Systems, apparatus, and methods are disclosed for performing scalable operations in a file system, including POSIX-like file systems. Metadata entries in a namespace or directory tree are sharded across multiple file metadata servers. An enumeration operation, such as listing a directory, is parallelized across the multiple file metadata servers, while retaining standard functionality transparently to clients. Other enumeration operations include no-output operations such as changing file attributes or deleting a file, and cumulative operations such as counting total disk space usage. The parallelization is compatible with tree-level parallelization and storage-level parallelization. Disclosed technologies can be applied to other fields requiring scalable enumeration, such as database and network applications.

Grider, Gary A.↗
DOE OSTI2021

Understanding Lustre Internals. Second Edition

The Lustre file system has become a preferred storage resource for systems on the Top500 list, and it is often the file system of choice for small- to medium-sized HPC systems that require parallel shared access to data. Several resources exist to help users deploy and configure Lustre, but the same cannot be said for resources that explain the inner workings of the Lustre source code. A previous ORNL technical report entitled "Understanding Lustre Filesystem Internals" (ORNL/TM-2009/117) provided an excellent summary of Lustre subsystem operations. However, that report is over a decade old and is based on Lustre version 1.6. Since that report was published, Lustre has evolved significantly. Several subsystems underwent significant code changes and many new features have been added to the file system, bringing the current Lustre version up to 2.15.This report aims to document and explain the internal workings of the latest version of the Lustre file system. It will provide more complete and up-to-date information than the previous technical report and should serve as a foundational document for anyone interested in Lustre software development. Key data structures will be described along with the APIs used for interaction among the various Lustre subsystems. Although the Lustre software is constantly being developed, the details in this document should remain relevant for the forseeable future.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

matsim-agents v1.0

matsim-agents is a multi-agent AI framework for atomistic materials simulation and discovery. It orchestrates large language models (LLMs), machine-learned interatomic potentials (MLIPs), and DFT codes into a single agentic loop running on laptops and DOE leadership-class supercomputers. MULTI-AGENT ORCHESTRATION A LangGraph state machine with three nodes: a Planner that converts a natural-language research objective into structured tasks; an Executor that dispatches atomistic tools and loops until the queue is empty; and an Analyst that summarizes results into a human-readable report. State is checkpointed after every step and human-in-the-loop gates can be inserted at any edge. HYPOTHESIS-DRIVEN DISCOVERY CHAT An interactive REPL (matsim-agents chat) that couples LLM dialogue with atomistic simulation. Chemical formulas are automatically detected in conversation turns and trigger a full crystal-phase exploration: structure generation → relaxation → stability scoring → result injection back into the conversation, creating a closed hypothesis-refinement loop. CRYSTAL PHASE ENUMERATION Given a composition, the phase explorer enumerates prototypes by stoichiometry: elemental (fcc/bcc/hcp/sc/diamond), binary 1:1 (rocksalt/CsCl/zincblende/ wurtzite/fluorite/rutile), ternary 1:1:3 (cubic perovskite), ternary 1:2:4 (perovskite + spinel), quaternary 1:1:2:6 (Fm-3m double perovskite). 2-D prototypes (graphene, h-BN, MoS2 2H/1T) and multilayer stacking are also supported via --include-2d and --num-layers. SUPERCELL GENERATION AND SITE DECORATION Auto-tiling to a minimum atom count (--min-atoms), explicit NxNxN tiling (--supercell), symmetry-distinct site decorations (--n-orderings), and isotropic lattice-scale sweeps (--lattice-scales) for volume bracketing. MLFF RELAXATION AND STABILITY SCORING HydraGNN (multi-headed GNN) drives structure relaxation via ASE with FIRE, BFGS, or BFGSLineSearch. Stability output: delta-E/atom ranking across phases and a max-residual-force dynamical-stability proxy. Other MLIPs (MACE, NequIP, Orb) can be plugged in through the same interface. DFT BACKENDS Quantum ESPRESSO pw.x and VASP 6.6 are first-class labellers. Both have validated GPU builds and SLURM/PBS launchers for three DOE platforms: Frontier (AMD MI250X, ROCm), Aurora (Intel PVC, oneAPI), Perlmutter (NVIDIA A100, CUDA). QE produces ~100 binaries (pw.x, ph.x, epw.x, ...). VASP supports scf, relax, vc-relax, and vc-relax-shape run types. ACTIVE-LEARNING LOOP matsim-agents al run CONFIG.yaml drives an iterative HydraGNN-DFT loop: MD generates candidates → ensemble/MC-dropout uncertainty selects the most informative → DFT labels them in parallel inside one allocation → dataset grows → HydraGNN retrains → repeat. DFT backend is a single YAML toggle (dft.backend: vasp | qe). LLM-generated seed structures are supported (no curated POSCAR library needed). Config uses ${VAR}, ${VAR:-default}, ${VAR:?msg} shell-style substitution for cross-user/cross-site portability. LLM BACKENDS Ollama (local, default), vLLM (HPC multi-GPU serving), OpenAI, Anthropic, HuggingFace Transformers+Accelerate. Selected at runtime via flag or env var with no code changes. HPC PORTABILITY Same Python entry points run on Frontier (ROCm 7.2), Aurora (oneAPI), and Perlmutter (CUDA 12). DFT and ML stacks are never co-loaded in the same shell; they couple through the scheduler and filesystem. Advanced multi-node launchers (serve, discovery-chat, single-relaxation, active-learning, QE warm-start) are provided for all three platforms. CODABENCH COMPETITION BUNDLE A self-contained benchmark: 159 atomistic test structures across 11 material classes, 5 tasks (formation energy, forces, ML relaxation, AI-DFT relaxation, phase stability ranking), public/private leaderboard split (30/70), and four ready-to-run baselines: MACE-MP-0, HydraGNN, UMA, AllScAIP.

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗