Data-Driven Dynamic Algorithm Dispatch with Large Language Models

We introduce a large language model (LLM)-driven approach for generating dynamic algorithmic dispatch heuristics in high-performance linear algebra. By combining prompt engineering with LLaMA 3 and a curated performance database, the model learns to synthesize selection heuristics that exploit structural patterns to identify fast algorithmic choices. A case study on LU factorization demonstrates the model's ability to replicate expert-designed strategies. This work, developed as part of the DARPA-MIT SmartSolve project, highlights the promise of LLMs for algorithmic discovery and the development of more adaptive, fast linear algebra software.

Accelerated Genetic Programming Hyper-Heuristics for Simulation-Based Scheduling via Agentic AI

Python is widely used in scientific research because it enables rapid development and provides rich ecosystems for data analysis, artificial intelligence (AI), and machine learning. However, customized research code can become prohibitively slow as experiments scale. This challenge is particularly acute in discrete-event project-scheduling simulations, where sequential state updates, nested loops, conditional evaluations, and object-oriented structures limit the benefits of compiled numerical and GPU-accelerated libraries. Addressing these bottlenecks typically requires iterative profiling, refactoring, testing, and validation, yet researchers may lack the time or specialized software-engineering expertise for low-level optimization. This paper presents a systematic refactoring approach using Claude agentic AI on real-world project-scheduling workloads in a high-performance computing (HPC) environment. Guided by representative benchmarks and correctness checks, the agent identifies bottlenecks, implements targeted optimizations, and evaluates their effects, while the researcher retains final control. Testing runtime reduced from 1,298 seconds to under 200 seconds without changing outputs, saving four million core-hours (NZ\$320,000) annually.

Scalable High-Fidelity Macromolecular Docking for GPU-Accelerated Supercomputers

Flexible macromolecular docking offers high-fidelity predictions of biomolecular interactions, but remains prohibitively expensive at scale. Among existing approaches, LightDock leverages Glowworm Swarm Optimization (GSO) for accuracy, yet suffers from limited parallelism, irregular computation, and severe load imbalance, preventing efficient execution on GPU supercomputers. We present SparkleDock, a scalable GSO-based docking framework enabling near-real-time flexible docking. We redesign GSO to expose massive fine-grained parallelism at the glowworm-agent level, and restructure the dominant energy scoring computation into a Tensor Core-compatible formulation, enabling efficient execution of irregular pairwise interactions through structured matrix operations. We further introduce a performance-model-driven scheduling for load balancing and out-of-core scaling across GPUs. SparkleDock achieves 9.7 $\times$ and 18.9 $\times$ speedups over LightDock on single A100 and H100 GPU, and delivers over two orders of magnitude acceleration at scale. On 512 GPUs, it reduces docking time from hours to seconds, enabling large-scale, high-fidelity virtual screening previously impractical with flexible docking.

Trusted Credentials, Untrusted Behavior: Benchmarking LLM-Agent Security in High-Performance Computing

Large language model (LLM) agents are starting to take on routine work in high-performance computing (HPC), including monitoring Slurm jobs, diagnosing failed builds, inspecting simulation output, and coordinating scientific workflows. To do this work, an agent commonly acts under its user's credentials and inherits the user's access to files and the scheduler. This arrangement creates a failure mode that ordinary account-level controls do not capture. Adversarial instructions in a log, tool description, shared file, or peer-agent message may redirect the agent beyond the task the user assigned, even though every resulting command is authenticated and permitted for that account. We refer to this as the hijacked authorized agent problem. Existing agent-security studies explain relevant mechanisms, such as indirect prompt injection and tool misuse, but generally evaluate them in web, enterprise, or personal-assistant settings. HPC security, by contrast, has mature controls for identity and isolation but does not ordinarily represent the intent of a particular task. This paper defines the threat model in the HPC setting, identifies attack surfaces created by schedulers, shared storage, multi-project accounts, and scientific workflows, and examines where current controls fall short. It concludes with a research agenda and a plan for an empirical benchmark, TaskBound.

An Agentic AI Framework to Accelerate Scientific Discovery in Plant Phenotyping

High-throughput plant phenotyping now generates image derived datasets far faster than scientists can analyze them. At Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory (APPL), automated stations image hundreds of plants daily across multiple remote sensing modalities; yet, trait extraction and interpretation remain manual, expert-bound, and strictly post-hoc, making analysis, not acquisition, the binding constraint on discovery. We present an end-to-end agentic AI framework that turns the facility from a data factory into an interactive autonomous, discovery platform, where scientists partner with AI agents to accelerate time to insight. A conversational Co-Scientist Agent translates a scientist's natural-language question into a structured analysis plan, and a headless Compute Agent dispatches Vision Transformer segmentation and trait extraction on the Frontier exascale supercomputer. The two agents run in separate security and resource domains and communicate over a secure, token-authenticated streaming channel, a design that accounts for the federation, data-movement, and provenance realities cloud-native agentic frameworks ignore, ensuring end-to-end provenance is captured for every interaction. The framework turns a days- to weeks-long analysis process into an interactive loop where agents reason over results, recommend next analyses, and respond to follow-up questions in seconds.

Twelve quick tips for designing AI-driven HPC workflows

High-performance computing (HPC) clusters remain the backbone of large-scale scientific computation, traditionally executing deterministic, linear pipelines optimised for predictable performance. However, the pervasive integration of artificial intelligence (AI) and foundation models into scientific research has introduced a fundamentally new computational paradigm. AI-driven workflows are characteristically iterative, data-driven, and probabilistic, introducing unique challenges regarding data gravity, heterogeneous resource management, and complex workflow orchestration. This guide provides twelve practical tips designed to help researchers design efficient, scalable, and reproducible AI-driven HPC workflows. By addressing critical system-level bottlenecks - such as containerisation for environment portability, strategic deployment of job arrays, explicit feedback loop mechanics, and I/O optimisation for small files - this article offers a framework for transitioning from rigid execution pipelines to adaptive, intelligent computational environments. While these architectural principles are broadly applicable across distributed environments, they are particularly tailored to the resource-intensive throughput demands of modern computational biology.

CodegenBench: Can LLMs Write Efficient Code Across Architectures?

While large language models (LLMs) have been extensively evaluated on code generation tasks for general-purpose programming and GPU-accelerated environments (e.g., PyTorch, CUDA), their capabilities in CPU-oriented high-performance computing (HPC) across diverse architectures remain underexplored. To bridge this gap, we introduce CodegenBench, a comprehensive benchmark suite designed to evaluate the generation of efficient parallel code across three distinct hardware platforms: x86_64, Sunway, and Kunpeng. Our benchmark comprises 106 standard Basic Linear Algebra Subprograms (BLAS) routines establishing a fundamental baseline, alongside 20 specialized computational kernels adapted for each of the unique supercomputing architectures (LeetSunway and LeetKunpeng). Our extensive evaluation reveals that while state-of-the-art LLMs can generate optimized code for ubiquitous architectures like x86_64, they exhibit significant performance degradation on domain-specific architectures with limited public documentation and training data, highlighting critical limitations in cross-platform generalization. Furthermore, our analysis of factors influencing code quality such as implementation length and task complexity indicates that current LLMs are most effective for moderately difficult problems requiring concise code snippets. We open-source our dataset and automated evaluation infrastructure to facilitate future research in LLM-driven high-performance code generation. The resources are available at https://anonymous.4open.science/r/CodegenBench-EDE1/ and https://anonymous.4open.science/r/CodegenBenchDataset-2551.