Trust, but Verify: Rigorously Profiling Best-Effort High-Performance Computing for Digital Evolution
Authors: Matthew Andres Moreno, Santiago Rodriguez Papa, Charles Ofria, Luis Zaman, Emily Dolson
Organizations: Department of Ecology and Evolutionary Biology; Center for the Study of Complex Systems; University of Michigan, Ann Arbor, MI, USA · Department of Computer Science and Engineering; Program in Ecology, Evolution, and Behavior; Michigan State University, East Lansing, MI, USA
Developments in high-performance computing (HPC) technology continue to drastically increase quantities of available processing power. In the context of digital evolution, this explosive growth offers opportunities to advance both hypothesis-driven explorations of multi-scale biological phenomena and application-driven evolutionary optimization targeting hard problem domains. A particular opportunity arises from emerging next-generation AI/ML hardware accelerator platforms, such as the 880,000-processor Cerebras Wafer-Scale Engine (WSE). Such hardware, however, constrains on-device data storage and movement --- a challenge compounded by vulnerability to failures arising over numerous device components. Best-effort relaxations that depart from a traditional deterministic computing paradigm can help accommodate such constraints, but complicate reproducibility and risk introducing artifactual biases. We explore these concerns, developing a framework to measure runtime behavior of best-effort code and examining case studies of best-effort computing in digital evolution projects. The first case study applies best-effort CPU-cluster multiprocessing to a multicellularity evolution model, which provides 92% scaling efficiency at 64 processes (2.1× speedup) and exhibits robust median quality of service, even under hardware anomalies. The second case study examines WSE-based simulations, demonstrating best-effort strategies to track spatiotemporal population history --- through sparse, asynchronous device-to-host sampling that tolerates hardware faults. In sum, across potential forms and scopes of best-effort relaxation, we argue that digital evolution is uniquely positioned to contribute in developing post-deterministic HPC paradigms.
Modern large-scale language model pre-training relies heavily on the single program multiple data (SPMD) paradigm, which requires tight coupling across accelerators. Due to this coupling, transient slowdowns, hardware failures, and synchronization overhead stall the entire computation, wasting significant compute time at scale. While recent distributed methods like DiLoCo reduced communication bandwidth, they remained fundamentally synchronous and vulnerable to these system stalls. To address this, we introduce Decoupled DiLoCo, an evolution of the DiLoCo framework designed to break the lock-step synchronization barrier and go beyond SPMD to maximize training goodput. Decoupled DiLoCo partitions compute across multiple independent learners'' that execute local inner optimization steps. These learners asynchronously communicate parameter fragments to a central synchronizer, which circumvents failed or straggling learners by aggregating updates using a minimum quorum, an adaptive grace window, and dynamic token-weighted merging. Inspired by chaos engineering'', we achieve significantly improved training efficiency in failure-prone environments with millions of simulated chips with strictly zero global downtime, while maintaining competitive model performance across text and vision tasks, for both dense and mixture-of-expert architectures.
The transition from sequential to parallel computing is essential for modern high-performance applications but is hindered by the steep learning curve of concurrent programming. This challenge is magnified for irregular data structures (such as sparse graphs, unbalanced trees, and non-uniform meshes) where static scheduling fails and data dependencies are unpredictable. Current Large Language Models (LLMs) often fail catastrophically on these tasks, generating code plagued by subtle race conditions, deadlocks, and sub-optimal scaling. We bridge this gap with ParEVO, a framework designed to synthesize high-performance parallel algorithms for irregular data. Our contributions include: (1) The Parlay-Instruct Corpus, a curated dataset of 13,820 tasks synthesized via a "Critic-Refine" pipeline that explicitly filters for empirically performant algorithms that effectively utilize Work-Span parallel primitives; (2) specialized DeepSeek, Qwen, and Gemini models fine-tuned to align probabilistic generation with the rigorous semantics of the ParlayLib library; and (3) an Evolutionary Coding Agent (ECA) that improves the "last mile" of correctness by iteratively repairing code using feedback from compilers, dynamic race detectors, and performance profilers. On the ParEval benchmark, ParEVO achieves an average 106x speedup (with a maximum of 1103x) across the suite, and a robust 13.6x speedup specifically on complex irregular graph problems, outperforming state-of-the-art commercial models. Furthermore, our evolutionary approach matches state-of-the-art expert human baselines, achieving up to a 4.1x speedup on specific highly-irregular kernels. Source code and datasets are available at https://github.com/WildAlg/ParEVO.
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.