Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2101.06737

Ten Simple Rules for Success with HPC, i.e. Responsibly BASHing that Linux Cluster

Jamie J. Alnasir
View original source ↗Read source document ↗Export metadata ↓

Abstract

High-performance computing (HPC) clusters are widely used in-house at scientific and academic research institutions. For some users, the transition from running their analyses on a single workstation to running them on a complex, multi-tenanted cluster, usually employing some degree of parallelism, can be challenging, if not bewildering, especially for users whose role is not predominantly computational in nature. On the other hand, there are more experienced users, who can benefit from pointers on how to get the best from their use of HPC. This Ten Simple Rules guide is aimed at helping you identify ways to improve your utilisation of HPC, avoiding common pitfalls that can negatively impact other users and will also help ease the load (pun intended) on your HPC sysadmin. It is intended to provide technical advice common to the use of HPC platforms such as LSF, Slurm, PBS/Torque, SGE, LoadLeveler and YARN, the scheduler used with Hadoop/Spark platform.

Explore related subjects

cs.DC

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jamie J. Alnasir. 2021-01-17. Ten Simple Rules for Success with HPC, i.e. Responsibly BASHing that Linux Cluster. https://doi.org/10.1371/journal.pcbi.1009207

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Weave: Fine-Grained Dynamic SM Scheduling in an MoE Megakernel for Compute-Communication Overlap

Mixture-of-Experts (MoE) inference under expert parallelism (EP) turns each MoE layer into a distributed computation with costly dispatch and combine communication. State-of-the-art systems reduce this cost through communication-computation overlap, splitting the GPU's SMs for communication and computation respectively. However, this approach still leaves GPU resources wasted along two dimensions. Spatially, the best SM split is determined by each layer's routing result and varies across layers and GPUs, so fixed policies mismatch the workload and waste either NVLink bandwidth or compute throughput. Temporally, complex MoE data dependencies introduce bubbles that leave SMs idle. We present Weave, to our knowledge the first MoE overlap system that performs fine-grained dynamic SM scheduling - deciding per layer and per GPU by routing results at runtime. Once routing completes, each layer's communication and computation volumes become known; Weave exploits this predictability through a lightweight cost model running inside the persistent megakernel: a spatial scheduler partitions SMs into communication workers and computation workers to match the communication/computation throughput ratio, and a temporal scheduler coordinates the two worker groups to minimize SM idleness. On 4x H100 SXM GPUs across six mainstream MoE models, Weave achieves a 2.89x geometric-mean MoE-layer speedup and a 1.33x geometric-mean end-to-end speedup over five state-of-the-art baselines.

cs.DC↗
arXiv2026

pytest-gpu-proof: Enabling Cloud-CPU Continuous Integration for GPU Code with Local GPU Attestation

GPU acceleration is now routine across robotics, but cloud-hosted GPU continuous integration (CI) runners are expensive, resulting in severe under-testing of GPU-accelerated code. We present pytest-gpu-proof, an open-source pytest plugin offering a practical middle ground. Tests can be run on a local machine, signed with a receipt of exactly what ran and what it produced, and integrated into standard CPU CI workflows (e.g., GitHub Actions). The tool is open source and on PyPI, and we are actively integrating it across our lab's software stack.

cs.DC↗
arXiv2026

When Fancy Eviction Fails: Rethinking Cache Replacement For LLM Prefix Reuse

Long-running LLM applications repeatedly send growing context, making prefix caching critical for reducing prefill cost. Yet prefix-cache behavior under agentic workloads remains poorly understood. We study production traces from two companies and evaluate 14 eviction algorithms across HBM-constrained and large memory-pool settings. Despite a large gap to Belady, sophisticated policies designed for traditional caches provide little benefit over LRU. The reason is structural: prefix reuse is dominated by the regular pacing of active sessions, making recency unusually predictive. Prefix caching nevertheless introduces new challenges, including heavy-tailed session footprints and highly variable miss costs as attention computation grows with sequence length. We introduce the compute-savings ratio and two offline oracles to quantify these effects. Our results show that effective prefix-cache management should retain recency as its foundation while selectively adding quick demotion for one-hit prefixes, compute-aware partial eviction for expensive misses, and capacity-dependent eviction granularity. We will release the traces and simulator to support future research.

cs.DC↗