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arXiv · 2101.06737

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

Jamie J. Alnasir
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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.

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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

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