Tutorials required cluster setup¶
This page describes the HPC/Slurm setup needed to follow along in our HPC (=cluster computing) kickstart courses. The target audience of this page is HPC system staff who would like to direct their users to follow along with this course. What is on this page is not actual “requirements” but “if you don’t match this, you will have to tell your users”. Perhaps it could be added to your quick reference.
This course is designed to be a gentle introduction to scaling up from a local workflow to running on a cluster. It is not especially focused on the high performance part but instead the basics and running existing things on a cluster. And just to make it clear: our main lesson isn’t just following our tutorials, but teaching someone how to figure things out on other clusters, too.
Our philosophy for clusters is:
Make everything possible automatic (for example, partition selection, Slurm options). A user should only need to specify what is needed - at least for tutorials.
Standardization is good: don’t break existing standard Slum things, it should be possible to learn “base Slurm” and use it across clusters (even if it’s not the optimal form)
These tutorials/our course will be quite easy to use for users of a cluster which have:
Slurm as the batch system
You can get a shell (likely via ssh)
gitinstalled without needing to load a module
Python 2 or 3 (any version) installed as
pythonwithout needing to load a module.
If you run your own cluster, create a quick reference such as Triton quick reference so that others following tutorials such as ours can quickly translate to your own cluster’s specifics. (Our hope is that all the possible local configuration is on there, so that you can translate it to your site, and that is sufficient to run).
Connection should be possible via ssh. You probably want a cheatsheet and installation help before our course.
Slurm is the workload manager.
Partitions are automatically detected in most cases. We have a
job_submit.lua script that detects these cases, so that for most
--partition never needs to be specified:
Partition is automatically detected based on run time (except for special ones such as debug, interactive, etc).
GPU partition is automatically detected based on
There are no other mandatory Slurm arguments such as account or cluster selection.
seff is installed.
We use this
slurm_tool wrapper, but we don’t require it (but it
might be useful for your users anyway, perhaps this is an opportunity
for joint maintenance):
You use Lmod and it works across all nodes without further setup.
Git: Git is used to clone our examples (and should have network access).
Python: We assume Python is available (version 2 or 3 - we make our examples run on both) without loading a module. Many of our basic examples use this to run simple programs to demonstrate various cluster features without getting deeper into software.
We expect this to be different for everyone. We expect most clusters have at least a home directory (small) and a work space (large and high-performance).
$HOME is the home directory, small and backed up, not for big
research, mounted on all nodes.
$WRKDIR is an environment variable that points to a per-user
scratch directory (large, not backed up, suitable for fast I/O across
We also strongly recommend group-based storage spaces for better data management.