Introduction: The workshop session will provide a quick tour covering high-level concepts, commands and processes for using Linux and HPC on our Beartooth cluster. It will cover enough to allow an attendee to access the cluster and to perform analysis associated with this workshop.
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A reservation can be considered a temporary partition.
It is a set of compute nodes reserved for a period of time for a set of users/projects, who get priority use.
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Important Dates:
After the 17th of June this reservation will stop and you will drop down to general usage if you have another Beartooth project.
The project itself will be removed after the 24th of June. You will not be able to use/access it. Anything you require please copy out of the project.
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The Beartooth Shell Access opens up a new browser tab that is running on a login node. Do not run any computation on these.
[<username>@blog2 ~]$The SouthPass Interactive Desktop (terminal) is already running on a compute node.
[<username>@t402 ~]$
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Login Node Policy
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Anything compute-intensive (tasks using significant computational/hardware resources - Ex: using 100% cluster CPU)
Long running tasks (over 10 min)
Any collection of a large # of tasks resulting in a similar hardware footprint to actions mentioned previously.
Not sure? Use
sallocto be on the safe side. This will be covered later.
Ex:salloc –-account=arccanetrain -–time 40:00See more on ARCC’s Login Node Policy here
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Since the cluster has to cater for everyone we can not provide a simple desktop environment that provides everything.
Instead we provide modules that a user will load that configures their environment for their particular needs within a session.
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Can be copied from: /project/biocompworkshop/arcc_notes
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07 07 Summary and Next Steps
Run over the goals we’ve looked at.
Point towards the previous workshops for additional details.
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We’ve covered the following high-level concepts, commands and processes:
What is HPC and what is a cluster - focusing on ARC’s Beartooth cluster.
An introduction to Linux and its File System, and how to navigate around using an Interactive Desktop and/or using the command-line.
Linux command-line commands to view, search, parse, sort text files.
Using vim as a command-line text editor.
Setting up your environment (using modules) to provide R/Python environments.
Accessing compute nodes via a SouthPass Interactive Desktop.
Requesting interactive sessions (from a login node) using
salloc.Setting up a workflow, within a script, that can then be submitted to the Slurm queue using
sbatch, and how to monitor jobs.
Further Assistance:
Everything covered can be found in previous workshops and additional information can be found on our Wiki.
ARCC personnel will be around in-person for the first three days to assist with cluster/Linux related questions and issues.
We will provide virtual support over Thursday/Friday. Submit questions via the Slack channel and these will be passed onto us, and we will endeavor to set up a zoom via our Office Hours.