BRC Cluster Workshop

User Tools

Site Tools

Trace:
update_2021_overview

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
update_2021_overview [2021/06/18 10:28]
root 		update_2021_overview [2021/12/14 17:18] (current)
root
Line 1: Line 1:
 ===== Update 2021 Overview ===== ===== Update 2021 Overview =====
  
-The cluster is being updated to Ubuntu 20.04. Along with the OS update comes several changes to the way the cluster works. This page summarizes those changes. Workshops will be held in June and July of 2021 to discuss these changes in detail. +The cluster is being updated to Ubuntu 20.04. Along with the OS update comes several changes to the way the cluster works. This page summarizes those changes. Workshops were held in June and July of 2021 to discuss these changes in detail. 
  
 Rather than shutting the cluster down and doing the upgrade in one swell foop, we are providing a new cluster (with a new login node) already upgraded to Ubuntu 20.04 "Focal Fossa". You can move to the new cluster when it is convenient (although you will have to move in the near future - defined as the next 3-4 months). Rather than shutting the cluster down and doing the upgrade in one swell foop, we are providing a new cluster (with a new login node) already upgraded to Ubuntu 20.04 "Focal Fossa". You can move to the new cluster when it is convenient (although you will have to move in the near future - defined as the next 3-4 months).
  
-The new cluster currently has 6 brand new compute nodes to which you can submit jobs using slurm as usual. These 6 nodes each have:+** From September 6th no new jobs will be allowed on the old cluster. Jobs which are already running on that date will be allowed to continue running, but the old cluster now has a 30-day time limit on all queues. ** 
 + 
 +Most of the old cluster nodes have now been moved to the new cluster. The new cluster includes 6 brand new compute nodes to which you can submit jobs using slurm as usual. These 6 nodes each have:
    
  
Line 34: Line 36:
  
 So, you should be more careful in specifying how many cores your job needs. See the "-c" or "--cpus-per-task" option to sbatch. So, you should be more careful in specifying how many cores your job needs. See the "-c" or "--cpus-per-task" option to sbatch.
 +
 +See [[Enforcing Core Counts]] for more details.
  
 === Enforcing Memory Allocation === === Enforcing Memory Allocation ===
Line 44: Line 48:
 You can change the amount of memory your job is allocated using either the "--mem" option, or the "--mem-per-cpu" option on sbatch. You can change the amount of memory your job is allocated using either the "--mem" option, or the "--mem-per-cpu" option on sbatch.
  
 +See [[Enforcing Memory Allocation]] for more details.
  
 ==== Environment Modules ==== ==== Environment Modules ====
  
-Environment modules allow you to control which software (and which version of that software) is available in your environment. For instance the new cluster has 4 different version of standard R installed: 3.5.3+Environment modules allow you to control which software (and which version of that software) is available in your environment. For instance the new cluster has 4 different versions of standard R installed: 3.5.3
 , 3.6.3, 4.0.5, 4.1.0. When you first log in and try to run R the OS will respond with "command not found". To activate R in your environment you would type: , 3.6.3, 4.0.5, 4.1.0. When you first log in and try to run R the OS will respond with "command not found". To activate R in your environment you would type:
  
Line 54: Line 59:
 </code> </code>
  
-That would then give you access to the most recent version of R available (4.1.0 in this case). +See [[Environment Modules]] for more details.
- +
-To use a different version you would have typed something like: +
- +
-<code> +
-module add R/3.6.3 +
-</code> +
- +
-To get a list of all available software you can type: +
- +
-<code> +
-module avail +
-</code> +
- +
-To get a full list of module commands: +
- +
-<code> +
-module --help +
-</code> +
- +
-There's a shorthand version of the module command: **ml**. To load a module you can use just: +
- +
-<code> +
-ml fastp +
-</code> +
- +
-to, for instance, load the fastp program. +
- +
-You can also issue the other module commands using ml: +
- +
-<code> +
-ml avail +
-ml list +
-ml purge +
-... +
-</code> +
- +
-More information about environment modules can be found here: https://modules.readthedocs.io/en/latest/+
  
 ==== Connecting to the Updated Cluster ==== ==== Connecting to the Updated Cluster ====
update_2021_overview.1624026489.txt.gz · Last modified: 2021/06/18 10:28 by root

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: Public Domain
Public Domain Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki