User Tools
environment_modules
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
environment_modules [2021/07/06 15:06] root |
environment_modules [2022/01/26 09:52] (current) root |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ===== Environment Modules ===== | ===== Environment Modules ===== | ||
| - | **This page applies only to the new cluster.** | + | Environment modules allow you to control which software (and which version of that software) is available in your environment. For instance, at the time of writing, |
| - | + | ||
| - | 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 | + | |
| - | , 3.6.3, 4.0.5, 4.1.0. When you first log in and try to run R the OS will respond with " | + | |
| < | < | ||
| Line 30: | Line 27: | ||
| </ | </ | ||
| - | There' | + | There' |
| < | < | ||
| Line 62: | Line 59: | ||
| - | ==== Where to Load Modules | + | ==== Where run Module |
| You have several options as to where to use " | You have several options as to where to use " | ||
| Line 93: | Line 90: | ||
| This would generate an error because of the latest version of R already being loaded. | This would generate an error because of the latest version of R already being loaded. | ||
| - | So, in your script you should | + | So, in your script you could unload R before loading the new version. |
| < | < | ||
| Line 151: | Line 148: | ||
| === Python and Perl === | === Python and Perl === | ||
| - | Since various OS level tools need python and perl there are version | + | Since various OS level tools need python and perl there are versions |
| - | * python 2.7.18 for older software that requires python2 | + | |
| - | * python 3.9.5 | + | * python 3.9.5 |
| - | * perl 5.34.0 | + | * perl 5.34.0 |
| The system-wide python is accessible only as " | The system-wide python is accessible only as " | ||
| Line 166: | Line 163: | ||
| === Installing R Packages === | === Installing R Packages === | ||
| - | If you try to install an R package (as an ordinary user) and get a " | + | If you try to install an R package (as an ordinary user) and get a " |
| + | |||
| + | < | ||
| + | * installing to library '/ | ||
| + | Error: ERROR: no permission to install to directory '/ | ||
| + | </ | ||
| + | |||
| + | Then you might need to create the correct directory for R to use for package installation | ||
| ~/ | ~/ | ||
| Where " | Where " | ||
| - | + | ||
| + | You can create the directory from the command line, like this: | ||
| + | |||
| + | < | ||
| + | cd | ||
| + | mkdir -p ~/ | ||
| + | </ | ||
| + | |||
| + | Or you can do it from within R, and then you won't need to know any details like the specific version number - the R program that you have started will fill them in for you: | ||
| + | |||
| + | < | ||
| + | dir.create(Sys.getenv(" | ||
| + | </ | ||
| + | |||
| + | === Rscript and the "# | ||
| + | |||
| + | If you have used | ||
| + | |||
| + | < | ||
| + | # | ||
| + | </ | ||
| + | |||
| + | as the first line of your R scripts so that you can run them just like programs on the old cluster, they will no longer work on the new cluster. This is because there is no interpreter at / | ||
| + | |||
| + | On the new cluster you should load an R module (possibly from within your .bashrc file so that R is always available when you log in), and then use: | ||
| + | |||
| + | < | ||
| + | # | ||
| + | </ | ||
| + | |||
| + | at the top of your R scripts. | ||
| + | |||
environment_modules.1625598379.txt.gz · Last modified: 2021/07/06 15:06 by root
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: Public Domain
