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RSModules

The RSModules package is a tool to help you to modify your environment by using modulefiles.
A modulefile contains all the settings needed to configure your shell to be able to use a certain application. A modulefile can modify environment variables, execute commands or even load other modules for dependencies.

You modify your environment $PATH, $LD_LIBRARY_PATH, $PYTHONPATH, $PERL5LIB, ... by loading and/or unloading modules.
You don't have to worry about manually modifying your $PATH or other environment variables when installing (multiple versions of) a package.
The moment you need a version or a package, just load the module.

The philosophy behind RSModules is to provide module implementation where speed is important and which is very easy to setup and administer.

Table of Contents

  1. Example
  2. Features
  3. Installation
  1. Modulefiles
  1. Using from perl
  2. Using from python
  3. PAQ

Example

An example says more than a thousand words:

[user@awesome ~]$ echo $PATH
/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
[user@awesome ~]$ which perl
/usr/bin/perl
[user@awesome ~]$ module av perl

  Module name | Description
              |                     
  perl/5.10.1 | 
D perl/5.14.1 | Perl 5.14.1 is a highly capable, feature-rich programming language with over 29 years of development.
  perl/5.8.9  | 


  * D means that the module is set as the default module.
  * Loaded modules are printed in bold.

[user@awesome ~]$ module load perl
[user@awesome ~]$ which perl
/usr/local/perl/5.14.1/bin/perl
[user@awesome ~]$ echo $PATH
/usr/local/perl/5.14.1/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
[user@awesome ~]$

Features

  • module available [--default] [--deprecated] [--regex][search string(s)] Shows all the (default, deprecated) modules or the modules that match the search strings.
  • module info [(partial)modulename] [(partial)modulename] [...] Shows info about the requested module(s).
  • module load [(partial)modulename] [(partial)modulename] [...] Loads the requested modules.
  • module switch [(partial)modulename from] [(partial)modulename to] Switch between the requested modules.
  • module unload [(partial)modulename] [(partial)modulename] [...] Unloads the requested modules.
  • module purge Unloads all loaded modules.
  • module refurbish Unloads all loaded modules and reloads all autoloaded modules
  • module refresh Reloads all loaded modules.
  • module undo Undo previous load/unload/switch/purge actions
  • module list Shows a list of all the loaded modules.
  • module autoload append|prepend|remove|list|purge [modulename(s)] Manages the auto loading of modules by adding them to your startup scripts.
  • module delete [(partial)modulename(s)] Deletes one or more modulefiles. But only if you have the permissions to do so.
  • module readme [(partial)modulename] Looks for a manpage or README file in the module installation folder and displays the contents of this file.
  • module cd [(partial)modulename] Changes your current working directory to the module installation folder. When you don't provide a modulename the working directory is changed to the module installation folder of the last loaded module.
  • module edit [(partial)modulename] Opens the modulefile in your $EDITOR or if this variable is not present in vi -e.
  • The output is not redirected to stderr, but to stdout. So you are able to use grep / rg on the output and it doesn't trigger errors in pipelines.
  • RSModules is fast because it's written in a compiled language and it is using cache files for listing the modules.
  • By using module info, users can easily discover what a module provides and how they use the software that is bundled with the module.
  • The RSModules binary has no dependencies. RSModules works on linux and macOS.
[user@awesome ~]$ ldd rsmodules
	not a dynamic executable
[user@awesome ~]$ file rsmodules
rsmodules: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, BuildID[sha1]=d46b88517c5a31aa8241b8cac1dd48f96c04d26c, stripped
[user@awesome ~]$
  • Support for bash, zsh, tcsh, csh, perl and python.
  • Tabcompletion support for bash, tcsh and csh.

Installation

Manual installation

RSModules has a few configuration options which are located in the setup scripts.

  • $RSMODULES_INSTALL_DIR: the environment variable points to the location where rsmodules is installed
  • $MODULEPATH: the environment variable that contains a : separated list of folders where module files can be found.

The scripts setup_rsmodules.sh and setup_rsmodules.sh need to be sourced when the user logs in. You either symlink these in /etc/profile.d/ or source them in the users init scripts (.bashrc, .cshrc, .zshrc, ...)

After you have added modulefiles, don't forget to update the module cache by running the command: update_modules_cache

In case you want to use RSModules inside your python or perl scripts, add the $RSMODULES_INSTALL_DIR to the $PYTHONPAH and/or $PERL5LIB environment variable(s). But this shouldn't be needed as the setup_rsmodules.(c)sh scripts do this for you.

Automatic installation

RSModules has a simple installation wizard.

  • First of all make sure that the environment variables $RSMODULES_INSTALL_DIR and $MODULEPATH are not set.
  • Then run the rsmodules command and the installation wizard will guide you around.

Depending on your permissions rsmodules will be either installed in your home directory or system wide.

The wizard sets $RSMODULES_INSTALL_DIR and $MODULEPATH in the setup_rsmodules.(c)sh files. For the root user these files will be symlinked in /etc/profile.d/. For non root users these files will be sourced from your .bashrc, .cshrc. On the next login the module command will be available

A dummy module will be created to help you around.

After you have added modulefiles, don't forget to update the module cache by running the command: update_modules_cache

Compiling from source

First you'll have to install Rust on your system:

[user@awesome ~]$ curl https://sh.rustup.rs -sSf | sh

Now run the following command in the root of the project:

[user@awesome ~]$ cargo build --release

The rsmodules binary can be found in the target/release/ folder.

Or you can create a distributable .tar.gz by running:

[user@awesome ~]$ ./create_dist.sh

The resulting .tar.gz file can be found in the releases/ folder.

Modulefiles

Modulefiles are very simple scripts. They are based on the rhai [https://github.com/jonathandturner/rhai#rhai-language-guide] scripting syntax.

Next to the default rhai syntax, the following functions are available:

  • setenv("variable","value");
  • getenv("variable");
  • unsetenv("variable");
  • prepend_path("variable","value");
  • append_path("variable","value");
  • remove_path("variable","value");
  • system("command");
  • system_unload("command"); This command is only executed when unloading a module
  • load("modulename");
  • unload("modulename");
  • conflict("modulename");
  • description("module description");
  • set_alias("name","value");
  • is_loaded("modulename");
  • source("shelltype", "/path/to/filename.shell-extension");
  • add_bin_to_info("binary_name");
  • deprecated("YYYY-MM-DD");

Note:

When using add_bin_to_info (you can add it multiple times to your scripts), module info <modulename> will only show the binaries that are added with this function, it will ignore the binaries in your PATH variables.

deprecated should be used when you plan to remove a module. This will warn the user that this module will be removed after the given date in YYYY-MM-DD format. After this date the module file will still exist but wont be usable anymore, it's your task to remove it (you can find deprecated modules by running: module av -R the modules marked with an 'R' in front of them are the ones you are looking for). Don't forget to run module cache make or update_modules_cache when you deprecated a module by adding the deprecated function call to the modulefile.

Example modulefile

description("InterProScan is the software package that allows sequences to be scanned against InterPro's signatures");
description("");
description("InterPro is a resource that provides functional analysis of protein sequences by classifying them into");
description("families and predicting the presence of domains and important sites. To classify proteins in this way,");
description("InterPro uses predictive models, known as signatures, provided by several different databases,");
description("(referred to as member databases), that make up the InterPro consortium.");

conflict("iprscan");

load("java/1.8.0_60");
load("perl");
load("python/2.7.2");
load("EMBOSS");
load("gcc");

prepend_path("PATH","/software/shared/apps/iprscan/5.23-62/bin/");
prepend_path("PATH","/software/shared/apps/iprscan/5.23-62/");

system("mkdir -p /scratch/tmp/iprscan_logs");
system("mkdir -p /scratch/tmp/iprscan_tmp");

system("source activate myprogram");
system_unload("source deactivate");

source("bash", "/software/shared/apps/iprscan/5.23-64/env.sh");
source("zsh", "/software/shared/apps/iprscan/5.23-64/env.zsh");

var x = getenv("SOMEVAR");

if x == "OKAY" {
    load("abyss");
} else {
    load("R");
    unsetenv("SOMEVAR");
}

if is_loaded("blast/2.2.17") {
    load("blast/2.5.0+");
}
note: As the time of writing rhai scripts don't support tabs, only spaces.

After you have created new modulefiles, don't forget to update the module cache by running the command:

[user@awesome ~]$ module cache make

You can also have a progress bar while updating the cache.

[user@awesome ~] update_modules_cache

Using from perl

When you source the file setup_rsmodules.(c)sh there is a path added to your $PERL5LIB environment variable. This gives you the possibility to use rsmodules from inside your perl scripts.

#!/usr/bin/perl

use rsmodules;

module("load blast");

print($ENV{"LOADEDMODULES"} . "\n");

module("list");

# this var is set with setenv("SOMEVAR","value") in the modulescript
print($ENV{"SOMEVAR"});

Using from python

When you source the file setup_rsmodules.(c)sh there is a path added to your $PYTHONPATH environment variable. This gives you the possibility to use rsmodules from inside your python scripts.

import os
from rsmodules import module

module("load","blast")

print(os.environ["LOADEDMODULES"])

module("list","")

#this variable is declared in a module file with setenv("SOMEVAR","value")
print(os.environ['SOMEVAR'])

PAQ

What does PAQ mean ?

Possibly asked questions :)

Why RSModules while tclmodules/cmodules and Lmod are around?

A couple of years ago I ran into some issues with tcl/c modules. Because I was annoyed by the fact that everything was printed to stderr, I started writing my own implementation of modules in C. When 90% of the features where ready (90% as in the other 10% takes also another 90% time ;) ). I found Lmod, so I stopped working on my little sideproject and started to try Lmod.

It was more or less decided to switch to Lmod. Until I was looking for a new sideproject to learn the programming language Rust. In no time I had 90% ;) of the code ready + some features our users have been asking for. (a way to see which executables a module provides, a short description in the module av output).

And that's how RSmodules was born.

Does this mean that tcl/c modules or Lmod are bad projects ?

Absolutely not ! Feel free to use whatever that suits your needs.

Why then didn't you contribute to these projects instead ?

I needed a side project to learn Rust and the project got a bit out of hand :)

What does the RS in RSModules mean ?

RS stands for rust

How fast is RSModules ?

[user@awesome ~]$ time module cache make

/software/shared/rsmodulefiles/ was succesfully indexed.

  * Total number of modules: 927
  * Number of default (D) modules: 151

real	0m4.781s
user	0m0.062s
sys   	0m0.168s
[user@awesome ~]$
The module files in the above example are located on a network share

Can I convert my tcl modulefiles to rhai modulefiles ?

Robert McLay, the Lmod developer, was so kind to write a script to translate tcl modulefiles to lua modulefiles. I have modified his script to output rhai modulefiles instead. So to answer the question, yes its possible. But its not possible to provide tcl module files in your $MODULEPATH and let RSModules translate them on the fly.

Will you add tabcompletion for zsh ?

Maybe, if I ever figure out how it works, feel free to contribute.

What happens when I load a module that is already loaded ?

The module is first unloaded and then reloaded again.

What happens when I load a different version of an already loaded module ?

The module is replaced with the newly loaded module:

[user@awesome ~]$ module load python
[user@awesome ~]$ module list

  Currently loaded modules:

  * python/3.5.1

[user@awesome ~]$ module load python/2.7.2

  The previously loaded module python/3.5.1 has been replaced with python/2.7.2

[user@awesome ~]$ module list

  Currently loaded modules:

  * python/2.7.2

[user@awesome ~]$

This is basicly the same as the module switch [from modulename] [to modulename] command.

I want to autoload some modules everytime I login. What do I need to do ?

The command module autoload is what you are looking for.

I want to remove a module through a script, but I don't want the interactive mode.

Call rsmodules directly and supply 'noshell' as the shell, example:

[user@awesome ~]$ /usr/local/bin/rsmodules noshell delete module/1.0 module/2.1
Removal of module/1.0 module/2.1 was succesful. Don't forget to update the module cache.
[user@awesome ~]$