Lmod 8.2.7

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 8
  • Dependencies to run Lmod:
    • lua-filesystem
    • lua-posix
    • lua-term
    • coreutils

Installation

The following procedure is the easiest way to install and configure Lmod V8.2.7 in a cluster.

  1. Install epel-release package and enable all the necessary repositories (epel and PowerTools for Centos 8) and install Lmod.

    $ dnf install epel-release
$ dnf upgrade -y
$ dnf --enablerepo=PowerTools,epel install Lmod

  2. Now, we will add our custom modulefiles path in the Lmod configuration files.

    With the 00-modulepath.sh.

    $ cd /etc/profile.d/
$ nano 00-modulepath.sh

    Go to where it says “export MODULEPATH=”

    • Before the || : add the following :/share/apps/modules/
    • Save the file.

    Your file should look like this:

    [ -z "$MODULEPATH" ] &&
  [ "$(readlink /etc/alternatives/modules.sh)" = "/usr/share/lmod/lmod/init/profile" -o -f /etc/profile.d/z00_lmod.sh ] &&
  export MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/share/apps/modules/ || :

    Now, with the 00-modulepath.csh.

    $ cd /etc/profile.d/
$ nano 00-modulepath.csh

    Go to where it says “setenv MODULEPATH”

    • Add the following at the end of the line :/share/apps/modules/
    • Save the file.

    Your file should look like this:

    if (! $?MODULEPATH && ( `readlink /etc/alternatives/modules.csh` == /usr/share/lmod/lmod/init/cshrc || -f /etc/profile.d/z00_lmod.csh ) ) then
  setenv MODULEPATH /etc/modulefiles:/usr/share/modulefiles:/share/apps/modules/
endif

    Note

    /share/apps/modules/ is our custom location for modules, you need to add in the configuration files your own path.

  3. Now, lets configure one last thing, these are the files needed to load pre-defined modules when an user logs into your cluster:

    $ cd /etc/profile.d/
$ nano z01_StdEnv.sh

    Inside the newly created z01_StdEnv.sh file, add the following:

    if [ -z "$__Init_Default_Modules" ]; then
   export __Init_Default_Modules=1;

   ## ability to predefine elsewhere the default list
   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"StdEnv"}
   export LMOD_SYSTEM_DEFAULT_MODULES
   module --initial_load --no_redirect restore
else
   module refresh
fi

    $ cd /etc/profile.d/
$ nano z01_StdEnv.csh

    Inside the newly created z01_StdEnv.csh file, add the following:

    if ( ! $?__Init_Default_Modules )  then
  setenv __Init_Default_Modules 1
  if ( ! $?LMOD_SYSTEM_DEFAULT_MODULES ) then
    setenv LMOD_SYSTEM_DEFAULT_MODULES "StdEnv"
  endif
  module --initial_load restore
else
  module refresh
endif

  4. We create the StdEnv.lua file, which has the modules that we want to load from the beginning. For this example, we will use SLURM and Munge.

    $ cd /share/apps/modules
$ nano StdEnv.lua

    Inside the newly created StdEnv.lua file, add the following:

    load("slurm","munge")

    Note

    Make sure you already have the modules created, Lmod supports both lua modulefiles and tcl modulefiles.

Lmod Module hierarchy

In this section, we will explain how your modules should be saved in order for Lmod to load them correctly.

  1. First, we go to our custom modulefiles path

    $ cd /share/apps/modules
$ ls
slurm/ munge/ gcc/ StdEnv.lua

    As you can see, all apps have their own directory.

    $ cd slurm/
$ ls
20.02.0

    This is a tcl modulefile, the name is the version of the program.

    $ cd /share/apps/modules/gcc
$ ls
5.4.0.lua

    This is a lua modulefile, as you see, Lmod supports both pretty well.

  2. Conclusion, each app needs its own directory (the directory should have the app’s name). And inside the directory, the modulefiles’ name should be the app’s version.

    Note

    If you make a lua modulefile, you need to add the file extension .lua to the modulefile, if it’s an tcl modulefile, no file extension is needed.

References

Robert McLay - Lmod: A New Environment Module System.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/
Robert McLay - How to use a Software Module hierarchy.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/080_hierarchy.html
Robert McLay - Converting from TCL/C Environment Modules to Lmod.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/073_tmod_to_lmod.html
Robert McLay - Lua Modulefile Functions.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html
Robert McLay - An Introduction to Writing Modulefiles.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/015_writing_modules.html
Robert McLay - How Lmod Picks which Modulefiles to Load.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/060_locating.html
Robert McLay - Providing A Standard Set Of Modules for all Users.
Retrieved May 15, 2020, from https://lmod.readthedocs.io/en/latest/070_standard_modules.html
Packages Search for Linux and Unix - Lmod-8.2.7-1.el8.x86_64.rpm.
Retrieved May 15, 2020, from https://centos.pkgs.org/8/epel-x86_64/Lmod-8.2.7-1.el8.x86_64.rpm.html
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