Creating local module directory

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Introduction

You can use your own custom modules to setup your environment to run programs that you have installed yourself. This tutorial will guide you through creating a custom module directory, adding versioned modules for programs, and automatically having these modules available to you upon login. The tutorial will assume you will be managing a set of modules for a whole group, though it is equally applicable to managing a personal set of modules.

Please note that on Euler, we are using environment modules in the old software stack and LMOD modules in the new software stack. On Leonhard we are using LMOD modules. When extending the centrally provided modules, please make sure that you use the correct module type for your own modules.

Extending the old software stack on Euler (environment modules)

You need to decide on the top-level directory (we will use the placeholder __TLD__ for the examples) in which to store the module files. You need to create the directory and set the user and group ownership:

[sfux@eu-login-01-ng ~]$ cd __TLD__
[sfux@eu-login-01-ng __TLD__]$ mkdir modules
[sfux@eu-login-01-ng __TLD__]$ chown sfux:sfux-group modules

Here you would need to replace sfux and sfux-group with your account name and personal group (or any other IAM group that is suitable for this purpose).

Now you need to let the module command know about your custom directory. Add the following line to your $HOME/.bash_profile file in case you are the only person using the additional modules. Or you can create a script that can be sourced in case multiple people use the additional modules.

module use __TLD__/modules

Extending the LMOD module hierarchy with local modules

Extending the LMOD module hierarchy is a bit more complex than extending a system of environment modules without hierarchy.

Euler

As described above, you would need to create a top level directory for your modules first (later we refer to this directory as __TLD__). Then download the local_modules.tar.gz file and untar it in your top level directory. This will provide the skeleton of directories for the module hierarchy:

[sfux@eu-login-12 my_modules]$ tar -xzvf local_modules.tar.gz
Compiler/
Compiler/gcc/
Compiler/gcc/8.2.0/
Compiler/gcc/8.2.0/openmpi/
Compiler/gcc/8.2.0/openmpi/3.0.1.lua
Compiler/gcc/8.2.0/openmpi/4.0.2.lua
Compiler/gcc/4.8.5/
Compiler/gcc/4.8.5/openmpi/
Compiler/gcc/4.8.5/openmpi/3.0.1.lua
Compiler/gcc/4.8.5/openmpi/4.0.2.lua
Compiler/gcc/6.3.0/
Compiler/gcc/6.3.0/openmpi/
Compiler/gcc/6.3.0/openmpi/3.0.1.lua
Compiler/gcc/6.3.0/openmpi/4.0.2.lua
Compiler/intel/
Compiler/intel/18.0.1/
Compiler/intel/18.0.1/openmpi/
Compiler/intel/18.0.1/openmpi/3.0.1.lua
Core/
Core/gcc/
Core/gcc/4.8.5.lua
Core/gcc/8.2.0.lua
Core/gcc/6.3.0.lua
Core/intel/
Core/intel/2018.1.lua
Core/intel/18.0.1.lua
MPI/
MPI/openmpi/
MPI/openmpi/3.0.1/
MPI/openmpi/3.0.1/gcc/
MPI/openmpi/3.0.1/gcc/8.2.0/
MPI/openmpi/3.0.1/gcc/4.8.5/
MPI/openmpi/3.0.1/gcc/6.3.0/
MPI/openmpi/3.0.1/intel/
MPI/openmpi/3.0.1/intel/18.0.1/
MPI/openmpi/4.0.2/
MPI/openmpi/4.0.2/gcc/
MPI/openmpi/4.0.2/gcc/8.2.0/
MPI/openmpi/4.0.2/gcc/4.8.5/
MPI/openmpi/4.0.2/gcc/6.3.0/
MPI/openmpi/4.0.2/intel/
MPI/openmpi/4.0.2/intel/18.0.1/

Now you can start to add your self created modules into the hierarchy depending on what compiler/MPI library they depend on.

  • Core layer: module files for software that does not depend on a centrally provided compiler or MPI library (self-contained binary release containing required runtime libraries, often commercial software like MATLAB, Ansys, Comsol, etc., or compilers themselves)
  • Compiler layer: modules for software that depends on a compiler but not on an MPI library
  • MPI layer: modules for software that depends on a particular compiler and MPI library

In order to use the local modules, you would need to use the following instructions:

  • Login to Euler
  • Change to the new software stack, using the command env2lmod
  • export MY_MODULE_PATH_ROOT=__TLD__
  • module use $MY_MODULE_PATH_ROOT/Core

Please note that in the third step, __TLD__ needs to be replaced with the path to the top level directory of your local modules.

Leonhard

This is work in progress and not yet documented.

LMOD cache

LMOD uses a local cache to speed up module avail and module spider queries. Therefore if a new module file is created, you cannot immediately see it with module avail as it takes a while until the cache is refreshed, but you can already load it with module load, because for loading a module the cache is not used to find the module.

If you would like to test a newly created module, then you can either remove the current cache files in

$HOME/.lmod.d/.cache

or you can use the option of the module command to bypass the cache:

module avail --ignore_cache

Example module files

Environment modules

For each software that you would like to create a module for, create a directory in the modules directory. This directory then contains the file whose name is the version number. In this example, we use PROGRAM as placeholder and 1.0 as version. The module file would therefore be stored in __TLD__/modules/PROGRAM and have the name 1.0

#%Module1.0
module-whatis "This is my software PROGRAM version 1.0"
set helpmsg "PROGRAM is used used to achieve the following task ..."
set topdir "__TLD__/apps/PROGRAM/1.0"
setenv IMPORTANT_VARIABLE "Some string"
prepend-path PATH $topdir/bin
prepend-path LD_LIBRARY_PATH $topdir/lib64
prepend-path C_INCLUDE_PATH $topdir/include

LMOD modules

For each software that you would like to create a module for, create a directory in the modules directory. This directory then contains the file whose name is the version number followed by the ending .lua. In this example, we use PROGRAM as placeholder and 1.0 as version. The module file would therefore be stored in __TLD__/modules/PROGRAM and have the name 1.0.lua

 
 -- -*- lua -*-
 -- 
 -- Any sort of comment can be put here
 --
 --
 whatis([[Name : This is my software PROGRAM version 1.0]])
 help([[PROGRAM is used to achieve the following task ...]])
 setenv("IMPORTANT_VARIABLE", "Some string")
 prepend_path("PATH", "__TLD__/apps/PROGRAM/1.0/bin")
 prepend_path("LD_LIBRARY_PATH", "__TLD__/apps/PROGRAM/1.0/lib64")
 prepend_path("C_INCLUDE_PATH", "__TLD__/apps/PROGRAM/1.0/include")