Module environment installation

Description	Installation of Module Environment
Related-course materials	HPC Administration Module1
Authors	Ndomassi TANDO (ndomassi.tando@ird.fr)
Creation Date	20/09/2019
Last Modified Date	20/09/2019

Summary

Definition
Installation
Configuration
Create a personal modulefile repository
Create a module file
Module commands
Links
License

Definition

URL: https://github.com/cea-hpc/modules

Environment Modules: provides dynamic modification of a user’s environment http://modules.sourceforge.net/

It allows the user to switch between several version of a program

Installation:

$ yum install tcl tcl-devel -y
$ wget https://github.com/cea-hpc/modules/releases/download/v4.2.1/modules-4.2.1.tar.gz
$ tar xvfz module-4.2.1.tar.gz
$ cd module-4.2.1
$ ./configure --prefix=/usr/local/modules-4.2.1
$ make
$ make install

Configuration:

Activate the Modules at shell startup:

Enable Modules initialization at shell startup. An easy way to get module function defined and its associated configuration setup at shell startup is to make the initialization scripts part of the system-wide environment setup in /etc/profile.d. To do so, make a link in this directory to the profile scripts that can be found in your Modules installation init directory:

$ ln -s /usr/local/modules-4.2.1/init/profile.sh /etc/profile.d/modules.sh
 $ ln -s /usr/local/modules-4.2.1/init/profile.csh /etc/profile.d/modules.csh

Define module path to enable by default:

Edit /usr/local/modules-4.2.1/modulerc configuration file.

Add there all the modulefile directories you want to activate by default at Modules initialization time.

Add one line mentioning each modulefile directory prefixed by the module use command:

$ module use /usr/local/modules-4.2.1/modulefiles
$ module use /path/to/other/modulefiles

Define the modulefiles to load by default

Edit /usr/local/modules-4.2.1/modulerc configuration file.

Add one line mentioning each modulefile to load prefixed by the module load command:

$ module load foo
$ module load bar

Define a personal module file repository:

Each user can create his personal module file repository

create your own repository

mkdir /home/path_to_my_modulefiles

Add the repository in your shell:

In your /home/user/.bashrc, add the following line:

module use –append /home/path_to_my_modulefiles

Define the module to launch at shell startup:

In your /home/user/.bash_profile, add the following line:

module load program

Create a modulefile:

We are going to split the modulefiles in two categories:

system: corresponding to the system programs

bioinfo: corresponding to the bioinformatics programs

$ mkdir /usr/local/modules-4.2.1/modulefiles/system
$ mkdir /usr/local/modules-4.2.1/modulefiles/bioinfo

For each program you will have to create a directory with the name of the program and a modulefile with the version number.

For example, the bioinformatics software ncbi-blast v 2.4.0+ will have the modulefile 2.4.0+ according to this path:

/usr/local/modules-4.2.1/modulefiles/bioinfo/ncbi-blast/2.4.0+

Module file template

Modulefiles are written in tcl language.

Here is a example for the program program 1.0

 #%Module1.0#####################################################################
       ##
       ##

       ## Define the  "module help …" command below:
       proc ModulesHelp { } {
       global name version prefix man_path
       puts stderr "\t[module-info name] - loads the compiler env variables"
       puts stderr "\tThe following env variables are set:"
       puts stderr "\t\t\$COMPILER, \$COMPILER_VER, \$CC, \$FC"
       puts stderr "\tThe following env variables are modified:"
       puts stderr "\t\t\$PATH, \$MANPATH, \$LD_LIBRARY_PATH"
       }
       ## Define the "module whatis …" comman with the line below
      module-whatis   "loads the [module-info name] environment"
       
        ## if some modules interfers with this one you can use conflict
       conflict bioinfo/program/2.0

        ## Set the version nuber of your program
         set     version      "1.0"

        ## Set the install path of your program
         set     topdir          /usr/local/bioinfo/program-1.0

        ## Define the PATH and other variable
        prepend-path   PATH             $topdir/bin
        prepend-path   LD_LIBRARY_PATH $topdir/lib
        setenv  CC     gcc    # setenv attributes only  one value  to the variable

### Example of modulefile:

 #%Module1.0#####################################################################
    ##
    ## modules modulefile
    ##
    ## modulefiles/modules.  Generated from modules.in by configure.
    ##
    proc ModulesHelp { } {
    global version modroot

    puts stderr "blast/2.4.0+ version 2.4.0 of blast"
     }

     module-whatis   "Loads version 2.4.0 of blast. BLAST finds regions of similarity between biological sequences"
     conflict bioinfo/blast/2.3.0+


    # for Tcl script use only
    set     version         2.4.0+
    set     topdir          /usr/local/ncbi-blast-2.4.0+





    prepend-path    PATH            $topdir/bin
    prepend-path    MANPATH         $topdir/man

Module commands:

See the available modules :

$ module avail

Obtain infos on a particular module:

$ module whatis + module name

Load a module :

$ module load + modulename

List the loaded module :

$ module list

Unload a module :

$ module unload + modulename

Unload all modules :

$ module purge

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).