Software modules on CentOS 7

Here’s how I did it.

yum install environment-modules -y

On my CentOS 7, this is what I get when I check the package information:

root@beta ~ ## > rpm -qi environment-modules
Name : environment-modules
Version : 3.2.10
Release : 10.el7
Architecture: x86_64
Install Date: Wed 28 Sep 2016 05:08:40 PM CEST
Group : System Environment/Base
Size : 220124
License : GPLv2+
Signature : RSA/SHA256, Wed 25 Nov 2015 03:27:36 PM CET, 
Key ID 24c6a8a7f4a80eb5
Source RPM : environment-modules-3.2.10-10.el7.src.rpm
Build Date : Fri 20 Nov 2015 06:44:07 AM CET
Build Host : worker1.bsys.centos.org
Relocations : (not relocatable)
Packager : CentOS BuildSystem <http://bugs.centos.org>
Vendor : CentOS
URL : http://modules.sourceforge.net/
Summary : Provides dynamic modification of a user's environment
Description :
The Environment Modules package provides 
for the dynamic modification of
a user's environment via modulefiles.

Each modulefile contains the information needed to configure 
the shell for an application. Once the Modules package is 
initialized, the environment can be modified on a per-module 
basis using the module command which interprets modulefiles. 
Typically modulefiles instruct the module command to alter 
or set shell environment variables such as PATH, MANPATH, etc. 
modulefiles may be shared by many users on a system
and users may have their own collection to supplement or 
replace the shared modulefiles.

Modules can be loaded and unloaded dynamically and atomically, 
in an clean fashion. All popular shells are supported, 
including bash, ksh, zsh, sh, csh, tcsh, as well as 
some scripting languages such as perl.

Modules are useful in managing different versions of applications.
Modules can also be bundled into metamodules that will load 
an entire suite of different applications.

NOTE: You will need to get a new shell after installing 
this package to have access to the module alias.

I made a first module as described on the Admin Magazine. Our gcc version is 4.8.5, so I customize the module file for this one.  In my case we “cd” to the default module folders, make a specific folder for the specific type of program, and copy the template

root@beta  ## > cd /usr/share/Modules/modulefiles
root@beta ## > mkdir compilers
root@beta ## > cp modules compilers/gcc-4.8.5

Then we edit the module info (compilers/gcc-4.8.5). The modified version looks like this:

#%Module1.0###################################
##
## modules compilers/gcc-4.8.5
##
## modulefiles/compilers/gcc-4.8.5. Sample gcc module
##
proc ModulesHelp { } {
 global version modroot

puts stderr "compilers/gcc-4.8.5 - sets the Environment for 
      GCC 4.8.5 "
}

module-whatis "Sets the environment for using 
    gcc-4.8.5 (C, Fortran)"

# for Tcl script use only
set topdir /usr/bin/gcc
set version 4.8.5
set sys linux86

setenv CC $topdir/bin/gcc
setenv GCC $topdir/bin/gcc
setenv FC $topdir/bin/gfortran
setenv F77 $topdir/bin/gfortran
setenv F90 $topdir/bin/gfortran
prepend-path PATH $topdir/include
prepend-path PATH $topdir/bin
prepend-path MANPATH $topdir/man
prepend-path LD_LIBRARY_PATH $topdir/lib

Will that be enough? To test it, I log in as a user on the machine and try to load the module:

yo@beta ~ $ > module avail

------------------/usr/share/Modules/modulefiles --------------
compilers/gcc-4.8.5 dot module-git module-info modules null use.own
yo@beta ~ $ > module help compilers/gcc-4.8.5

----------- Module Specific Help for 'compilers/gcc-4.8.5' --------

compilers/gcc-4.8.5 - sets the Environment for GCC 4.8.5 
yo@beta ~ $ > module whatis compilers/gcc-4.8.5 
compilers/gcc-4.8.5 : Sets the environment 
       for using gcc-4.8.5 (C, Fortran)
yo@beta ~ $ > module load compilers/gcc-4.8.5
yo@beta ~ $ > module list
Currently Loaded Modulefiles:
 1) compilers/gcc-4.8.5

So yes, it’s enough. I start creating happily modules and I find out that the most crucial part (as expected) seems to be where is the software compiled, the architecture, and the libraries needed.

If you don’t have clear still what to do with modules or how to handle them, you can check the Confluence page (pay attention to the table of commands on Basic Module Usage) the the FAQ of Sourceforge, the Linux Software Modules page of Illinois University, The Viriginia Tech page or the Michigan University page. Even Wikipedia has a link about it. Or you can google it yourself 🙂

To install it in our SLURM cluster, since we had previously a collection of programs in /usr/local, we only need to rsync the corresponding folder

rsync -av /usr/share/Modules/modulefiles/ 
        $i:/usr/share/Modules/modulefiles/

After that, unfortunately, if you lauch a job that calls module load SLURM gives this error

/var/spool/slurmd/job00682/slurm_script: 
/usr/bin/modulecmd: No such file or directory

But the error has a very easy workaround as found on the confluence wiki

from

#!/bin/bash

to

#!/bin/bash -login

The error, as explained, is due to the use of the bash shell, instead of the SLURM shell.

 

Advertisements

About bitsanddragons

A traveller, an IT professional and a casual writer
This entry was posted in bits, centos, linux, slurm. Bookmark the permalink.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s