Environment Module System Upgrade for Radon and Peregrine1

January 6, 2016
Peregrine1, Radon

The upgrade of the environment module system to Lmod on Peregrine1 and Radon was completed by the afternoon of Wednesday, January 6, 2016. Starting a new SSH session or logging out and back in will update your module system to Lmod - any sessions that were open from before the upgrade will still be using the old module system. If you encounter any issues or have any questions about the new module system please contact us at rcac-help@purdue.edu.

Original:

On Wednesday, January 6, 2016 the environment module system on Peregrine1 and Radon will be upgraded to Lmod. This new system has been in use on the Rice and Snyder clusters since they were put into production. It has also been available as an opt-in service on the other clusters for several months.

What is Lmod?

Lmod is a Lua based environment modules system developed by TACC (Texas Advanced Computing Center). This system is used on TACC clusters such as Stampede and Lonestar. Lmod is also used at several other universities and centers. Lmod offers all the same functionality as the current environment modules system and uses the same commands and syntax. However, Lmod offers new and unique functionality that can be leveraged to offer an easier to use and understand software environment on ITaP clusters.

Will I have to change anything?

No. Lmod offers exactly the same functionality as the current module system. No changes to your job submission scripts will be necessary - all the old commands will still work as they have before. It does, however, offer several new features and new functionality.

What are the new features of Lmod?

At the moment Lmod is mostly a one-for-one replacement of the current environment modules system. In the future, ITaP will expand on the functionality of Lmod to improve usability of our software stack.

One of the most exciting features of Lmod is the spider command. This command allows you to discover software available on the clusters that you might not otherwise find.

For example, finding the bioinformatics software bowtie2 is not easy. This software is not managed by ITaP and is not in the normal software availability. Nonetheless, it is available to the general cluster public if you happen to know how to find it. Lmod makes finding such software much easier:

$ module spider bowtie2

----------------------------------------------------------------------------
  bowtie2:
----------------------------------------------------------------------------
     Versions:
....
        bowtie2/2.2.3

----------------------------------------------------------------------------
  To find detailed information about bowtie2 please enter the full name.
  For example:

     $ module spider bowtie2/2.2.3
----------------------------------------------------------------------------

$ module spider bowtie2/2.2.3

----------------------------------------------------------------------------
  bowtie2: bowtie2/2.2.3
----------------------------------------------------------------------------

    This module can only be loaded through the following modules:

      bioinfo

With this command you can discover that this software is available by first loading the bioinfo module.

One of the other features lmod offers is the ability to prevent software conflicts. Loading multiple MPI libraries or compilers, for example, may result in conflicting commands and libraries being used. Lmod will not allow the accidental loading of multiple, conflicting software simultaneously. For example:

$ module load intel
$ module load pgi

Lmod has detected the following error: You can only have one compiler module loaded at a time.
You already have intel loaded.
To correct the situation, please enter the following command:

  module swap intel pgi/11.8-0

Please submit a consulting ticket if you require additional assistance.

Originally posted: December 3, 2015  4:01pm