We have software installed on our system. Whenever you open a shell, the paths in your shell will point to this software. At the moment (January 2016) we have Ubuntu Precise (12.04) installed, and our software resides here:


The software that is installed on the system might change over time. When never version of packages/libraries are around, we might upgrade the software that is installed there. On the other hand, sometimes never version of software are available, but they do not support all features that we want (yet). In that case, we can install the software in a separate place, and you can load a module which will set your paths such that you can use this newer software.

Accessing the module system

The first thing you need to do is to execute the following line:

. /axiom2/projects/software/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/Modules/3.2.10/init/bash

Now you can access the modules that are available (list them) by using the following command:

module avail 

The current output of that command is:

-------------------------- /axiom2/projects/software/arch/linux-precise/Modules/versions ---------------------------
--------------------- /axiom2/projects/software/arch/linux-precise/Modules/3.2.10/modulefiles ----------------------
dot modules pydpiper/develop-f52c98c quarantine-eeyore
module-git null pydpiper/master-v1.12 R/R-3.2.3
module-info pydpiper/develop-27cd8f18f pydpiper/master-v1.15 use.own

R (versions)

mincLmer is broken in R-3.2.3 because of changes in the underlying LmerTest package.

Potentially fixable by loading the old lmerTest manually within an R session:

library(lmerTest, lib.loc = "/axiom2/projects/software/arch/linux-precise/lib/R/library/")

We currently have R-3.2.3 available as a module. Load it as follows:

module load R/R-3.2.3

When you have done that, your paths are set to point to R-3.2.3, and you can type "R" in the command line to use that version

Quarantines and Pydpiper

For information about registration quarantines and pydpiper versions look here: PydPiper at MICe with quarantines