Software on M3

Modules

M3 is a shared computing environment, and uses a modular system to manage software. This system provides an easy mechanism for updating your environment such as the PATH, MANPATH, and LD_LIBRARY_PATH environment variables, so that your environment uses the correct version of software and libraries installed on MASSIVE. This also prevents other users installing software that may intefere with your personal software installs. You can find a list of our installed modules here.

There are some useful commands to know when using modules.

# You can see what modules we have by using module avail
module avail <software-name>

# To use a module
module load <module-name>

# You can see which modules are already loaded into your environment
module list

# To learn more about a particular module
module show <module-name>

# To stop using a module
module unload <module-name>

# To stop using all loaded modules
module purge

Requesting an install

If you require additional software please email help@massive.org.au with the following details:

  • software

  • version

  • URL for download

  • urgency

  • if there are any licensing restrictions we need to impose

Containers and Docker on M3

Many fields are beginning to distribute fully self contained pieces of software in a container format with Docker. Unfortunately Docker is unsuited as a container format for shared user systems, however it is relatively easy to convert most Docker containers for scientific work flows to the Singularity format. If you wish to run software based on a Docker container, please email help@massive.org.au and let us know where we can obtain the container and we will be happy to convert it for you.

Python and conda on M3

While there are Python modules installed on MASSIVE, you are unable to update or install your own Python packages into them. This means it is usually best practice to use a conda or virtual environment to run Python on M3. Learn more about Python best practices at Running Python and conda on M3.

Software for the Monash Bioinformatics Platform (MBP)

The Monash Bioinformatics Platform (MBP) maintains a software stack on M3. For more information, see the Bioinformatics community page.

Software Deprecation: Java

30 September 2020

Please be advised of upcoming changes to the Java software modules on the system.

On Thursday, the 15th of October, 2020, we will be removing these two java software modules:

  • java/1.7.0_67

  • java/1.8.0_77

This change is necessary as critical security vulnerabilities are present in these two versions of Java.

In their place, please use:

  • java/openjdk-1.8.0_242

  • java/openjdk-1.14.02

This change requires updating the java version that underpins the following 26 specific versions of software modules:

Module Name

Version/s

beagle

2.1.2 3.1.2

fastqc

0.11.7

gatk

3.4 3.7 4.0.1.1 4.0.11.0 4.1.2.0

gem

3.3

juicer

1.6.2

mauve

20150213

maven

3.3.9

nighres

1.1.0b1

nilearn

0.6.2

picard

2.9.2 2.19.0

R

3.5.1 3.5.2-openblas 3.5.3-mkl 3.6.0-mkl 3.6.2-mkl 4.0.0-openblas

snpeff

4.3t

swig

3.0.12 4.0.1

xnat-desktop

1.0.40

Ahead of the removal of these older java modules, on October 8, 2020 (Thursday), these modules will be updated to use java/openjdk-1.8.0_242. As the difference of this java is the patch number (from the old _77 to the updated _242), we do not expect this to affect the correct operation of these modules. We have conducted simple tests to ensure that the commands for each of these modules work under the patched java.

Please advise us if there are any issues: help@massive.org.au