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 |
|
fastqc |
|
gatk |
|
gem |
|
juicer |
|
mauve |
|
maven |
|
nighres |
|
nilearn |
|
picard |
|
R |
|
snpeff |
|
swig |
|
xnat-desktop |
|
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