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Linux Environment Modules

The VDI uses the Linux environment modules. The “module” command is available for loading additional software packages into the command line environment.  For more information see: Gadi Environment Modules. When loading modules where the version used matters (e.g. scripts), it’s recommended that you explicitly state which version of each module to load. This will help avoid unexpected surprises if the default version changes when a new version of the module is deployed in the future.

The following are a list of software available using Linux Environment Modules:

Package

Version

PackageVersion

cartopy(py3.7)

0.18.0

igv

2.8.6

cdo 

1.9.8

Jupyterlab(py3.7)

2.1.4

dask(py3.7)

2.19.0

llvm

10.0.0

gcc(8.3.1)Matlab2019b

gdal(py2.7)

gdal(py3.7)

3.0.2 3.1.0

3.0.2 3.1.0

ncl

6.6.2

geos

3.8.0

nco

4.9.2

git

2.24.1

netcdf

4.7.4

4.7.4p

hdf4

4.2.14

hdf5

1.10.5

1.10.5p

proj
ESMF8.0.1

The following Python modules are also available under the Linux environment modules:

Package

Version

PackageVersion

h5py(py3.7)

2.10.0

python-partd1.1.0
mpi4py(py3.7)3.0.3python-pillow7.2.0
netcdf4-python(py3.7)1.5.3python-psutil5.7.0

python3

3.7.4

python-pyshp2.1.0

python-bokeh

2.1.1

python-shapely

1.7.0

python-click7.1.2python-snappy0.5.4
python-cloudpickle1.5.0python-sortedcontainers2.2.2
python-fastparquet0.4.0

python-tables

3.6.1
python-fsspec0.7.4

python-tblib

1.6.0

python-graphviz

0.14

python-thrift0.13.0
python-heapdict1.0.1python-toolz0.10.0
python-jinja22.11.2python-tornado6.0.4
python-locket0.2.0python-typing-extensions3.7.4.2
python-msgpack1.0.0python-zict2.0.0

python-owslib

0.20.0

python2

2.7.17

We also have a more extensive area for python software which will be addressed in NCI's Jupyter and Python software documentation (in dev) .


Software Activation

Some commercial software requires activation of a licence before it can be used. Often this activation process ties the software to the machine that it is running on. This has the following implications in the virtual desktop environment that you need to be aware of:

  • Each time that you start a new desktop session, you are allocated a random node in the desktop pool. Even if you terminate a desktop session and then immediately start a new one, you are not guaranteed to get the same node. Hence, the licensing system may think that you are trying to use the software on another computer and refuse to operate.

  • The desktop session might end while you are not actively using it, e.g. the maximum session lifetime is reached while it is running in the background. In such circumstances, you won’t have an opportunity to deactivate the licence.

  • From time to time we rebuild the nodes upon which the desktops are running. This may cause the licensing system to think that the hardware has changed and is a different computer.

MATLAB

There are various licence activation options offered by MathWorks for MATLAB. Of these, any of the non-network options such as “Standalone Named User” and “Designated Computer” are affected by the activation issues described above. You might be able to deactivate a MATLAB licence without having access to the node it was activated on by visiting the MathsWorks licence centre online. Please contact MathWorks for any licensing queries or issues.

No matter what method you use to run MATLAB, always ensure that you are using the product within the terms of your MathWorks licence agreement.

Login Named User

MathWorks provides an alternative licensing mode which permits you to use an already activated licence on another machine for the duration that the application is running. This avoids the above issues since the licence is not actually being permanently installed on the desktop. Therefore, this is the recommended method for using MATLAB on the virtual desktops if the option is available for your licence.

Before you can use this method for the first time, you must complete the following:

  1. Your licence must have already been activated on another machine (eg. your local workstation) as a “Standalone Named User” type. Note that this option is only available to “Individual” and “Group” licences. Don’t activate a licence for the first time on a virtual desktop.

  2. Enable the “Login Named User” (LNU) option for the licence by visiting the following URL.  For group licences, your licensing administrator may have to complete this procedure for you.
    https://www.mathworks.com/licensecenter/lnu

If you are a member of an academic institution which has a “Total Academic Headcount” (TAH) licence then ignore the above steps.  Simply ask your local MATLAB licence administrator to register your email address.

Then, whenever you want to run MATLAB:

  1. Start the application from the desktop applications menu:

    Alternatively, open a terminal window and enter the following commands:

    $ module load matlab matlab -licmode online
  2. Enter your MathWorks account login details in the following dialog:

Network Licensing

If your organisation has a network based MATLAB licence server, you might be able to use it from the virtual desktops to avoid any activation issues. You will need to contact your local licensing administrator to organise access from the virtual desktop pool.

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