'UNSW - Science

UNSW - Science - HPC

Frequently Asked Questions about Software

As well as on this FAQ page the individual software pages provides information about the software installed on the clusters.

How do I choose which version of software I use?

To select a specific version of a piece of software you can use the module command. This allow you to choose between different installed versions of software.

How do I request the installation or upgrade of a piece of software? 

If you wish to have a new piece of software installed or software that is already installed upgraded please send an email to the UNSW IT Servicedesk (ITServiceCentre@unsw.edu.au) from your UNSW email account with details of what software change you require and the cluster that you would like it changed on.

Can I install software myself to test it before requesting that it be installed on the system? 

If you wish to try a new piece of software before requesting it to be installed for every cluster user you can install it in your cluster home drive for yourself by following the instructions on the installing software for yourself page.

What can I do when Java tells me that there is not enough space?

This happens because the default memory alllocation for Java is too small for you. To use more memory instead type
java -Xmx1g or export _JAVA_OPTIONS=-Xmx1g and run Java normally.

I normally use the graphical version of Matlab on Windows how can I start using using Matlab on a cluster?

The underlying version of Matlab installed on the clusters is essentially the same as the version of Matlab you use on your Windows machine although you may need to use the module command to select the version of Matlab that you wish to use. You will then need to save the commands that you want to run in Matlab as a batch file. Further information on the specifics of using Matlab on the clusters is available on the Matlab software page.

Is it possible to use the graphical (GUI) version of Matlab or other software on a cluster?

Yes it is possible to run the graphical version of the software installed on the cluster by starting an interactive job after starting a graphical session.

What are the Boost C++ libraries?

The Boost libraries are a broad collection of C++ libraries. More information is available at www.boost.org.

What are the advantages of using the Intel Compilers or Libraries?

More information about exactly what is contained in the Intel Compilers and Modiles can be found on the Intel software page. Apart from providing functions that are not available in the GNU compilers the main advantage of the Intel package is that the code has been optimised by Intel for running on each different Intel CPU chipset.

I requested 2Gb of memory for my simple Matlab job but I get an 'Out of Memory' error message?

By default when MATLAB is started it will launch a Java virtual machine (JVM) as some functions in MATLAB require the JVM even though many do not. Recent versions of glibc have a new method for allocating memory on multicore machines. The result is that the new glibc causes multithreaded code (such as the JVM) to request a larger virtual address space than previously with older versions of glibc.

If the subset of MATLAB used by your code does not require the JVM, then you may be able to disable the JVM with the MATLAB option -nojvm and keep your job under 2gb otherwise you will need to increase the value of vmem to at least 4gb. If you are using Matlab 2014b then you should request at least 6gb (for reference the Matlab 2014b benchmark requires at least 8gb of memory to run).

Why does SAS sometimes open in graphical mode and sometimes open in text mode? 

By default when you start SAS on the cluster it will try to open in graphical mode unless you use the "-nodms" flag. When you use SAS to run a program from the command line or in a job script it will assume the "-nodms" flag and open in text mode.

Why do my SAS jobs run out of space? 

By default SAS uses /tmp to store working files. However when you use a cluster node the /tmp directory is quite small and can be easily filled up as opposed to the directory $TMPDIR which has much more space. The SAS page has information about how to tell SAS to use $TMPDIR via the -work flag.

How do I load or install extra Stata commands? 

For information on how to load extra Stata commands, visit the Stata information page.