The policies regarding the installation of software is on this page. In general, scientific software is installed as requested with the caveats noted in that section.
Ocelote is built on CentOS 6 which is the foundation for all compilers, libraries, and applications. Some workloads need CentOS 7 for its newer kernel. A number of GPU nodes have been reprovisioned with a CentOS 7 image. To access one of these nodes, modify the PBS select statement to include os7=True. Note the upper case T
A list of installed software is kept at this page.
Many popular software packages are installed and available as modules. There may be several versions of a package available.
|Display all the software and versions installed on the system|
|module list||Display the software you have loaded in your environment|
|module load modulename||Load a software module in your environment|
|module purge||Unload all the software modules from your environment|
|module unload modulename|
Unload a specific software package from your environment
|module help||Display a help menu for the module command|
To submit a request to have software installed on the UA HPC systems use the HPC Software Install Request form: https://it.arizona.edu/hpc-software-install-request
There is no expected timeframe for how long it takes to install software. There are many variables. If you haven't heard back in a week, it is reasonable for you to follow up with firstname.lastname@example.org
You can install software packages into your home directories with the space that is allocated to you with your HPC account. However you cannot install software that requires root permission, or use a method like "yum install" that accesses system paths.
Follow this link for detailed information on how to install your own software
Follow this link for more information on using Perl.
Follow this link for more information on using Python.
Follow this link for more information on using R.
Follow this link for more information on using Matlab
Anaconda is available as a module and comes with Glueviz, JupyterLab, Jupyter Notebook, Spyder, Orange and RStudio. It also supports the conda commands for building a personal environment.
Apache Spark is a fast and general-purpose cluster computing system. However it has not been installed for support in a multi-node environment as yet. That functionality is planned for the future. It provides high-level APIs in Java, Scala, Python and R, and an optimized engine that supports general execution graphs. It also supports a rich set of higher-level tools including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Spark Streaming.
There are some simple tests here.
El GatoElGato is now running CentOS 7. The compilers available are:
Intel/2019.3: "module load intel"
For AVX2 support, compile with the -xHOST option. Note that -xHOST alone does not enable aggressive optimization, so compilation with -O3 is also suggested. The -fast flag invokes -xHOST, but should be avoided since it also turns on interprocedural optimization (-ipo), which may cause problems in some instances.
For GNU compilers, AVX support is only available in version 4.6 or later. For AVX support, compile with -mavx