The policies regarding the installation of software
are on this page. In general, scientific software is installed as requested with the caveats noted in that section
. There are over 100 software applications installed as modules so you should look there before submitting an installation request. As an alternative, you are always welcome to install your own software or other software in your file space.
Puma, Ocelote, and El Gato are built with CentOS 7 along with the system libraries, compilers and utilities that are needed for HPC operations.
Software packages are available as modules and are accessible from the compute nodes of any of our three clusters. They are not available on the login nodes so you will need to be in an interactive session to access them. A list of installed software is kept
on this page
, but may not be as current as using the
module avail command as shown below.
If multiple versions of software are available on the system, the newest is made the default. This means loading a module without specifying the version will select the most recent. We strongly recommend including version information in your module statements. This ensures that you maintain a consistent environment for your analyses in the event of a software upgrade.
To see, access, and get information on individual software packages available on the system, use the module commands detailed below. If you have trouble accessing the module command, see our FAQ section.
|Display all the software and versions installed on the system|
|Display all installed versions of the software "module_name"|
|Display the software you have loaded in your environment|
|Displays some descriptive information about a specific module|
|Load a software module in your environment|
|Unload a specific software package from your environment|
|Unload all the software modules from your environment|
|Display a help menu for the module command|
Puma, Ocelote, and El Gato all run CentOS7 and have the following compilers available:
Common Software Packages
Follow the links below for detailed information on using the listed software packages.
Installing additional software
To submit a request to have software installed on the UA HPC systems, use
. (This link might be under construction, so send an email to hpc-consult) There is no expected timeframe for how long it takes to install software
, there are many variables that determine this. If you haven't heard back in a week, it is reasonable for you to follow up
with a support ticket
may also install software packages into
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.
For information on
Using and Customizing Perl
Follow this link for more information on using Perl.
Using and Customizing Python
Follow this link for more information on using Python.
Using and Customizing R
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"
- GCC 5.4.0: "module load gnu"
- GCC 8.3.0: "module load gnu8"
- LLVM 5.0.1" "module load llvm5"
- There are standard Red Hat versions of mpich, mvapich, mvapich2 and openmpi. Some extra options are invoked when you load one - use module avail to see the specific name.
- The same four MPI are available with more detailed options for gcc, intel and open64. Again use module avail for the appropriate choices.
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
installing software locally, see our online guide for an example.