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Overview

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 ElGato are built with CentOS 7 along with the system libraries, compilers and utilities that are needed for HPC operations. 

Contents

Available Software

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.

Module Commands

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.

Module CommandDescription

$ module avail

 Display all the software and versions installed on the system

$ module avail module_name

Display all installed versions of the software "module_name" 

$ module list

Display the software you have loaded in your environment

$ module what-is module_name

Displays some descriptive information about a specific module

$ module load module_name

Load a software module in your environment
$ module unload module_nameUnload a specific software package from your environment

$ module purge

 Unload all the software modules from your environment

$ module help

 Display a help menu for the module command

Compilers

Puma, Ocelote, and El Gato all run CentOS7 and have the following compilers available:

CompilerVersionModule Command
Intel 2020.1$ module load intel/2020.1
Intel2020.4$ module load intel/2020.4
gcc5.4.0

$ module load gnu/5.4.0

gcc7.3.0$ module load gnu7/7.3.0
gcc8.3.0$ module load gnu8/8.3.0
This one is loaded by default

Common Software Packages

Using Matlab

This page provides information on using Matlab on HPC and diagnosing common problems.

Using and Installing Python

Different versions of Python are available on HPC, both as system modules as well as system software on each compute node. Python 2 is available but is no longer supported by the Python Foundation, so we recommend you use Python 3. Python version 3 requires the python3 command or pip3 to differentiate. It is very different from Python version 2, so do not assume that Python 3 will work for you or that all older modules will work with version 3.

Using and Installing Perl

One of the best things about Perl is the number of packages provided by the user community. Installing packages generally requires root access but that is not a viable solution in the HPC environment.

Using and Customizing R Packages

Create your own custom libraries where you can install and manage packages locally.

Installing Software

While users cannot add or update system software or libraries using tools that require root privileges such as yum, many software packages can be installed locally without needing to be a superuser. Frequently linux packages make use of the "configure, make, make install" method and an example of how to do this is shown under Example Installation on this page.

Installing additional software

To submit a request to have software installed on the UArizona HPC systems, use our HPC Software Install Request form. There is no expected time frame 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

You 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 installing software locally, see our online guide for an example.

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