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Table of Contents

Policies

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title	Software

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	Getting Help
	Getting Help
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Overview

The policies regarding the installation of software

is

are on this page. In general, scientific software is installed as requested with the caveats noted in that section.

Installed software

A list of installed software is kept at this page.

Warning

On Ocelote, many libraries like FFTW and MPICH came with the Cluster Manager. As a consequence, they have different naming from the other clusters. For example, module load blas on the older clusters will need to be module load blas/gcc/64. There are frequently versions of these libraries that have several compilation options, for example, blas was created with four different compilers on Ocelote.

Modules

Many popular software packages are installed and available as modules. There may be several versions of a package available.

Installing additional software

To submit a request to have software installed on the UA HPC systems use the HPC Software Install Request form: http://uits.arizona.edu/forms/hpc-software-install-request

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

Using and Installing Python

Follow this link for more information on using Python.

Using and Installing Perl

Follow this link for more information on using Perl.

Modules

Module CommandDescription module

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.

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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 can be seen by clicking the link below, but may not be as current as using the module avail command (more information under Module Commands).

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	Software Resources
	Software Resources
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Module Commands

Tip
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 Command	Description
`$ module avail`	Display all the software and versions installed on the system

module


`$ 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 load modulename


`$ 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 purge Unload all the software modules Unload a specific software package

$ module unload module_name Unload a specific software package from your environment

module unload modulename

$ module purge

Unload all the software modules from your environment

module

GCC is available without loading a module. gcc --version shows that it is 5.2.0. If you also need the GNU Scientific Libraries (gsl), that is available using module load gsl which will get you version 2.1

The Intel Compiler suite 2016 is available in both 32 and 64 bit versions. The math kernel libraries (mkl) are provided as separate modules, also in 32 and 64 bit versions.

MPI compilers. There are more choices now so pay attention.

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 compilers are available with more detailed options for gcc, intel and open64. Again use module avail for the appropriate choices.

AVX2 The new cluster has Intel V3 Haswell processors. A key feature of these is AVX2. Read this Intel document.

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

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$ module help

Display a help menu for the module command

Example for Using Modules

To display a list of the available packages when your logged in to one of the HPC login nodes:

module avail

To load the latest installed version of the "Trinity" software:

module load trinity

To list the software you currently have loaded:

module list

To unload all modules if you want to start over. Logging out will also unload modules.

module purge

Compilers

ICE
There are several compilers available for your use. Remember when you run your code and you need to do a module load, that you use the same version of compiler that the code was originally compiled with.

GCC is available by default. gcc --version shows that it is 4.4.4 That version was installed at cluster installation and has not been updated to maintain consistency between compiling software and subsequently running it. If you also need the GNU Scientific Libraries (gsl), that is available using module load gsl which will get you version 1.15

The Intel 2012 compiler suite is available as a module. module load intel will load the 2012 suite. It is the default for the same reason as gcc. The math kernel libraries (mkl) are provided when you module load intel (any version) - no separate step is required.

The Intel 2013 compiler suite is also available as an optional module. module load intel/2013.5.192 will provide that version if needed.

The latest Intel suite is now available with module load intel/xe.2016.u2. Unlike earlier versions, you do not need to separately load the MPI capable compiler. For detailed information, refer to the Intel documentation:
https://software.intel.com/en-us/articles/intel-parallel-studio-xe-2016-release-notes

MPI compilers

intel-mpi/2012.0.032 is the default version which matches the non-mpi version. Use module load intel-mpi

intel-mpi/2013.5.192 is available by specifying module load intel-mpi/2013.5.192

openmpi version 1.4.4 is available by specifying module load openmpi

mpich2 is available at version 1.4.1p1 by default or you can get version 3.1.4 with module load mpich2/3.1.4

El Gato

The principles are similar for ElGato except that the intel and intel-mpi compilers are only available for the 2013 versions.
openmpi is available both for version 1.6.5 and version 1.8.1
El Gato has a separate web site with easy to follow instructions.

Ocelote

Compilers

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

Compiler	Version	Module Command
Intel	2020.1	`$ module load intel/2020.1`
Intel	2020.4	`$ module load intel/2020.4`
gcc	5.4.0	`$ module load gnu/5.4.0`
gcc	7.3.0	`$ module load gnu7/7.3.0`
gcc	8.3.0	`$ module load gnu8/8.3.0 This one is loaded by default`

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Common Software Packages

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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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