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Overview

The policies regarding the installation of software

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

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To submit a request to have software installed on the UA HPC/HTC 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.

The Running Jobs page has examples of how to run some of the applications.

 

Module Commands

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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. 

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

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 CommandDescription

$ module avail

 Display all the software and versions installed on the system

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 module list

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$ module avail module_name

Display all installed versions of the software "module_name" 

$ module list

Display the software you have loaded in your environment

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 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

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 module purge

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$ module unload module_nameUnload a specific software package from your environment

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 module unload modulename

$ module purge

 Unload all the software modules from your environment

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$ module help

 Display a help menu for the module command

 

Example for Using Modules

First log in to the login node:
ssh netid@login.hpc.arizona.edu

To display a list of the available packages:
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

Installing Your Own Software

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.

 

Compilers

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 wth module load  mpich2/3.1.4

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

 

El Gato

The principals 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.

 

 

 

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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

Follow the links below for detailed information on using the listed software packages.

Perl

Python

R

Matlab

Anaconda

Installing additional software

To submit a request to have software installed on the UA HPC systems, use our HPC Software Install Request form. (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

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.