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Overview

The policies regarding the installation of software

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

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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

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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

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$ module avail

 Display all the software and versions installed on the system

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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 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 unload module_nameUnload a specific software package from your environment

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$ module purge

 Unload all the software modules from your environment

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$ module help

 Display a help menu for the module command

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 Perl

Follow this link for more information on using Perl.

Using and Installing Python

Follow this link for more information on using Python.

Using R Packages

You can install your own R packages which is similar to using virtualenv with Python

  1. Make directory to store packages
    $ mkdir -p ~/R/library
  2. Tell R where the directory is by creating an environment file:
    $ echo 'R_LIBS=~/R/library/' >> ~/.Renviron
  3. For example to install and load the package "ggplot2":
    $ module load R
    $ R
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    > install.packages("ggplot2")
    > library(ggplot2)
  4. After this you'll only need the library command to load your custom package
  5. For more information:
    http://www.r-bloggers.com/installing-r-packages/

Using Matlab

MATLAB performs its own hardware discovery and it might try to access all the cores and the memory of the node even if the full node wasn't allocated. That will result in scheduler killing the job. To prevent that the full Ocelote node of 28 cores and 168GB of memory should be allocated to run a MATLAB job.

Like any other application, MATLAB has to be loaded as a module before you can use it. To see all the installed versions of the MATLAB use command module avail matlab.

The typical procedure for performing calculations on UA HPC systems is to run your program non-interactively on compute nodes. The easiest way to run MATLAB non-interactively is to use input/output redirection. This method uses Linux operators < and > to point MATLAB to the input file and tell where to write the output (see the example script). The other method is to invoke MATLAB from the PBS script and execute specified statement using -r option. For details please refer to the manual page of matlab command:

https://www.mathworks.com/help/matlab/ref/matlablinux.html

Code Block
#!/bin/bash
#PBS -N job_name
#PBS -W group_list=group_name
#PBS -q standard
#PBS -l select=1:ncpus=28:mem=168gb:pcmem=6gb
#PBS -l walltime=01:00:00
#PBS -l cput=28:00:00

cd $PBS_O_WORKDIR

module load matlab

matlab -nodisplay -nosplash < script_name.m > output.txt

The options -nodisplay and -nosplash in the example prevent MATLAB from opening elements of GUI. To view the full list of options for matlab command load the MATLAB module and type matlab -h in Linux prompt, or use the link above to the manual page on MathWorks website."

Spark

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.

Compilers

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MPI compilers

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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.

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  • 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.

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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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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.