Compilers

MPI compilers

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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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
   ...
   > 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

#!/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."