Data analysis and visualization

Frequently used packages | License use guidelines

Many data analysis and visualization software packages are freely available for use on CISL-managed resources. These include some developed and supported by NCAR and CISL. The Cheyenne user software and Casper user software web pages list the software environment modules that are already installed on those systems.


Frequently used packages

These are among the more frequently used data analysis and visualization packages available to Casper and Cheyenne users. To request installation of other packages, contact CISL.

  • GrADS – The Grid Analysis and Display System (GrADS) is an interactive desktop tool for visualizing earth science data.
  • IDL – IDL is Interactive Data Language, which is used for data visualization and analysis. Documentation is available here.

MATLAB Toolboxes
Image Processing Toolbox
MATLAB Compiler
Mapping Toolbox
Neural Network Toolbox
Optimization Toolbox
Parallel Computing Toolbox
Signal Processing Toolbox
Statistics Toolbox
Wavelet Toolbox

  • MATLAB – This is a high-level language and interactive environment for data analysis, statistics, and image processing. Several MATLAB toolboxes are provided (list at right). See the MathWorks web site for documentation and note the information below about Octave, an alternative to MATLAB.
  • NCL – NCAR Command Language is an interpreted language that CISL designed for scientific data analysis and visualization. See NCL for how to use this in the Cheyenne environment.
  • ParaView* – This is an open-source application for building visualizations and analyzing data, either interactively in 3D or through batch processing. See ParaView.org for documentation.
  • PyNGL and PyNIO – Python packages that CISL developed for scientific visualization, file input/output, and data analysis.
  • VAPOR* – The Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers is a desktop platform that provides an interactive 3D visualization environment for exploring geosciences CFD data sets. See VAPOR.

Many additional applications and tools that are commonly used by atmospheric and Earth system scientists are available on NCAR HPC resources and through the CISL Research Data Archive. These include Mathematica, Vis5d, and VTK.

MATLAB alternative - Octave

Many MATLAB codes run with very little or no modification under Octave, a free interactive data analysis software package with syntax and functionality that are similar to MATLAB's. Since using Octave is not constrained by license issues, we encourage MATLAB users to try it, particularly those who have long-running MATLAB jobs. Depending on compute intensity, Octave usually runs slower than MATLAB but it may be suitable for most data analysis work and you won't risk having jobs killed because of a lack of licenses.

To use Octave interactively, start an interactive job and load the module.

module load octave

Run octave to start the command line interface, or run the following command to use the GUI.

octave --force-gui

License use guidelines

The CISL user community shares a limited number of licenses for running MATLAB, MATLAB Toolboxes, and some other applications.

Follow these guidelines to ensure fair access for all users:

  • Avoid monopolizing these licenses.
  • If you need to use multiple licenses at one time, be considerate of others and finish your session as quickly as possible.
  • Close applications when you are done to free up licenses for others to use.

CISL reserves the right to kill jobs/tasks of users who monopolize these licenses.

To see how many licenses are being used, run licstats at your command line.

licstats

Run it with option -h for additional information.

licstats -h

 

* Those marked with an asterisk should be run only on the Casper nodes because of their graphics and GPU requirements. Others can be used on Cheyenne. Check the man pages for any program to get additional information.