Analysis and visualization software

Using applications | License use guidelines | Applications and analysis packages

These are frequently used data analysis and visualization software packages available to Cheyenne users, in some cases via the Yellowstone system and Geyser or Caldera nodes. See a more complete list below.

To request installation of other packages, contact cislhelp@ucar.edu.

  • GrADS and OpenGrADS—The Grid Analysis and Display System (GrADS) is an interactive desktop tool for visualizing earth science data. OpenGrADS is built on top of GrADS and augments its functionality.
  • 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.
  • 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 Yellowstone 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.
  • 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 for how to use this in the Yellowstone environment.

Using applications

To run most applications in the Cheyenne environment, you first load a module. See Essential module commands for how to identify and load modules. Also see Running interactive applications to learn how to start interactive jobs to use these programs.

When you work with these applications, use your temporary /glade/scratch space for data analysis. Then, after post-processing, save the data that you need long-term to the High Performance Storage System (HPSS) tape archive. Using the tape archive only for long-term storage helps conserve your storage allocation and allows the HPSS system to run more efficiently for everyone.


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

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 very 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, follow the instructions below to start an interactive job, then 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

Applications and analysis packages

  • CDAT - Climate Data Analysis Tools
  • CDO - Climate Data Operators
  • Gnuplot
  • IDL - Interactive Data Language
  • JasPer
  • MATLAB and toolboxes
  • NCAR Graphics
  • NCL - NCAR Command Language
  • Ncview
  • Octave
  • R
  • VAPOR* - Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers
  • VisIt*
  • VTK* - Visualization ToolKit

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

Related training courses

NCAR courses