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Data analysis and visualization

Many data analysis and visualization software packages are freely available for use on CISL-managed resources. These packages include some developed and supported by NCAR and CISL.

Frequently used packages

These are among the more frequently used data analysis and visualization packages available on NCAR systems. To request installation of other packages, contact the NCAR Research Computing help desk.

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

Please follow these license use guidelines for Matlab

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 licstatus at your command line. You will see columns showing how many licenses you're using, the total number of licenses in use, and the total number of licenses. 

licstatus

This is a high-level language and interactive environment for data analysis, statistics, and image processing. Several MATLAB toolboxes are provided (list below). See the MathWorks web site for documentation and note the information just below about Octave, an alternative to MATLAB. Related: MATLAB Parallel Computing Toolbox

MATLAB toolboxes

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

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

NCL

NCAR Command Language is an interpreted language that CISL designed for scientific data analysis and visualization.

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.

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.

Advanced visualization support

Researchers who need help visualizing data to demonstrate the results of their scientific computing can request expert assistance and collaboration from CISL. This service is available to researchers who want help using specialized applications on data analysis and visualization resources that CISL manages.

CISL visualization staff have particular expertise in CISL-developed software such as VAPOR and NCL but are open to assisting with other applications. They have helped science teams produce numerous visualizations for conferences, publications, and scientific journals as well as science and broadcast news programs.

See these sites for some examples:

Requesting support

To ask for assistance, please use this request form. Indicate clearly that the request is for "Advanced Visualization Support" and describe how the proposed visualization project meets the following criteria:

  • The assistance will culminate in a visualization deliverable or deliverables within a defined time period.

  • The deliverable(s) will help demonstrate science results and findings.

  • A member or members of the science team will participate actively in the production of the deliverable(s).

  • Data to be visualized must have been generated on a CISL high-performance computing system.

  • CISL data analysis and visualization resources will be used in creating the deliverables.

Requests for advanced visualization support are evaluated based on those criteria to ensure the most productive use of the limited available staff time. To further help us evaluate your request, please briefly address the following questions when submitting the request form:

  1. What does the scientist want to communicate about the data with a visualization?

  2. What type of visualization is needed (2D or 3D animation, still images)?

  3. What model or instrument produced the data?

  4. How big are the data?

  5. In what file format are the data stored?

The CISL visualization staff will follow up with requesters directly if additional details are needed.

Starting visualization applications

CISL visualization experts can help as described above with using applications such as NCL and VAPOR.

See the Casper documentation to learn how to submit the necessary jobs and start the applications on that data analysis and visualization cluster.