Software notes

MATLAB | NCAR Graphics | NetCDF | ParaView | VAPOR GUI

Review the information below to get the best results when working with these packages in the Yellowstone environment.


MATLAB

See Running visualization programs for how to run MATLAB and other applications through TurboVNC.

If you need to work with MATLAB's Parallel Computing Toolbox, you can use either of two modes:

Also see MATLAB and NetCDF below.


NCAR Graphics

Before linking in the NCAR Graphics Library, load the NCAR Command Language (NCL) module.

module load ncl

When you compile your program, you may need to include some or all of the following arguments in your compilation flag:

-lncarg -lncarg_gks -lncarg_c -lX11 -lXext -lcairo -lfontconfig -lpixman-1 -lfreetype -lexpat -lpng -lz -lpthread -lbz2 -lXrender -lgfortran

The NCAR Graphics compilation commands ncargf77 (Fortran 77 code) and ncargf90 (Fortran 90 code) provide all of those options.


NetCDF

MATLAB and NetCDF

MATLAB natively supports NetCDF format. At the MATLAB prompt, enter help netcdf for information on native commands.

We recommend using the native commands, but some third-party toolboxes are available on Yellowstone:

  • To add the MEXNC interface and SNCTOOLS codes, run ncstartup from your MATLAB command line. If you have not updated your script to be compatible with SNCTOOLS -r4028, you may need to invoke a previous version. Run help ncstartup at your MATLAB command line for details.
  • To add the M_MAP toolbox, run m_map_startup.

If necessary, you can still add the deprecated, unsupported NetCDF Toolbox by running old_netcdf_startup from your MATLAB command line. However, you do this at your own risk.

Python and NetCDF

After you load the python module, use one of the following commands to add the libraries that you will need in order to load NetCDF files from Python.

module load pynio
module load netcdf4python
module load all-python-libs

For additional Python documentation, see our Python page and the PyNIO documentation.

R and NetCDF

These packages are available on Yellowstone for working with NetCDF in R.

  • ncdf
  • ncdf4

Invoke the library command to load the packages into your R session.

Example:

library(ncdf)

ParaView

To use the serial version of ParaView, first load paraview.

module load paraview

Running ParaView in parallel is nontrivial. For example, you need to spawn pvserver with mpiexec, then connect to pvserver with the paraview client.


VAPOR GUI

To use the VAPOR GUI for visualization, see Using VAPOR in the Yellowstone environment.

To use the VAPOR CLI utilities, you must first load the VAPOR module as described on that page.

Be sure to stop the TurboVNC server when you are finished.