Running data processing and analysis applications and utilities on the cluster

This section covers the use of all interactive (as opposed to batch mode) data processing software. This includes linux utilities such as tar and gzip, graphical applications such as MATLAB and ncview and any programs and scripts written by the user for data processing or analysis. Data transfer is discussed in a separate topic.

Where and how to run applications

SSH access to the storage servers has been disabled, to reduce the impact of data processing activities on I/O performance. Instead of running data processing applications on storage servers, four new compute servers called nemo1, nemo2, nemo3 and nemo4 have been provided. A number of scientific software applications are available through the "setup" command in the C-shell. The "setup" command by itself lists all available versions of all applications. Paths and environment variables associated with the current version of an application can be setup in your C-shell environment by using the command "setup" followed by the application name. For example, "setup matlab" sets up the current version of MATLAB. Similarly, "setup new matlab" and "setup old matlab" set up the shell environment for new and old versios of MATLAB.

The "modules" system was originally installed on the ClusterVision cluster and its associated storage servers. The "module" command works in a simiar way to "setup", and makes a number of additional libraries and applications available. For example "module avail" shows all available applications and libraries, and "module add netcdf" adds paths to NetCDF libraries and utilities to your shell environment.

MATLAB

The current version of MATLAB is R2009bSP1 . Launch MATLAB with the command "matlab", or "matlab -nodesktop" if you want a command line instead of the GUI. The previous version is R2006a ("setup old matlab") and the new version is R2010b ("setup new matlab"). Version R2006a does not have 64-bit architecture support, and must be launced with the command "matlab -arch=glnx86 ", which tells MATLAB to use the 32-bit architecture version. For more info on Matlab see ESSCComputing>Software>MatlabHelp.