The GridEngine Run Utility

10/07 22:17 run is a utility that allows users to abandon the practice of writing or dealing with submit scripts. It is tightly-integrated with Modules so that users can forget about which type of parallel library they use (OpenMPI, MVAPICH, DDI, Linda, Threads, etc.), what cryptic options they need to pass to the scheduler (-j y -R y -l h_rt=10:00:00,h_vmem=16G... etc, etc.), and transparently handles interactive graphical applications that need to make use of HPC resources. run was written by Brian Smith for the University of South Florida. It is licensed under the GPL and will be available on this site for download soon.

Example: Running Matlab through Module Integration

Let's say you want to get a graphical Matlab session up and running. First, ensure that your Workstation is correctly configured for displaying X11 applications by following our guide here.

Once you log into the system and have XWin32 (or your preferred X server) running, issue the following command:

[user@host ~]$ run matlab/r2009b

This will transparently start an interactive session with the scheduler and subsequently launch Matlab.

Example: Running VASP

VASP is an Electronic Structure package that normally is run as a batch job submitted to the queue via a job script. With run, we no longer need to know any of this:

[user@host ~]$ run -n 16 -t 10:00:00 vasp/4.6.34
Your job 30709 ("vasp/4.6.34-user-9408cf7") has been submitted
[user@host ~]$

This will automatically submit a VASP job to the queue in batch mode, using your current directory as its search path for its INCAR file. The anticipated runtime of 10 hours is reported with the -t directive. That we require 16 processors is expressed with the -n directive. Knowledge of what MPI library VASP was compiled with, what options should be passed to OpenMPI for optimal execution, and other details are taken care of behind the scenes.

• More information coming soon!!!