There are two sets of methods of running programs and jobs on the HBS compute Grid: using default submission (wrapper) scripts or by writing custom submission commands. In this section we will cover the former method, which is the most straightforward way to submit a job on the Grid.
One can take advantage of using default submission scripts via NoMachine, and using pre-defined Unix command wrappers. In this manner the scripts appear as menu items (NoMachine) or very similar to unix programs (command line). The user selects the program to run as well as the resource requirements (number of CPUs). These are submitted to and run as either interactive or batch jobs under the LSF scheduler, depending on which interface you use. Please refer to the NoMachine and Command Line subsections for detailed instructions on how to run the default submission scripts.
These default scripts are often called "wrapper" scripts, as they are witten as a wrapper around the native binary. This wrapper includes the necessary options to call the program with predefined resources requirments (e.g. 2 cores of CPU). But with this ease of use, there is the tradeoff in flexibility: there are limited choices in what programs can be run and the resources requested.
The other method, using custom submission scripts, offers maximum flexibility but involves writing custom, one-line unix commands or simple text-based submission scripts. This method is described in the Custom Submission Scripts section.
Last Updated 1/7/2020