Part 3 - Job submission: AMBER

From this page onward, we're going to do more job submission exercises with serious jobs. In this part, we're going to experiment with an application template, AMBER, which is deployed on the NGS.

We're going to try job submission to the job queue which is controled by a job manager.
Instead of using globus-job-run command, we use globus-job-submit to put the job on the queue first, wait until it's processed and executed, and then get back the result.

Before actually submitting the job, we need to prepare the input data files required by the AMBER appliation. Fortunately, NGS provided a set of example input data files for this application, and we can just copy them into our home directory and use them. To keep the home directory clean, we create a subdirectory amber for this application. Let's do this on RAL.

let's submit the example AMBER job to the queue. The executable of this application is /usr/ngs/AMBER_10_0, and the arguments following it specify the parameters required by this application. And note that we specify cy.out as our output file under the amber subdirectory.

The returned URI https://ngs.rl.ac.uk:50043/29402/1224687026/ is an ID that we must use to query the status of the job running and to get the result. To query the job running status (note that you need to put the URI from your console rather than copy this one):

Since the job is finished, we can get the result now:

This application does not give any output, because we specified to save the output into file cy.out under the amber subdirectory. Let's check it's there:

Finally, we need to clean the cached result for the job: