Job Submission: AMBER

In this exercise, we simple try to submit a ready-made example job AMBER with example input data.
Choose Applications menu in the NGS Portal page (skip if you're there), select All in category list as shown below, and click button Find Personal Applications.

Move mouse cursor to AMBER in the job list that we have saved, and click load.

Scroll down to the bottom of the page until you see a red box labelled Submit My Job, and two buttons in the box, and .

Now let's submit this job to the queue. Click button , and it may take several seconds before the page is reloaded with the following messages:

• Data staged ok
• Job submitted ok
• Job updated ok

In the My Job Summary box, we can see that the Job Status is set as SUBMITTED. And if we click on the anchor on the right: <Check Job Status>, the Job Status is changed to DONE. (It is possible that it's changed to PENDING or ACTIVE instead of DONE in which case it needs more time to finish execution. We can keep checking this until we get a DONE status.)

Now scroll down to the bottom again, and we'll see some logging message in the red box:

Submission Log
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/amber/examples/serial_example/prmtop
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/amber/examples/serial_example/in.md
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/amber/examples/serial_example/cytosine.out.save
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/amber/examples/serial_example/crd.md.23

This shows that four data files are staged/copied from the example directory to our working directory before submission, and they're used by the AMBER application as input datasets.

In the end, we're going to check that the job is executed with some expected results. By default specification of this example, the job will produce a data file named cytosine.out in our working folder. Let's see if it is there.

Go to Browse Host menu link, which is at the top-left corner of the page, and select gsiftp://ngs.rl.ac.uk:2811 from the list and click , open amber subdirectory if it is there, and the file cytosine.out.save will be there if we're lucky. Click the filename to download and open it with the browser or an editor. You can compare the content with the sample output file cytosine.out.save.