Job Submission: GROMACS with JSDL

In this exercise, we're going to see how to change parameters so that we can use our own dataset, and also have a brief look at JSDL(Job Submission Description Language).

On the Applications page, click button Find Personal Applications. Move your mouse cursor to GROMACS with version 3.3.1 in the job list, and click load.

Scroll down the page to find Stage Data: Edit section. Click on the Edit anchor to open the staging page.
Then click on button , wait until the Stage Log page comes out where you'll see the following log messages.

Staged Ok: gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/spc216.pdb
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/grompp.mdp
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/index.ndx
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/topol.top
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/conf.gro

Suppose that we want to use our own data files. We can simply try this by renaming the staged files. Now let's rename conf.gro to myconf.gro.
Select Browse Host menu on the top-left corner of the page. In the input box, choose ngs.rl.ac.uk and click button . Find the file conf.gro in your working directory, click the rename link. Enter myconf.gro in the edit box and click button, and then button.

Now that we have our own data file, we need to modify the arguments to the application to let it know what to use.

Select menu item Arguments in My Job: list on the left side of the page, and find argument conf.gro in the edit box, change it to myconf.gro.
And we can also change the output filename from testgrom.tpr to mygrom.tpr. Then, click the button. You will see the changes shown below.

Now let's take a look at the JSDL and see what's there. Click menu item <JSDL/>, what we see in the scrollable text box is the complex JSDL profile. It is in XML, and we can roughly sort out a simple tree structure like this:

• JobDescription
  • JobIdentification
  • Application
    • ApplicationName
    • ApplicationVersion
    • POSIXApplication
  • Resources
  • DataStaging

What we are interested here is to find out the arguments in this JSDL document. Scroll down until you see <jsdl-posix:POSIXApplication> element, and you'll find the following:

<jsdl-posix:Argument>myconf.gro</jsdl-posix:Argument>
<jsdl-posix:Argument>mygrom.tpr</jsdl-posix:Argument>

So, our modifications are shown here. And we can now submit the job.

Select menu item Submit/Run on the left, scroll down to the end of the page, and click .
untick the Stage data when submitting jobs checkbox, and then you get:

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

Check the job status until we get COMPLETED.

After completion, the GROMACS application places four files in our home directory. We can Browse Host and connect to ngs.rl.ac.uk to see the files.

• deshuf.ndx
• mygrom.tpr
• mdout.mdp