Job Submission: NAMD with data staging

NAMD is another example application that we can make use of directly. This time, we're going to see how to stage in our datasets rather than using the example data files.

Choose Applications menu in the NGS Portal page, and click button Find Personal Applications.
Move your mouse cursor to NAMD 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.

On this page, there're two options that we can specify. First, we can specify a different stage-to target other than the default gsiftp://ngs.rl.ac.uk:2811, which we don't need to change for now. Secondly, we can select our data files to be processed by the application, just by following Go Browse Host and Select Files/Dirs. But again, we don't need to do it right now because the files we need (NAMD input files) for the example job submission are already prepared, see the list below. And we can see the staging target is set as WORKINGDIR which is our home directory on host ngs.rl.ac.uk.

Now let's click on button , and it may take a few seconds to transfer the data files. Once it is finished, you'll be redirected to the Stage data log page with the following information:

Staged Ok: gsiftp://ngs.rl.ac.uk/apps/namd/examples/alanin.psf
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/namd/examples/alanin.pdb
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/namd/examples/alanin.params
Staged Ok: gsiftp://ngs.rl.ac.uk/apps/namd/examples/alanin

You can now check your working directory to make sure the files are copied over. To do this, select Browse Host menu on the top-left corner of the page. In the input box, choose ngs.rl.ac.uk and click button . And you'll find those files in your working directory:

• alanin.psf
• alanin.pdb
• alanin.params
• alanin

Up to now, we have copied over the example files into our working directory for submission. If we want to use our own data, we can open these files and modify the data and save back the files. To do this, we can click on the filenames to download the files to our local machine, edit the file with an editor or replace the file with another one, and finally upload(following the upload link above the file list) it back to our working directory.

Now let's go back to the NAMD job page by clicking Submit/Run menu item at the bottom left corner. One thing that we need to note is that we must remove the tick on

Stage all data when submitting job:

Otherwise, the data files are staged again and our modifications are lost.

Click , and until we see a reloaded page the following messages:

• Job submitted ok
• Job updated ok

Now let's check job status. Click on <Check Job Status>, and it reports either PENDING, or until finally COMPLETED.

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

• al_par.out