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Data Exercise 2.1: Using OSDF for Large Shared Data

This exercise will use a BLAST workflow to demonstrate the functionality of OSDF for transferring input files to jobs on OSG.

Because our individual blast jobs from previous exercises would take a bit longer with a larger database (too long for an workable exercise), we'll imagine for this exercise that our pdbaa_files.tar.gz file is too large for transfer_input_files (larger than ~1 GB). For this exercise, we will use the same inputs, but instead of using transfer_input_files for the pdbaa database, we will place it in OSDF and have the jobs download from there.

OSDF is connected to a distributed set of caches spread across the U.S. They are connected with high bandwidth connections to each other, and to the data origin servers, where your data is originally placed.

OSDF Map

Setup

  • Make sure you're logged in to ap40.uw.osg-htc.org
  • Copy the following files from the previous Blast exercises to a new directory in /home/<username> called osdf-shared:
    • blast_wrapper.sh
    • blastx
    • mouse_rna.fa.1
    • mouse_rna.fa.2
    • mouse_rna.fa.3
    • Your most recent submit file (probably named blast_split.sub)

Place the Database in OSDF

Copy to your data to the OSDF space

OSDF provides a directory for you to store data which can be accessed through the caching servers. First, you need to move your BLAST database (pdbaa_files.tar.gz) into this directory. For ap40.uw.osg-htc.org, the directory to use is /ospool/PROTECTED/[USERNAME]/

As the PROTECTED directory name indicates, your files placed in the directory will only be accessible by your own jobs.

Modify the Submit File and Wrapper

You will have to modify the wrapper and submit file to use OSDF:

  1. HTCondor knows how to do OSDF transfers, so you just have to provide the correct URL in transfer_input_files. Note there is no servername (3 slashes in :///) and we instead is is just based on namespace (/ospool/PROTECTED in this case):

    transfer_input_files = blastx, $(inputfile), osdf:///ospool/PROTECTED/<USERNAME>/pdbaa_files.tar.gz

  2. Confirm that your queue statement is correct for the current directory. It should be something like:

    queue inputfile matching mouse_rna.fa.*

And that mouse_rna.fa.* files exist in the current directory (you should have copied a few them from the previous exercise directory).

Submit the Job

Now submit and monitor the job! If your 100 jobs from the previous exercise haven't started running yet, this job will not yet start. However, after it has been running for ~2 minutes, you're safe to continue to the next exercise!

Considerations

  1. Why did we not place all files in OSDF (for example, blastx and mouse_rna.fa.*)?

  2. What do you think will happen if you make changes to pdbaa_files.tar.gz? Will the caches be updated automatically, or is there a possiblility that the old version of pdbaa_files.tar.gz will be served up to jobs? What is the solution to this problem? (Hint: OSDF only considers the filename when caching data)

Note: Keeping OSDF 'Clean'

Just as for any data directory, it is VERY important to remove old files from OSDF when you no longer need them, especially so that you'll have plenty of space for such files in the future. For example, you would delete (rm) files from /ospool/PROTECTED/ on when you don't need them there anymore, but only after all jobs have finished. The next time you use OSDF after the school, remember to first check for old files that you can delete.

Next exercise

Once completed, move onto the next exercise: Using OSDF for outputs