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Overview

There are some conditions where transferring to the worker node via HTCondor is not practical - for example, when the required input datasets are larger than the local scratch space available on the remote worker node. One way to do this is to create a tarball (a .tar.gz file) and instruct your job to pull it remotely as secondary payload. This tutorial will show you how to do this using a helper framework named SkeletonKey in conjunction with Parrot and Chirp.

Conventions

  • In the examples used on this page, text in red is being used as a placeholder and will need to be replaced with user specific information (e.g. username )
  • Names of servers are denoted using blue text (e.g. login.osgconnect.org)
  • Directory or file names are denoted using green text (e.g. ~/my_file)

Preliminaries

Before going through the examples, login to login.osgconnect.net and setup a work area:

Initial Setup

All of the files that we ask you to type below are present in the tutorial folder, ~/tutorial-chirp-access. You may edit them in place instead of typing; or you can type them fresh to reinforce your experience.

Remote data access

This example will guide you through creating a job that will read and write from a filesystem exported by Chirp. Chirp securely exposes a local filesystem path over the network so that remote jobs can access local data. SkeletonKey is a helper for setting up the secure access.

Create the application tarball

A tarball is a single-file archive of one or more files and folders that can be unpacked into its original form, much like a zip file. Tools for working with tarballs are universal to UNIX/Linux servers, while zip/unzip are perhaps less common.

First, create a new folder to contain your payload. You will then use this folder to create your tarball.

Create a shell script, ~tutorial-stash-chirp/data_app/data_access.sh with the following lines:

data_access.sh

Notice the use of the $CHIRP_MOUNT environment variable in this script. The SkeletonKey helper defines $CHIRP_MOUNT as the local path to the directory being exported from the Chirp server. 

Next, make sure the data_access.sh script is executable and create a tarball:

Creating tarball

Then copy the tarball to your public directory in Stash. Ensure that it can be read by anyone:

Making tarball available

 

Note that this makes data_app.tar.gz available via HTTP, at http://stash.osgconnect.net/+username/data_app.tar.gz. This illustrates the integration of file access in OSG Connect and Stash, and SkeletonKey will make use of this.

Create a job wrapper

Open a file called ~/tutorial-stash-tchirp/data_access.ini and add the following lines, replacing username with the appropriate values. This file is a SkeletonKey configuration profile.

data_access.ini


Run SkeletonKey on ~/tutorial-stash-chirp/data-access.ini. This creates a job wrapper named run_job.py — an executable that you will submit to Condor as a job, which performs setup and then invokes your real application.

Generate job wrapper

Verification

As always, run the job wrapper locally to verify that it's working correctly before submitting to the grid. Note that run_job.py contains ad hoc security credentials for accessing your data, and as such should NOT be world readable.
Verifying job wrapper

The job wrapper will virtually mount your ~/stash (/stash/user/username) folder through Parrot and Chirp, and data_access.sh will deposit output there. Even though the job runs locally and is very short, it may take surprisingly long because of the "remote" access setup. In real-world jobs the setup time is negligible compared to the job run time itself.

 Verify that the file was written correctly:

Job Verification


The output should match the output given in the example above with the exception of the date and time. Once the output is verified, delete the output file:

Cleanup

Submitting jobs to OSG Connect

Create a file called ~/tutorial-stash-chirp/osg-connect.submit with the following contents. Replacing PROJECT_NAME with an appropriate value:

OSG-Connect submit file


Submit the job to HTCondor. This will put 100 instances of the job onto the grid, because of the "Queue 100":

OSG-Connect submit file

Verify that the jobs ran successfully:

OSG-Connect submit file




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