Monday Exercise 4.2: Log in to the OSG Submit Machine

The goal of this exercise is to log in to a different submit host so that you can start submitting jobs into the OSG instead of the local cluster here at UW-Madison. Additionally, you will learn about the tar and scp commands, which will allow you to efficiently copy files between the two submit nodes.

If you have trouble getting ssh access to the submit machine, ask the instructors right away! Gaining access is critical for all remaining exercises.

Log in to the OSG submit machine

For some of the remaining exercises today, you will be using a machine named training.osgconnect.net. The username and password are listed on your 'Accounts' paper that you received yesterday. If you no longer have it, please ask the instructors for help.

Once you have your account details, ssh in to the machine and take a look around.

IMPORTANT

For performance reasons, you will be doing all of your work on training.osgconnect.net out of your local scratch directory, /local-scratch/<USERNAME>/ replacing <USERNAME> with your own username.

Do NOT use your home directory for job submission.

Preparing files for transfer

When transferring files between computers, it's best to limit the number of files as well as their size. Smaller files transfer more quickly and if your network connection drops, restarting the transfer is less painful than it would be if you were transferring large files.

Archiving tools (WinZip, 7zip, Archive Utility, etc.) can compress the size of your files and place them into a single, smaller archive file. The tar command is a one-stop shop for creating, extracting, and viewing the contents of tar archives (called tarballs) whose usage is as follows:

Using the above knowledge, log into learn.chtc.wisc.edu, create a tarball that contains today's exercise 4.1 directory, and verify that it contains all the proper files.

Comparing compressed sizes

You can adjust the level of compression of tar by prepending your command with GZIP=--<COMPRESSION>, where <COMPRESSION> can be either fast for the least compression, or best for the most compression (the default compression is between best and fast).

  1. Use wget to download the following files from our web server:
    1. Text file: http://proxy.chtc.wisc.edu/SQUID/osgschool19/random_text
    2. Archive: http://proxy.chtc.wisc.edu/SQUID/osgschool19/pdbaa.tar.gz
    3. Image: http://proxy.chtc.wisc.edu/SQUID/osgschool19/obligatory_cat.jpg
  2. Use tar on each file and use ls -l to compare the sizes of the original file and the compressed version.

Which files were compressed the least? Why?

Transferring files

Using secure copy

Secure copy (scp) is a command based on SSH that lets you securely copy files between two different hosts. It takes similar arguments to the cp command that you are familiar with but also takes additional host information:

[email protected] $ scp <source 1> <source 2>...<source N> <remote host>:<remote path>

For example, if I were logged in to learn.chtc.wisc.edu and wanted to copy the file foo from my current directory to my local scratch directory on training.osgconnect.net, the command would look like this:

[email protected] $ scp foo training.osgconnect.net:/local-scratch/<USERNAME>/

Additionally, I could also pull files from training.osgconnect.net to learn.chtc.wisc.edu. The following command copies bar from my local scratch directory on training.osgconnect.net to my current directory on learn.chtc.wisc.edu:

[email protected] $ scp training.osgconnect.net:/local-scratch/<USERNAME>/bar .

You can also copy folders between hosts using the -r option. If I kept all my files from Monday's exercise 1.3 in a folder named monday-1.3 on learn.chtc.wisc.edu, I could use the following command to copy them to my local scratch directory on training.osgconnect.net:

[email protected] $ scp -r monday-1.3 training.osgconnect.net:/local-scratch/<USERNAME>/

Try copying the tarball you created earlier in this exercise on learn.chtc.wisc.edu to training.osgconnect.net.

Secure copy from your laptop

During your research, you may need to retrieve output files from your submit host to inspect them on your personal machine, which can also be done with scp! To use scp on your laptop, follow the instructions relevant to your machine's operating system:

Mac and Linux users

scp should be included by default and available via the terminal on both Mac and Linux operating systems. Open a terminal window on your laptop and try copying the tarball containing today's exercise 4.1 from training.osgconnect.net to your laptop.

Windows users

WinSCP is an scp client for Windows operating systems.

  1. Install WinSCP from https://winscp.net/eng/index.php
  2. Start WinSCP and enter your SSH credentials for training.osgconnect.net
  3. Copy the tarball containing today's exercise 4.1 to your laptop

Extra challenge: Using rsync

scp is a great, ubiquitous tool for one-time transfers but there are better tools if you find yourself transferring the same set of files to the same location repeatedly. Another common tool available on many Linux machines is rsync, which is like a beefed-up version of scp. The invocation is similar to scp: you can transfer files and/or folders, but the options are different and when transferring folders, make sure they don't have a trailing slash (/, this means to copy all the files within the folder instead of the folder itself):

[email protected] $ rsync -Pavz <source 1> <source 2>...<source N> <remote host>:<remote path>

rsync has many benefits over scp but two of its biggest features are built-in compression (so you don't have to create a tarball) and the ability to only transfer files that have changed. Both of these feature are helpful when you're having connectivity issues so that you don't have to restart the transfer from scratch every time your connection fails.

  1. Use rsync to transfer the folder containing today's exercise 1.1 to training.osgconnect.net
  2. Create a new file in your exercise 1.1 folder on learn.chtc.wisc.edu with the touch command:

    [email protected] $ touch <filename>
    
  3. Use the same rsync command to transfer the folder with the new file you just created. How many files were transferred the first time? How many files were transferred if you run the same rsync command again?

Next exercise

Once completed, move onto the next exercise: Running jobs in the OSG