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OSG Exercise 1.2: Log In to the OS Pool Access Point

The main goal of this exercise is to log in to an Open Science Pool Access Point so that you can start submitting jobs into the OS Pool instead of the local cluster at UW–Madison. But before doing that, you will first prepare a file on learn to copy to the OS Pool Access Point. Then you will learn how to efficiently copy files between the CHTC and OS Pool Access Points.

If you have trouble getting ssh access to the OS Pool Access Point, ask the instructors right away! Gaining access is critical for all remaining exercises.

Part 1: On the CHTC Access Point

The first few sections below are to be completed on learn.chtc.wisc.edu, the UW–Madison CHTC Access Point. This is still the same Access Point you have been using since yesterday.

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 fails, 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 Unix tar command is a one-stop shop for creating, extracting, and viewing the contents of tar archives (called tarballs). Its usage is as follows:

  • To create a tarball named <archive filename> containing <archive contents>, use the following command:

    [email protected] $ tar -czvf <archive filename> <archive contents>
    

    Where <archive filename> should end in .tar.gz and <archive contents> can be a list of any number of files and/or folders, separated by spaces.

  • To extract the files from a tarball into the current directory:

    [email protected] $ tar -xzvf <archive filename>
    
  • To list the files within a tarball:

    [email protected] $ tar -tzvf <archive filename>
    

Using the guidance above, log into learn.chtc.wisc.edu, create a tarball that contains the OSG exercise 1.1 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).

While still logged in to learn.chtc.wisc.edu:

  1. Create and change into a new folder for this exercise, for example osg-ex12
  2. Use wget to download the following files from our web server:
    1. Text file: http://proxy.chtc.wisc.edu/SQUID/osgschool21/random_text
    2. Archive: http://proxy.chtc.wisc.edu/SQUID/osgschool21/pdbaa.tar.gz
    3. Image: http://proxy.chtc.wisc.edu/SQUID/osgschool21/obligatory_cat.jpg
  3. 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?

Part 2: On the Open Science Pool Access Point

For many of the remaining exercises, you will be using an OSG Connect Access Point, which submits jobs into the Open Science Pool. For the School, the default server is named login04.osgconnect.net; however, if you had an OSG Connect account from before the School (you know who you are), you may be using login05.osgconnect.net, so just change the examples as needed.

To log in to the OSG Connect Access Point, use the username and SSH key that you made when you set up OSG Connect. If you have any issues logging in to login04 (or login05, if that’s you), please ask for help right away!

So please ssh in to the server and take a look around:

  1. Log in using ssh login04.osgconnect.net (or login05, if that’s you)
  2. Try some Linux and HTCondor commands; for example:
    • Linux commands: hostname, pwd, ls, and so on
    • What is the operating system? uname and (in this case) cat /etc/redhat-release
    • HTCondor commands: condor_version, condor_q, condor_status -total

Transferring files

In the next exercise, you will submit the same kind of job as in the previous exercise. Wouldn’t it be nice to copy the files instead of starting from scratch? And in general, being able to copy files between servers is helpful, so let’s explore a way to do that.

Using secure copy

Secure copy (scp) is a command based on SSH that lets you securely copy files between two different servers. It takes similar arguments to the Unix cp command but also takes additional information about servers. Its general form is like this:

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

<remote path> may be omitted if you want to copy your sources to your remote home directory and [[email protected]] may be omitted if your usernames are the same across both servers. For example, if you are logged in to login04.osgconnect.net and wanted to copy the file foo from your current directory to your home directory on learn.chtc.wisc.edu, and if your usernames are the same on both servers, the command would look like this:

[email protected] $ scp foo learn.chtc.wisc.edu:

Additionally, you could pull files from learn.chtc.wisc.edu to login04.osgconnect.net. The following command copies bar from your home directory on learn.chtc.wisc.edu to your current directory on login04.osgconnect.net; and in this case, the username (Net ID) for learn is specified:

Also, you can copy folders between servers using the -r option. If you kept all your files from the HTCondor exercise 1.3 in a folder named htc-1.3 on learn.chtc.wisc.edu, you could use the following command to copy them to your home directory on login04.osgconnect.net:

Using this information, try this: From login04.osgconnect.net, try copying the tarball you created earlier in this exercise on learn.chtc.wisc.edu to login04.osgconnect.net.

Secure copy to your laptop

During your research, you may need to transfer output files from your submit server to inspect them on your personal computer, which can also be done with scp! To use scp on your laptop, follow the instructions relevant to your computer‘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 the OSG exercise 1.1 from login04.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 login04.osgconnect.net
  3. Copy the tarball containing OSG exercise 1.1 to your laptop

Extra challenge: Using rsync

(This last section is about a more advanced tool; you may skip this section if you want.)

scp is a common and useful tool for file transfers between computers, 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 servers is rsync, which has more features than scp and is correspondingly more complex. The invocation is similar to scp: You can transfer files and/or folders, but the options are different and, when transferring folders, pay close attention to a trailing slash (/), because it means different things to include or omit that single character!

Here is the general format of an rsync command:

rsync -Pavz <source 1> <source 2>...<source N> [[email protected]]<remote server>:<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 features are helpful when you have network issues so that you do not need to restart the transfer from scratch every time your connection fails.

  1. Log in to login04.osgconnect.net
  2. Use rsync to transfer the folder containing OSG exercise 1.1 on learn.chtc.wisc.edu to login04.osgconnect.net
  3. In a separate terminal window, log in to learn.chtc.wisc.edu
  4. Create a new file in your OSG exercise 1.1 folder on learn.chtc.wisc.edu with the touch command:

    [email protected] $ touch <filename>
    
  5. From login04.osgconnect.net, 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