Wednesday Exercise 2.2: Using Python, Pre-Built

In this exercise, you will install Python, package your installation, and then use it to run jobs. It should take about 20 minutes.

Background

We chose Python as the language for this example because: a) it is a common language used for scientific computing and b) it has a straightforward installation process and is fairly portable.

Running any Python script requires an installation of the Python interpreter. The Python interpreter is what we're using when we type python at the command line. In order to run Python jobs on a distributed system, you will need to install the Python interpreter (what we often refer to as just "installing Python"), within the job, then run your Python script.

There are two installation approaches. The approach we will cover in this exercise is that of "pre-building" the installation (much like we did with OpenBugs this morning). We will install Python to a specific directory, and then create a tarball of that installation directory. We can then use our tarball within jobs to run Python scripts.

Interactive Job for Pre-Building

The first step in our job process is building a Python installation that we can package up.

  1. Create a directory for this exercise on learn.chtc.wisc.edu and cd into it.
  2. Download the Python source code from https://www.python.org/.

    [email protected] $ wget https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tgz
    
  3. Of our options - submit server, interactive job, personal computer - which should we use for this installation/packaging process? Once you have a guess, move to the next step.

  4. Due to the number of people on our submit server, we shouldn't use the submit server. Your own computer probably doesn't have the right operating system. The best place to install will be an interactive job. For this job, we can use the same interactive submit file as Exercise 1.4, with one change. What is it?

  5. Make a copy of the interactive submit file from Exercise 1.4 and change the transfer_input_files line to the Python tarball you just downloaded. Then submit it using the -i flag.

    [email protected] $ condor_submit -i build.submit
    
  6. Once the interactive job begins, we can start our installation process. First, we have to determine how to install Python to a specific location in our working directory.

    1. Untar the Python source tarball and look at the README.rst file in the Python-3.7.0 directory. You'll want to look for the "Build Instructions" header. What will the main installation steps be? What command is required for the final installation? Once you've tried to answer these questions, move to the next step.
    2. There are some basic installation instructions near the top of the README. Based on that short introduction, we can see the main steps of installation will be:

      ./configure
      make
      make test
      sudo make install
      

      This looks a lot like the OpenBUGS installation from earlier today! It turns out that this three-stage process (configure, make, make install) is a common way to install many software packages. Also like the OpenBUGS installation, the default installation location for Python requires sudo (administrative privileges) to install. However, we'd like to install to a specific location in the working directory so that we can compress that installation directory into a tarball. How did we do this with OpenBugs?

    3. With OpenBugs we used the -prefix option with the configure script. Let's see if the Python configure script has this option by using the "help" option (as suggested in the README.rst file):

      [email protected] $ ./configure --help
      

      Sure enough, there's a list of all the different options that can be passed to the configure script, which includes --prefix. (To see the --prefix option, you may need to scroll towards the top of the output.) Therefore, we can use the $(pwd) command in order to set the path correctly, just as we did earlier today.

  7. Now let's actually install Python!

    1. From the job's main working directory, create a directory to hold the installation.

      [email protected] $ cd $_CONDOR_SCRATCH_DIR
      [email protected] $ mkdir python
      
    2. Move into the Python-3.7.0 directory and run the installation commands. These may take a few minutes each.

      [email protected] $ cd Python-3.7.0
      [email protected] $ ./configure --prefix=$(pwd)/../python
      [email protected] $ make
      [email protected] $ make install
      

      Note

      The installation instructions in the README.rst file have a make test step between the make and make install steps. As this step isn't strictly necessary (and takes a long time), it's been omitted above.

    3. If I move back to the main job working directory, and look in the python subdirectory, I should see a Python installation.

      [email protected] $ cd ..
      [email protected] $ ls python/
      bin  include  lib  share
      
    4. I have successfully created a self-contained Python installation. Now it just needs to be tarred up!

      [email protected] $ tar -czf prebuilt_python.tar.gz python/
      
  8. Before exiting, we might want to know how we installed Python for later reference. Enter the following commands to save our history to a file:

    [email protected] $ history > python_install.txt
    
  9. Exit the interactive job.

Python Script

  1. Create a script with the following lines called fib.py.

    import sys
    import os
    
    if len(sys.argv) != 2:
        print('Usage: %s MAXIMUM' % (os.path.basename(sys.argv[0])))
        sys.exit(1)
    maximum = int(sys.argv[1])
    n1 = n2 = 1
    while n2 <= maximum:
        n1, n2 = n2, n1 + n2
    print('The greatest Fibonacci number up to %d is %d' % (maximum, n1))
    
  2. What command line arguments does this script take? Try running it on the submit server.

Wrapper Script

We now have our Python installation and our Python script - we just need to write a wrapper script to run them.

  1. What steps do you think the wrapper script needs to perform? Create a file called run_fib.sh and write them out in plain English before moving to the next step.
  2. Our script will need to
    1. untar our prebuilt_python.tar.gz file
    2. access the python command from our installation to run our fib.py script
  3. Try turning your plain English steps into commands that the computer can run.
  4. Your final run_fib.sh script should look something like this:

    #!/bin/bash
    
    tar xzf prebuilt_python.tar.gz 
    python/bin/python3 fib.py 90
    

    or

    #!/bin/bash
    
    tar xzf prebuilt_python.tar.gz 
    export PATH=$(pwd)/python/bin:$PATH 
    python3 fib.py 90
    
  5. Make sure your run_fib.sh script is executable.

Submit File

  1. Make a copy of a previous submit file in your local directory (the OpenBugs submit file could be a good starting point). What changes need to be made to run this Python job?

  2. Modify your submit file, then make sure you've included the key lines below:

    executable = run_fib.sh
    transfer_input_files = fib.py, prebuilt_python.tar.gz
    
  3. Because we pre-built our Python installation on a machine running Scientific Linux, version 6.something, we should request machines with similar characteristics. Add the following line to your submit file as well:

    requirements = (OpSys == "LINUX" && OpSysMajorVer == 6 )
    
  4. Submit the job using condor_submit.

  5. Check the .out file to see if the job completed.