Software Exercise 5.2: 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¶

Objective: Install software (Python) to a folder and run it in a job using a wrapper script.

Why learn this?: This is very similar to the previous exercise.

Interactive Job for Pre-Building¶

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

Create a directory for this exercise on the Access Point and cd into it.

Download the Python source code from https://www.python.org/.

username@ap1 $ wget https://www.python.org/ftp/python/3.10.5/Python-3.10.5.tgz

First, we have to determine how to install Python to a specific location in our working directory.
1. Untar the Python source tarball (tar -xzf Python-3.10.5.tgz) and look at the README.rst file in the Python-3.10.5 directory (cd Python-3.10.5). 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 three-stage process (configure, make, make install) is a common way to install many software packages. 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.
3. You can often use an option called -prefix with the configure script to change the default installation directory. Let's see if the Python configure script has this option by using the "help" option (as suggested in the README.rst file):
```
username@host $ ./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 to a custom installation directory.
Now let's actually install Python!
1. From the original working directory, create a directory to hold the installation.
```
username@host $ cd  ../
username@host $ mkdir python310
```
2. Move into the Python-3.10.5 directory and run the installation commands. These may take a few minutes each.
```
username@host $ cd Python-3.10.5
username@host $ ./configure --prefix=$PWD/../python310
username@host $ make
username@host $ 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.
```
username@host $ cd ..
username@host $ ls python310/
bin  include  lib  share
```
4. I have successfully created a self-contained Python installation. Now it just needs to be tarred up!
```
username@host $ tar -czf prebuilt_python.tar.gz python310/
```
We might want to know how we installed Python for later reference. Enter the following commands to save our history to a file:
```
username@host $ history > python_install.txt
```

Python Script¶

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))

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.

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.
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
Try turning your plain English steps into commands that the computer can run.

Your final run_fib.sh script should look something like this:

#!/bin/bash

tar -xzf prebuilt_python.tar.gz 
python310/bin/python3 fib.py 90

or

#!/bin/bash

tar -xzf prebuilt_python.tar.gz 
export PATH=$(pwd)/python310/bin:$PATH 
python3 fib.py 90

Make sure your run_fib.sh script is executable.

Submit File¶

Make a copy of a previous submit file in your local directory (the submit file from the Use a Wrapper Script exercise might be a good candidate). What changes need to be made to run this Python job?

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

Submit the job using condor_submit.
Check the .out file to see if the job completed.