Run Python Scripts on OSG

Overview

This guide will show you two examples of how to run jobs that use Python in the Open Science Grid. The first example will demonstrate how to submit a job that uses base Python. The second example will demonstrate the workflow for jobs that use specific Python packages, including how to install a custom set of Python packages to your home directory and how to add them to a Python job submission.

Before getting started, you should know which Python packages you need to run your job.

Running Base Python on the Open Science Grid

Several installations of base Python are available via the Open Science Grid's Software Module System. To see what Python versions are available on the Open Science Grid run module avail while connected to our login node.

Create a bash script to run Python

To submit jobs that use a module to run base Python, first create a bash executable - for this example we'll call it run_py.sh - which will include commands to first load the appropriate Python module and then run our Python script called myscript.py.

For example, run_py.sh:

#!/bin/bash

# Load Python
module load python/3.7.0

# Run the Python script 
python3 myscript.py

If you need to use Python 2, load the appropriate module and replace the python3 above with python2.

Create an HTCondor submit file

In order to submit run_py.sh as part of a job, we need to create an HTCondor submit file. This should include the following:

  • run_py.sh specified as the executable
  • use transfer_input_files to bring our Python script myscript.pyto wherever the job runs
  • include requirements that request OSG nodes with access to base Python modules

All together, the submit file will look something like this:

universe    = vanilla     
executable  = run_py.sh

transfer_input_files = myscript.py

log         = job.log
output      = job.out
error       = job.error

# Require nodes that can access the correct OSG modules
Requirements = (HAS_MODULES =?= true) && (OSGVO_OS_STRING == "RHEL 7")

request_cpus    = 1 
request_memory  = 2GB
request_disk    = 2GB

queue 1

Once everything is set up, the job can be submitted in the usual way, by running the condor_submit command with the name of the submit file.

Running Python Jobs That Use Additional Pacakges

It's likely that you'll need additional Python packages (aka libraries) that are not present in the base Python installations made available via modules. This portion of the guide describes how to create a Python "virtual environment" that contains your packages and which can be included as part of your jobs.

Install Python packages

While connected to your login node, load the Python module that you want to use to run jobs:

 $ module load python/3.7.0

Next, create a virtual environment. The first command creates a base environment:

 $ python3 -m venv my_env

You can swap out my_env for a more descriptive name like scipy or word-analysis.

This creates a directory my_env in the current working directory with sub-directories bin/, include/, and lib/.

Then activate the environment and install packages to it.

$ source my_env/bin/activate

Notice how our command line prompt changes to:

(my_env)$

The activation process redefines some of the shell variables such as PYTHON_PATH, LIBRARY_PATH etc.

After activation, packages can be installed using pip which is a tool to install Python packages.

(my_env)$ pip install numpy
......some download message...
Installing collected packages: numpy
Installing collected packages: numpy
Successfully installed numpy-1.16.3

Install each package that you need for your job using the pip install command. Once you are done, you can leave the virtual environment:

(my_env)$ deactivate

The above command resets the shell environmental variables and returns you to the normal shell prompt (with the prefix my_env removed).

All of the packages that were just installed should be contained in a sub-directory of the my_env directory. To use these packages in a job, the entire my_env directory will be transfered as a tar.gz file. So our final step is to compress the directory, as follows:

$ tar czf my_env.tar.gz my_env

Create executable script to use installed packages

In addition to loading the appropriate Python module, we will need to add a few steps to our bash executable to set-up the virtual environment we just created. That will look something like this:

#!/bin/bash

# Load Python
# (should be the same version used to create the virtual environment)
module load python/3.7.0

# Unpack your envvironment (with your packages), and activate it
tar -xzf my_env.tar.gz
python3 -m venv my_env
source my_env/bin/activate

# Run the Python script 
python3 myscript.py

# Deactivate environment 
deactivate

Modify the HTCondor submit file to transfer Python packages

The submit file for this job will be similar to the base Python job submit file shown above with one addition - we need to include my_env.tar.gz in the list of files specified by transfer_input_files. As an example:

universe    = vanilla     
executable  = run_py.sh

transfer_input_files = myscript.py, my_env.tar.gz

log         = job.log
output      = job.out
error       = job.error

# Require nodes that can access the correct OSG modules
Requirements = (HAS_MODULES =?= true) && (OSGVO_OS_STRING == "RHEL 7")

request_cpus    = 1 
request_memory  = 2GB
request_disk    = 2GB

queue 1

Other Considerations

This guide mainly focuses on the nuts and bolts of running Python, but it's important to remember that additional files needed for your jobs (input data, setting files, etc.) need to be transferred with the job as well. See our Introduction to Data Management on OSG for details on the different ways to deliver inputs to your jobs.

When you've prepared a real job submission, make sure to run a test job and then check the log file for disk and memory usage; if you're using significantly more or less than what you requested, make sure you adjust your requests.

Getting Help

For assistance or questions, please email the OSG User Support team at support@opensciencegrid.org or visit the help desk and community forums.

 

This page was updated on Mar 31, 2020 at 13:45 from examples/manage-python-packages.md.