Overview

This guide will show you two examples of how to run jobs that use Python in the Open Science Pool. 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 Pool

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 run our Python script called myscript.py.

For example, run_py.sh:

#!/bin/bash

# Run the Python script 
python3 myscript.py

If you need to use Python 2, 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 a standard OSG Connect Singularity image that has Python installed.

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

universe    = vanilla

+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-20.04:latest"

executable  = run_py.sh

transfer_input_files = myscript.py

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

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 Packages

It's likely that you'll need additional Python packages that are not present in the base Python installations. This portion of the guide describes how to install your packages to a custom directory and then include them as part of your jobs.

Install Python packages

While connected to your login node, start the base Singularity container that has a copy of Python inside:

 $ singularity shell /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-20.04:latest

Next, create a directory for your files and set the PYTHONPATH

 Singularity> mkdir my_env
 Singularity> export PYTHONPATH=$PWD/my_env

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

Now we can use pip to install Python packages.

Singularity> pip3 install --target=$PWD/my_env 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.

If you would like to test the package installation, you can run the python3 command and then try importing the packages you just installed. To exit the Python console, type "quit()"

Once you are done, you can leave the virtual environment:

Singularity> exit

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

# Unpack your envvironment (with your packages), and activate it
tar -xzf my_env.tar.gz
export PYTHONPATH=$PWD/my_env

# Run the Python script 
python3 myscript.py

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

+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-20.04:latest"

executable  = run_py.sh

transfer_input_files = myscript.py, my_env.tar.gz

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

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 Research Facilitation team at support@osg-htc.org or visit the help desk and community forums.

 

This page was updated on Sep 15, 2022 at 15:41 from examples/manage-python-packages.md.