Run Python Scripts on OSG
This guide will show you to how run jobs that use Python in the Open Science Grid. Our
first example will show how to submit a job that runs a script that only uses base Python.
If your jobs use specific Python packages, the second half of this guide will show you how to install these packages to your home directory and add them to a basic Python job submission.
Before we begin, you should know which Python packages you need to run your job.
Running Python on the Open Science Grid
You can see the versions of Python available in the Open Science Grid's Software
Module System, by running
module avail on the submit node.
To use a module, you "load" it and then use the
python command to run a Python script.
However, we're not actually going to do this on the submit node. Instead, we'll put
these commands into a script, so they can be executed wherever the job runs:
#!/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
In order to submit this script as part of a job, you'll need to create an HTCondor submit file. This should include the following:
bashscript above will be the job's "executable" - for this example we'll call it
- The Python script (
myscript.py, above) will need to be transferred to wherever the job runs, and should be listed in "transfer_input_files".
- It's also important to include the requirement(s) that request OSG servers that have access to the base Python module used in the wrapper script.
All together, a 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
condor_submit command with the name of the submit file.
Adding Python Packages to a Job
It's likely that you'll need additional Python packages that aren't present in the default OSG software modules. This portion of the guide describes how to create a Python "virtual environment" that contains your packages and can be included as part of your jobs.
Install needed Python packages
First, load the Python module that you want to use to run jobs.
$ module load python/3.7.0
Now, we will go through the steps to create a virtual environment. The first
command creates the base environment. You can swap out
my_env for a more descriptive name like
$ python3 -m venv my_env
This creates a directory
my_env in the current working directory
We now need to activate the environment and install our packages to it.
$ source my_env/bin/activate
Notice how your command line prompt changes to:
The activation process redefines some of the shell variables such as PYTHON_PATH, LIBRARY_PATH etc.
After activation, we are ready to add the packages with
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:
The above command resets the shell environmental variables and returns you to the
normal shell prompt (the prefix
All of the packages that were just installed should be contained in a sub-directory
my_env directory. To use these packages in a job, we will transfer the
my_env directory as a tar.gz file. So our final step is to compress the
directory, as follows:
$ tar czf my_env.tar.gz my_env
Executable script and submit file
When our job actually runs, we will want to include the same steps as the previous shell script (load the Python module, run Python), but will need to add a few steps 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
The submit file for this job will be similar to above, but you need to make sure
to add the
tar.gz file with your environment to the list of "transfer_input_files:
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
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
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.
This page was updated on Sep 16, 2019 at 17:00 from examples/manage-python-packages.md.