In this tutorial, we learn how to create and use Python virtualenv on the OSG. As an example, we create a virtual environment that holds NLTK (Natural Language Tool Kit) library and then run an NLTK analysis using the virtualenv.
It is easiest to start with the
tutorial command. In the command prompt, type
$ tutorial python-virtualenv # Copies input and script files to the directory python-virtualenv.
This will create a directory
tutorial-virtualenv. Inside the directory, you will see the
text_nltk_venv.sh # Job wrapper script text_nltk_venv.submit # HTCondor job description file simple_text_analysis.py # Python program to analyze the text nltk_data.tar.gz # NLTK reference data nltk_env.tar.gz # Virtual environment for NLTK inside python2.7 create_virtenv.sh # Script to create the virtual environment
text_nltk_venv.submit is the job submission file,
text_nltk_venv.sh.sh is the wrapper shell script,
simple_text_analysis.py is the Python program that does the text analysis using NLTK library,
nltk_data.tar.gz is the reference
data for NLTK analysis, and
nltk_env.tar.gz is the virtual environment that contains Python2.7 and NLTK packages. The shell script
create_virtenv.sh creates the virtual environment for NLTK package with Python 2.7.
Installation of a Python package via virtual environment
The shell script
create_virtenv.sh completes the following tasks:
1. Creates a virtual environment called `nltk_env` 2. Activates the virtual environment 3. Installs the package `NLTK` into the virtual environment 4. Produces a compressed file of the virtual environment
Let us go through the above steps as outlined in
create_virtenv.sh. We create the virtual environment with Python version 2.7 which is available on the submit node (login.osgconnect.net) as distributed environmental modules [REF].
The module command is used to load Python2.7
$ module load python/2.7
and create an isolated virtual environment called
nltk_env using the tool
virutalenv-2.7 (Feel free to choose a different name instead of
$ virtualenv-2.7 nltk_env New Python executable in nltk_env/bin/python Installing setuptools, pip...done.
This creates a directory
nltk_env in the current working directory with sub-directories bin/, include/, and lib/.
Take a look at the list of site-packages
$ ls nltk_env/lib/python2.7/site-packages/ easy_install.py _markerlib pip-6.0.8.dist-info setuptools easy_install.pyc pip pkg_resources setuptools-12.0.5.dist-info
In the above listing, there is no
nltk package. So we need to install the package
NLTK in the virtual environment. We first activate the virtual environment
$ source nltk_env/bin/activate (nltk_env)$
The activation process redefines some of the shell variables such as PYTHON_PATH, LIBRARY_PATH etc. Furthermore, it changes the shell prompt by adding the name of the virtual environment (nltk_env in the present example) as prefix.
After activation, we are ready to add the packages with
pip which is a tool to install Python packages.
(nltk_env)$ pip install nltk ......some download message... Installing collected packages: nltk Running setup.py install for nltk Successfully installed nltk-3.2.1
Let us check weather the installed package exist under site-packages directory
(nltk_env)$ ls nltk_env/lib/python2.7/site-packages/ | grep nltk nltk nltk-3.2.1-py2.7.egg-info
We finished the installation of NLTK package. Now it is okay to come out of the virtual environment, type (nltk_env)$ deactivate
The above command resets the shell environmental variables and returns you to the normal shell prompt (the prefix
Now the virtual environment is ready. Next step is to make this virtual environment available on the remote worker machine when the job is being executed. So it is good to compress the whole directory
nltk_env and send it along with the HTCondor job.
$ tar xzf nltk_env.tar.gz nltk_env
Job submission and execution files
Let us take a look at the job description file
#The UNIVERSE defines an execution environment. You will almost always use VANILLA. Universe = vanilla # EXECUTABLE is the program your job will run It's often useful # to create a shell script to "wrap" your actual work. Executable = text_nltk_venv.sh transfer_input_files = nltk_data.tar.gz, nltk_env.tar.gz, simple_text_analysis.py # The LOG file is where HTCondor places information about your # job's status, success, and resource consumption. log = job.log # The standard output and error messages output = job.out error = job.error # Set the requirement that the OASIS modules are available on the remote worker machine requirements = (HAS_CVMFS_oasis_opensciencegrid_org =?= TRUE) # QUEUE is the "start button" - it launches any jobs that have been # specified thus far. Queue 1
Note that we transfer the compressed virtual environment file
nltk_env.tar.gz. On the remote worker machine, the virtual environment is uncompressed and activated before actual the Python program is executed via the wrapper script
#!/bin/bash # Extract the "nltk_env" and "nltk_data" tar -xzf nltk_env.tar.gz tar -xzf nltk_data.tar.gz # Load Python 2.7 (should be the same version used to create the virtual environment) module load python/2.7 # Create the virtual environment on the remote hosts (redefines the env variables) virtualenv-2.7 nltk_env # Activate virtual environment source nltk_env/bin/activate # Run the Python script python simple_text_analysis.py > simple_text_analysis.out # Deactivate virtual environment deactivate # Clean up the data on the remote machine rm nltk_env.tar.gz nltk_data.tar.gz rm -rf nltk_env nltk_data
Running the simulation
We submit the job using
condor_submit command as follows
$ condor_submit text_nltk_venv.submit //Submit the condor job script "text_nltk_venv.submit"
Now you have submitted a job that performs NLTK analysis of English text. The present job should be finished quickly (less than an hour). You can check the status of the submitted job by using the
condor_q command as follows
$ condor_q username # The status of the job is printed on the screen. Here, username is your login name.
After the job completion, you will see the output file
This page was updated on Dec 19, 2018 at 07:02 from tutorials/tutorial-python-virtualenv/README.md.