set environment variable in python script

Question

I have a bash script that sets an environment variable an runs a command

LD_LIBRARY_PATH=my_path
sqsub -np $1 /homedir/anotherdir/executable

Now I want to use python instead of bash, because I want to compute some of the arguments that I am passing to the command.

I have tried

putenv("LD_LIBRARY_PATH", "my_path")

and

call("export LD_LIBRARY_PATH=my_path")

followed by

call("sqsub -np " + var1 + "/homedir/anotherdir/executable")

but always the program gives up because LD_LIBRARY_PATH is not set.

How can I fix this?

Thanks for help!

(if I export LD_LIBRARY_PATH before calling the python script everything works, but I would like python to determine the path and set the environment variable to the correct value)

Answer 1

bash:

LD_LIBRARY_PATH=my_path
sqsub -np $1 /path/to/executable

Similar, in Python:

import os
import subprocess
import sys

os.environ['LD_LIBRARY_PATH'] = "my_path" # visible in this process + all children
subprocess.check_call(['sqsub', '-np', sys.argv[1], '/path/to/executable'],
                      env=dict(os.environ, SQSUB_VAR="visible in this subprocess"))

Answer 2

You can add elements to your environment by using

os.environ['LD_LIBRARY_PATH'] = 'my_path'

and run subprocesses in a shell (that uses your os.environ) by using

subprocess.call('sqsub -np ' + var1 + '/homedir/anotherdir/executable', shell=True)

Answer 3

There are many good answers here but you should avoid at all cost to pass untrusted variables to subprocess using shell=True as this is a security risk. The variables can escape to the shell and run arbitrary commands! If you just can't avoid it at least use python3's shlex.quote() to escape the string (if you have multiple space-separated arguments, quote each split instead of the full string).

shell=False is always the default where you pass an argument array.

Now the safe solutions...

Method #1

Change your own process's environment - the new environment will apply to python itself and all subprocesses.

os.environ['LD_LIBRARY_PATH'] = 'my_path'
command = ['sqsub', '-np', var1, '/homedir/anotherdir/executable']
subprocess.check_call(command)

Method #2

Make a copy of the environment and pass is to the childen. You have total control over the children environment and won't affect python's own environment.

myenv = os.environ.copy()
myenv['LD_LIBRARY_PATH'] = 'my_path'
command = ['sqsub', '-np', var1, '/homedir/anotherdir/executable']
subprocess.check_call(command, env=myenv)

Method #3

Unix only: Execute env to set the environment variable. More cumbersome if you have many variables to modify and not portabe, but like #2 you retain full control over python and children environments.

command = ['env', 'LD_LIBRARY_PATH=my_path', 'sqsub', '-np', var1, '/homedir/anotherdir/executable']
subprocess.check_call(command)

---

Of course if var1 contain multiple space-separated argument they will now be passed as a single argument with spaces. To retain original behavior with shell=True you must compose a command array that contain the splitted string:

command = ['sqsub', '-np'] + var1.split() + ['/homedir/anotherdir/executable']