I've tried googling the answer but with no luck.
I need to use my works supercomputer server, but for my python script to run, it must be executed via a shell script.
For example I want job.sh
to execute python_script.py
How can this be accomplished?
Just make sure the python executable is in your PATH environment variable then add in your script
python path/to/the/python_script.py
Details:
#!/bin/sh python python_script.py
chmod u+x job.sh
./job.sh
Suppose you have a python file hello.py
Create a file called job.sh
that contains
#!/bin/bash
python hello.py
mark it executable using
$ chmod +x job.sh
then run it
$ ./job.sh
Modify your script hello.py
and add this as the first line
#!/usr/bin/env python
mark it executable using
$ chmod +x hello.py
then run it
$ ./hello.py
Imho, writing
python /path/to/script.py
Is quite wrong, especially in these days. Which python? python2.6? 2.7? 3.0? 3.1? Most of times you need to specify the python version in shebang tag of python file. I encourage to use
#!/usr/bin/env python2 #or python2.6 or python3 or even python3.1for compatibility.
In such case, is much better to have the script executable and invoke it directly:
\n#!/bin/bash \n\n/path/to/script.py \n
This way the version of python you need is only written in one file. Most of system these days are having python2 and python3 in the meantime, and it happens that the symlink python points to python3 , while most people expect it pointing to python2 .
Save the following program as print.py
:
#!/usr/bin/python3
print('Hello World')
Then in the terminal type:
chmod +x print.py
./print.py
You should be able to invoke it as python scriptname.py
eg
# !/bin/bash
python /home/user/scriptname.py
Also make sure the script has permissions to run.
You can make it executable by using chmod u+x scriptname.py
.
This works best for me: Add this at the top of the script:
#!c:/Python27/python.exe
(C:\\Python27\\python.exe is the path to the python.exe on my machine) Then run the script via:
chmod +x script-name.py && script-name.py
This works for me:
Create a new shell file job. So let's say: touch job.sh
and add command to run python script (you can even add command line arguments to that python, I usually predefine my command line arguments).
chmod +x job.sh
Inside job.sh
add the following py files, let's say:
python_file.py argument1 argument2 argument3 >> testpy-output.txt && echo "Done with python_file.py"
python_file1.py argument1 argument2 argument3 >> testpy-output.txt && echo "Done with python_file1.py"
Done with python_file.py
Done with python_file1.py
I use this usually when I have to run multiple python files with different arguments, pre defined.
Note: Just a quick heads up on what's going on here:
python_file.py argument1 argument2 argument3 >> testpy-output.txt && echo "completed with python_file.py" .
python python_file.py
, plain and simple. Next up, the >> will print and store the output of this .py file in the testpy-output.txt file.I use this and it works fine
#/bin/bash
/usr/bin/python python python_script.py
Since the other posts say everything (and I stumbled upon this post while looking for the following).
Here is a way how to execute a python script from another python script:
Python 2:
execfile("somefile.py", global_vars, local_vars)
Python 3:
with open("somefile.py") as f:
code = compile(f.read(), "somefile.py", 'exec')
exec(code, global_vars, local_vars)
and you can supply args by providing some other sys.argv
Here I have demonstrated an example to run python
script within a shell
script. For different purposes you may need to read the output from a shell command
, execute both python
script and shell
command within the same file.
To execute a shell command from python
use os.system()
method. To read output from a shell command
use os.popen()
.
Following is an example which will grep all processes having the text sample_program.py inside of it. Then after collecting the process IDs (using python) it will kill them all.
#!/usr/bin/python3
import os
# listing all matched processes and taking the output into a variable s
s = os.popen("ps aux | grep 'sample_program.py'").read()
s = '\n'.join([l for l in s.split('\n') if "grep" not in l]) # avoiding killing the grep itself
print("To be killed:")
print(s)
# now manipulating this string s and finding the process IDs and killing them
os.system("kill -9 " + ' '.join([x.split()[1] for x in s.split('\n') if x]))
References:
If you have a bash script and you need to run inside of it a python3 script (with external modules), I recommend that you point in your bash script to your python path like this.
#!/usr/bin/env bash
-- bash code --
/usr/bin/python3 your_python.py
-- bash code --
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