CODEWITHSUNDEEP
pythonsubprocess
JakobJakobson13
JakobJakobson13

Reputation: 145

Start background process in python via subprocess and write output to file

Dear stackoverflow users,

I'm looking for a solution for a probably quite easy problem. I want to automate some quantum chemical calculations and ran into a small problem.

Normally you start your quantum chemical programm (in my case it's called orca) with your input file (*.inp) on a remote server as a background process and pipe the output into an outputfile (*.out) via

nohup orca H2.inp >& H2.out &

or something similar.

Now I wanted to use a python script (with some templating) to write the input file automatically. At the end the script should start the calculation in a way that I could log out of the server without stopping orca. I tried that with

subprocess.run(["orca", input_file], stdout=output_file)

but so far it did not work. How do I "emulate" the command given at the top with the subprocess module?

Regards

Update I have one file that is called H2.xyz. The script reads and splits the filename by the point and creates an input file name H2.inp and the output should be written into the file H2.out.

Update 2 The input file is derived from the *xyz file via

xyzfile = str(sys.argv[1])
input_file = xyzfile.split(".")[0] + ".inp"
output_file = xyzfile.split(".")[0] + ".out"

and is created within the script via templating. In the end I want to run the script in the following way:

python3 script.py H2_0_1.xyz

Upvotes: 5

Views: 13156

Answers (4)

Sven-Eric Krüger
Sven-Eric Krüger

Reputation: 1327

For me (Windows, Python 2.7) the method call works very fine like this:

with open('H2.out', 'a') as out :
    subprocess.call(['orca', infile], stdout=out,
                                      stderr=out,
                                      shell=True)   # Yes, I know. But It's Windows.

On Linux you maybe do not need shell=True for a list of arguments.

Upvotes: 1

Sharku
Sharku

Reputation: 1092

I had the same problem not long ago. Here is my solution:

commandLineCode = "nohup orca H2.inp >& H2.out &"
try:
    proc = subprocess.Popen(commandLineCode,
                            stdin=subprocess.PIPE,
                            stdout=subprocess.PIPE,
                            stderr=subprocess.PIPE,
                            cwd = workingDir)

except OSError:
    print("Windows Error occured")
    print(traceback.format_exc())

timeoutInSeconds = 100
try:
    outs, errs = proc.communicate(timeout = timeoutInSeconds)
except subprocess.TimeoutExpired:
    print("timeout")
    proc.kill()
    outs, errs = proc.communicate()

stdoutDecode = outs.decode("utf-8")
stderrDecode = errs.decode("utf-8")

for line in stdoutDecode.splitlines():
    # write line to outputFile
if stderrDecode:
    for line in stderrDecode.splitlines():
        # write line to error log

The OSError exception is pretty important since you never now what your OS might do wrong.

For more on the communicate() command which actually starts the process read: https://docs.python.org/3/library/subprocess.html#subprocess.Popen.communicate

Upvotes: 0

Simon K.
Simon K.

Reputation: 66

Is the usage of subprocess important? If not, you could use os.system.

The Python call would get really short, in your case

os.system("nohup orca H2.inp >& H2.out &")

should do the trick.

Upvotes: 0

Adelina
Adelina

Reputation: 11941

Why not simply:

subprocess.Popen(f'orca {input_file} >& {output_file}',
                 shell=True, stdin=None, stdout=None, stderr=None, close_fds=True)

More info: Run Process and Don't Wait

Upvotes: 1

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