Python subprocess not executing program correctly

Question

I'm trying to execute a Fortran program in a shell from Python. I'm using subprocess to call the Fortran program and pass arguments (two input files are required). This is how I do it:

COMMAND = '/path/to/FORTRAN/program << !\n' + INPUT_FILE1 + '\n' + INPUT_FILE2 +'\n!'
return = subprocess.call(COMMAND, shell=True)

Unfortunately, the Fortran program exits with:

? FORTRAN Runtime Error:
? Attempt to read past end of file
? READ(UNIT=22,...

This is not an issue with the input files or the Fortran program. When I execute this in my shell:

$>/path/to/FORTRAN/program << !
>INPUT_FILE1
>INPUT_FILE2
>!

everything works as expected (no Attempt to read past end of file).

I don't have access to the Fortran source, so I cannot check what is going on in there. I think it has to do with the way I'm calling the program through subprocess - I just can't figure out what.

I'm using Python 2.6.6.

Quick explanation: The Fortran program will prompt for two input files, but it doesn't recognize them as command-line options (they cannot be provided with the call to the program). If you want to run it from - say a shell script (batch mode) - you need to capture the return command to execute the command, but also provide the two files. The << ! opens a "list" for lack of a better term. The following commands are handed to the program which waits with its execution until ! is typed.

I have used this approach multiple times successfully (different Fortran code), and with this one, using a C shell script (not Python).

I don't know enough about running FORTRAN from a terminal - what's the significance of <<? Is that reading from stdin or otherwise? Perhaps the problem is that you're submitting the input files as arguments, but it expected a buffer it's going to parse. Hard to say without more info about the program in question. — g.d.d.c
– g.d.d.c, Commented Mar 28, 2013 at 21:06
I tried to reproduce by calling a small program that dumps its stdin, and both the command-line and subprocess work in this case. — Armin Rigo
– Armin Rigo, Commented Mar 28, 2013 at 21:50

jfs · Accepted Answer · 2013-05-16 15:31:39Z

1

You could try "\r\n" (tty newline):

from subprocess import Popen, PIPE

p = Popen(["/path/to/FORTRAN/program"], stdin=PIPE,
          bufsize=1, close_fds=True)
p.communicate("INPUT_FILE1\r\nINPUT_FILE2")
rc = p.returncode

with/without "\r\n" at the end.

answered May 16, 2013 at 15:31

jfs

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3 Comments

Schorsch Over a year ago

this worked, with a slight modification: I used p.communicate("INPUT_FILE1\nINPUT_FILE2") without the \r. What is the difference between the communicate and the stdin.write, as suggested by @Armin-Rigo? Or is this rather a different question ...

jfs Over a year ago

In this case it should be equivalent to .stdin.close(); .wait(). The difference might be in the initial .write() part.

jfs Over a year ago

Though looking at the source I don't see any difference except bufsize=1 (line-buffered) and close_fds=True (the latter should be default on posix)

Community · Accepted Answer · 2017-05-23 10:33:42Z

1

I had what may have been a similar problem a while back, and the solution turned out to be adding a small pause. Take a look at this and see whether that technique helps.

edited May 23, 2017 at 10:33

CommunityBot

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answered Mar 29, 2013 at 20:18

LAK

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Comments

Armin Rigo · Accepted Answer · 2013-03-29 21:21:42Z

1

Maybe it's caused by the shell invoked with shell=True, if that doesn't invoke bash on your system. You can avoid depending on the extended shell syntax <<, and instead build the whole call on your own, as in:

popen = subprocess.Popen(["/path/to/FORTRAN/program"], stdin=subprocess.PIPE)
popen.stdin.write('123\n')
time.sleep(0.1)    # hack, following LAK's suggestion
popen.stdin.write('456\n')
popen.stdin.close()
result = popen.wait()

edited Mar 29, 2013 at 21:21

answered Mar 28, 2013 at 21:54

Armin Rigo

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1 Comment

Schorsch Over a year ago

I've tried your updated proposal - and played with the sleep command a little - without success. For now I fixed it by writing the command to a shell script and executing that from Python. Maybe a bit convoluted, but it works.

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