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I usually execute a Fortran file in Linux (manually) as:

  1. Connect to the server
  2. Go to the specific folder
  3. ifort xxx.for -o xxx && ./xxx (where 'xxx.for' is my Fortran file and 'xxx' is Fortran executable file)

But I need to call my fortran file (xxx.for) from python (I'm a beginner), so I used subprocess with the following command:

cmd = ["ssh", sshConnect, "cd %s;"%(workDir), Fortrancmd %s jobname "%s -o %s" exeFilename "%s && %s ./ %s%s"%(exeFilename)]

But I get an error, and I'm not sure what's wrong. Here's the full code:

import string import subprocess as subProc from subprocess import Popen as ProcOpen from subprocess import PIPE import numpy import subprocess userID = "pear" serverName = "say4" workDir = "/home/pear/2/W/fortran/" Fortrancmd = "ifort" jobname = "rad.for" exeFilename = "rad" sshConnect=userID+"@"+servername cmd=["ssh", sshConnect, "cd %s;"%(workDir), Fortrancmd %s jobname "%s -o %s" exeFilename "%s && %s ./ %s%s"%(exeFilename)] **#command to execute fortran files in Linux **#ifort <filename>.for -o <filename> && ./<filename> (press enter) **#example:ifort xxx.for -o xxx && ./xxx (press enter) print cmd

How can I write a python program that performs all 3 steps described above and avoids the error I'm getting?

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6 Answers 6

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there are some syntax errors...

original:

cmd=["ssh", sshConnect, "cd %s;"%(workDir), Fortrancmd %s jobname "%s -o %s" exeFilename "%s && %s ./ %s%s"%(exeFilename)]

I think you mean:

cmd = [ "ssh", sshConnect, "cd %s;" % (workDir,), "%s %s -o %s && ./%s" % (Fortrancmd, jobname, exeFilename, exeFilename) ]

A few notes:

  • a tuple with one element requires a comma at the end of the first argument see (workDir,) to be interpreted as a tuple (vs. simple order-of-operations parens)
  • it is probably easier to contruct your fortan command with a single string format operation

PS - For readability it is often a good idea to break long lists into multiple lines :)

my advice

I would recommend looking at this stackoverflow thread for ssh instead of using subprocess

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2

For the manual part you may want to look into pexpect or for windows wexpect. These allow you to perform subprocesses and pass input under interactive conditions.

However most of what you're doing sounds like it would work well in a shell script. For simplicity, you could make a shell script on the server side for your server side operations, and then plug in the path in the ssh statement:

ssh user@host "/path/to/script.sh"
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1

one error:
you have an unquoted %s in your list of args, so your string formatting will fail.

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Here is a complete example of using the subprocess module to run a remote command via ssh (a simple echo in this case) and grab the results, hope it helps:

>>> import subprocess >>> proc = subprocess.Popen(("ssh", "remoteuser@host", "echo", "1"), stdout=subprocess.PIPE, stderr=subprocess.PIPE) >>> stdout, stderr = proc.communicate()

Which in this case returns: ('1\n', '')

Note that to get this to work without requiring a password you will likely have to add your local user's public key to ~remoteuser/.ssh/authorized_keys on the remote machine.

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You could use fabric for steps 1 and 2. This is the basic idea:

from fabric.api import * env.hosts = ['host'] dir = '/home/...' def compile(file): with cd(dir): run("ifort %s.for -o %s" %(file,file)) run("./%s > stdout.txt" % file)
  • Create fabfile.py
  • And you run fab compile:filename
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do you have to use python?

ssh user@host "command"

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