CODEWITHSUNDEEP
pythonfortransubprocessos.system
falconskull
falconskull

Reputation: 303

Can't seem to get fortran executable to run correctly through python

I have read a bunch of different topics on SO and other sites and cannot get a direct answer to my question/problem. Currently I have this python script that runs completely fine, with the exception of no calls made to run a fortran program are working correctly. I have tried using subprocess commands, os.system commands, opening bash script files that are opened through python, and no luck. Here are some examples and errors I'm getting.

One attmept:

subprocess.Popen(["sh", "{0}{1}".format(SCRIPTS,"qlmtconvertf.sh"), "qlmt"], shell=False, stdout=subprocess.PIPE)

This gives an error that the program has trouble reading the file correctly.

    forrtl: severe (24): end-of-file during read, unit 1, file /home/akoufos/lapw/Ar/lda/bcc55_mt1.5_lo_e8_o4/DOS/lat70/qlmt

Another attempt:

subprocess.Popen(["./{0}{1}".format(SOURCE,"qlmtconvertf"), "qlmt"], shell=False, stdout=subprocess.PIPE)

This gives an error of not finding the file.

    File "/home/akoufos/lapw/Scripts_Plots/LAPWanalysis.py", line 59, in DOS
subprocess.Popen(["./{0}{1}".format(SOURCE,"qlmtconvertf"), "qlmt"], shell=False, stdout=subprocess.PIPE)
    File "/usr/lib64/python2.7/subprocess.py", line 672, in __init__
errread, errwrite)
    File "/usr/lib64/python2.7/subprocess.py", line 1202, in _execute_child
raise child_exception
    OSError: [Errno 2] No such file or directory

Yet another attempt:

os.system("{0}{1}".format(SOURCE,"qlmtconvertf qlmt"))

This gives an error equivalent to the first example. In all examples SOURCE="/home/myusername/lapw/Source/", where the fortran source files are, SCRIPTS="/home/myusername/lapw/Scripts_Plots/", where I have other files and the python scripts in, qlmtconvertf is a compiled fortran program, and qlmt is a file the qlmtconvertf reads. This source code works completely fine if I call it in the shell, like I have done countless times, but I'm trying to automate calling these codes. I have written a bash script as well, that does what I need, but I'm trying to do everything through python instead. Any ideas, suggestions, or answers to what I am doing incorrectly and what is going on would be greatly appreciated. Thank you all in advance.

EDIT: I got it working with the suggestion given below by Francis. I had to keep the complete paths (i.e. /home/username/etc) and the os.path.join to call the program correctly.

    import os.path
    LAPW = "/home/myusername/lapw/"
    SOURCE = os.path.join(LAPW,'Source')
    SCRIPTS = os.path.join(LAPW,'Scripts_Plots')
    QLMTCONVERT = os.path.join(SOURCE,'qlmtconvertf')
    qargs = [QLMTCONVERT,'qlmt']
    #CALLING PROGRAM
    subprocess.Popen(qargs, stdout=subprocess.PIPE).communicate(input=None)

To get it to work correctly I had to also close the 'qlmt' file I had created during the python script. Also I am working in the directory that contains the 'qlmt' file.

(edit Also added .communicate(input=None) to the end of the subprocess. This was unnecessary for this process call, but it was important for a latter one I made in the script that tried to use a file the process was creating. From my understanding the .communicate talks to the process and basically waits for it to finish before the next python line is executed. Similar to .wait(), but more advanced. If someone who understands this more wants to elaborate, please feel free. edit)

I'm not exactly sure why this method worked, but using strings as inputs for the subprocess was giving errors. If any one has any insight on this I would be very thankful if you could pass on your knowledge. Thank you everyone for the help.

Upvotes: 2

Views: 1954

Answers (1)

Francis Avila
Francis Avila

Reputation: 31621

I think you forgot a slash in your filenames:

"{0}{1}".format(SOURCE,"qlmtconvertf qlmt") == '/home/myusername/lapw/Sourceqlmtconvertf qlmt'

I assume you mean this?

"{0}/{1}".format(SOURCE,"qlmtconvertf qlmt") == '/home/myusername/lapw/Source/qlmtconvertf qlmt'

I recommend using os.path.join rather than direct string construction for pathname creation:

import os.path

executable = os.path.join(SOURCE, 'qlmtconvertf')
args = ['qlmt']

subprocess.Popen(executable+args, stdout=subprocess.PIPE)

Upvotes: 3

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