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I am running a Python code that contains print statements via SLURM. Normally when I run the Python code directly via "python program.py" the print statements appear in the terminal. When I run my program via SLURM, as expected the print statements do not appear in the terminal. How can I save the print statements to a file so I can check them as the program is running? Below is my submission script that I submit via "sbatch submit.sh". Notice that I've already tried two methods to write the output either to test1.out or test2.out. Please let me know where I'm going wrong!

#!/bin/bash

#SBATCH -J mysubmission
#SBATCH -p New
#SBATCH -n 1
#SBATCH -t 23:59:00
#SBATCH -o test1.out

module load gnu python

python program.py > test2.out
Ian
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  • Are you sure you know what directory the files are being created in? Try a fully qualified pathname. – RobertB Oct 16 '15 at 19:51
  • I see test1.out and test2.out are both created in the directory where I run sbatch. But these files are blank. I'll try adding path names though. – Ian Oct 16 '15 at 19:52
  • Adding path names didn't solve the problem. – Ian Oct 16 '15 at 19:54
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    Force your output to go to stdout by using: `sys.stdout.write` instead of print. Consider using `logging` module. – RobertB Oct 16 '15 at 19:55
  • I'll try that. Is there no way to get print to appear in the output files though? – Ian Oct 16 '15 at 19:56
  • I've heard *nix can be tricky with that. Not sure really, I'm on Windows :( http://stackoverflow.com/questions/3263672/python-the-difference-between-sys-stdout-write-and-print – RobertB Oct 16 '15 at 19:57
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    sys.stdout.write works. Thanks! – Ian Oct 16 '15 at 20:05

4 Answers4

21

By default, print in Python is buffered, meaning that it does not write to files or stdout immediately, and needs to be 'flushed' to force the writing to stdout immediately.

See this question for available options.

The simplest option is to start the Python interpreter with the -u option.

From the python man page:

-u Force stdin, stdout and stderr to be totally unbuffered. On systems where it matters, also put stdin, stdout and stderr in binary mode. Note that there is internal buffering in xreadlines(), readlines() and file-object iterators ("for line in sys.stdin") which is not influenced by this option. To work around this, you will want to use "sys.stdin.readline()" inside a "while 1:" loop.

damienfrancois
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7

You can use:

python -u program.py > test2.out

And all your output will be saved to test2.out file.

סטנלי גרונן
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Evgenia Galytska
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4

You can put

sys.stdout.flush()

after the print statements of interest. Or since python 3.3

print("hey", flush=True)

is an option. Using unbuffered IO (with python -u) could reduce performance if you print frequently, especially on a shared filesystem.

Jonatan Öström
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0

Above solutions did not yield live output for me. (You need to flush print and sync the file change.) Here is a code that you can simply prepend to your python script.

#!/usr/bin/env python3.7
import sys
import builtins
import os
sys.stdout = open("stdout.txt", "w", buffering=1)
def print(text):
    builtins.print(text)
    os.fsync(sys.stdout)

print("This is immediately written to stdout.txt")

That's it.

Explanation

Redirect stdout and write the file buffer after every newline.

sys.stdout = open("stdout.txt", "w", buffering=1)

Overwrite the print function and sync the flushed file also on the operating system side.

 def print(text):
    builtins.print(text)
    os.fsync(sys.stdout)
Manu
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