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How do I save print statements when running a program in SLURM?

Tags:

python

slurm

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
like image 661
Ian Avatar asked Oct 16 '15 19:10

Ian


3 Answers

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.

like image 125
damienfrancois Avatar answered Oct 20 '22 21:10

damienfrancois


You can use:

python -u program.py > test2.out

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

like image 8
Evgenia Galytska Avatar answered Oct 20 '22 21:10

Evgenia Galytska


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.

like image 6
Jonatan Öström Avatar answered Oct 20 '22 19:10

Jonatan Öström