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Asked: 2024-09-21T22:16:21+05:30 In:

How can I capture the output from print statements when executing a script using SLURM?

Hey everyone! I’m currently working on a research project that involves running some scripts on a cluster managed by SLURM. I’m trying to figure out the best way to capture the output from the print statements in my Python scripts when they’re executed using SLURM.

I’ve tried redirecting output to a file, but I’m not seeing the print statements show up as I’d expected. Can anyone share their experience or best practices on how to capture that output effectively? Any tips or examples would be really helpful! Thanks in advance!

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    3 Answers

    1. “`html





      Capturing Output in SLURM

      Capturing Output from Python Scripts on SLURM

      Hi there! I’ve faced a similar issue when working with SLURM and Python scripts. Here’s how you can effectively capture the output from your print statements:

      1. Redirecting Output

      When submitting your job with SLURM, you should use the --output option in your SLURM script. For example:

      sbatch --output=output.log my_script.py

      This will direct all standard output (stdout) from your script to output.log file.

      2. Error Output

      If you also want to capture error messages (stderr), you can use:

      sbatch --output=output.log --error=error.log my_script.py

      This way, any errors will be logged separately in error.log.

      3. Combining stdout and stderr

      If you want both stdout and stderr in the same file, you can do the following:

      sbatch --output=output.log --error=output.log my_script.py

      4. Example SLURM Script

      Here’s a simple example of a SLURM script:

      #!/bin/bash
#SBATCH --job-name=my_python_job
#SBATCH --output=output.log
#SBATCH --error=error.log
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1

module load python
python my_script.py

      5. Check Output

      After your job finishes, check the output.log file to see the print statements from your Python script. If the log file is not being created or is empty, make sure your script is executing correctly and that print statements are being reached.

      Hope this helps! Good luck with your research project!



      “`






    2. SLURM Output Capture

      Capturing Output in SLURM

      Hi there!

      I totally understand the struggle with capturing output from print statements in Python scripts when running on SLURM. Here are some tips that might help you out:

      • When you submit your SLURM job using the sbatch command, you can use the following options to redirect the output:
      • Standard Output: Use #SBATCH -o output.txt in your script to capture standard output, which includes print statements.
      • Error Output: Use #SBATCH -e error.txt to capture any errors that occur during execution.
    3. Make sure to check the output files specified. They should be in the same directory from which you submitted your job.
    4. For example, if your SLURM script looks like this:
      5.         #!/bin/bash
        #SBATCH -o output.txt
        #SBATCH -e error.txt
        #SBATCH --job-name=my_python_job
        #SBATCH --time=01:00:00
        #SBATCH --ntasks=1
        #SBATCH --cpus-per-task=1

        module load python/3.8
        python my_script.py
    5. After your job finishes, check output.txt for your print statements!

      6. If you need to capture the output while the job is still running, you can use the squeue command to monitor job status and output.

      Hope this helps! Let me know if you have any more questions.


  • “`html

    When running Python scripts on a SLURM-managed cluster, capturing the output from print statements is crucial for debugging and logging your work. The simplest way to capture stdout and stderr output is by using the SLURM job script options. You can set options such as #SBATCH --output=output.txt to redirect standard output to a specific file. By default, only the standard output (stdout) will be captured unless you also specify #SBATCH --error=error.txt for standard error (stderr) output. Additionally, ensure that your print statements are not being suppressed by any other logging configuration or interpreter settings.

    If you find that your print statements are still not showing up, consider explicitly flushing the output buffer by calling sys.stdout.flush() or using the flush=True argument in your print statements in Python 3. This ensures that the output is written immediately to the file instead of being buffered. Another option is to modify the job script to include a simple print statement at the end that confirms the job completion, which can help ascertain that the code executed as expected. Following these practices should help you effectively capture all necessary output while using SLURM.

    “`

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