Why is there no entry in the Slurm output file until the job ends?

The reason why you might not see any output in your Slurm output file until the job completes is often due to buffering.

Here's a breakdown of why this happens and how to address it:

1. Buffering:

- Standard Output (stdout) and Standard Error (stderr): Programs often buffer their output before writing it to the output stream. This is for performance reasons, as writing small chunks of data frequently can be inefficient.

- Slurm's Handling: Slurm inherits this behavior. When a job is running, the output is often buffered by the application itself, the shell, or by Slurm's I/O handling mechanisms.

2. Flushing the Buffers:

- Implicit Flushing: Buffers are automatically flushed when they are full, when the program exits, or when you explicitly tell them to flush.

- Problem: If the job runs for a long time and doesn't produce enough output to fill the buffer, or if it doesn't explicitly flush the output, you won't see anything in the output file until the job ends.

3. Solutions:

- Explicitly Flush Output:

- In many programming languages, you can explicitly flush the output buffer. For example:

- Python: Use sys.stdout.flush() or print(..., flush=True).

- C/C++: Use fflush(stdout).

- Bash: Use stdbuf -o0 or unbuffer (from the expect package) to disable buffering for standard output.

- Example (Python):

import sys
print("This will be written immediately.", flush=True) sys.stdout.flush()

- Use stdbuf or unbuffer:

- These utilities can modify the buffering behavior of commands. You might need to install the expect package to use unbuffer.

- Example:

sbatch --output=myjob.out myjob.sh

- To disable output buffering for the script, modify the submission script (myjob.sh) by prepending stdbuf -o0 to the command:

#!/bin/bash
#SBATCH --job-name=testjob
#SBATCH --output=testjob.out

stdbuf -o0 ./my_program

- Set –unbuffered in srun (if applicable): If you're using srun, you can specify the --unbuffered option.

- Check Slurm Configuration: While less common, check your Slurm configuration (slurm.conf) for any settings that might affect output buffering. This is usually handled at the application or shell level, but it's worth verifying.

4. Example Job Submission Script (myjob.sh):

#!/bin/bash
#SBATCH --job-name=my_long_job
#SBATCH --output=my_long_job.out

for i in {1..10}; do
  echo "Step $i" && date
  sleep 5
done

echo "Job Complete" && date

- To see output immediately in this script, either modify the script to flush the buffer, or disable the buffer with stdbuf as shown above.

By addressing buffering, you can ensure that your Slurm output files are populated with information in near real-time, helping you monitor the progress of your jobs.

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