/var/spool/slurmd/job12662118/slurm_script: Line 136: Permem: Unbound Variable

Decoding the "permem: unbound variable" Slurm Error: A Comprehensive Guide

The error message "/var/spool/slurm/job12662118/slurm_script: line 136: permem: unbound variable" indicates a problem within your Slurm job script. This error arises when your script attempts to use the variable permem, but Slurm hasn't defined it. This usually happens because the variable is misspelled, not properly set, or used incorrectly within the script's context. This guide will help you troubleshoot and resolve this common Slurm issue.

Understanding the Error: The core issue is that Slurm cannot find a value assigned to the permem variable on line 136 of your Slurm script. This is a crucial variable if you're attempting to manage memory allocation within your Slurm job submission. The absence of this variable prevents Slurm from understanding your memory requests and properly executing your job.

Common Causes and Solutions

Here's a breakdown of the most frequent causes and their respective solutions:

1. Typographical Errors:

• Problem: The most straightforward reason is a simple typo. You might have misspelled permem as perMem, PERMEM, or something similar. Slurm is case-sensitive.
• Solution: Carefully review line 136 and ensure that permem is spelled correctly. Double-check for any extra spaces or characters around the variable name.

2. Incorrect Variable Placement/Scope:

• Problem: The permem variable might be defined within a function or conditional statement that isn't executed before line 136. Its scope might be limited, making it inaccessible where you're trying to use it.
• Solution: Check the script's structure. Make sure that the permem variable is defined before line 136 within the main script's body, outside any functions unless specifically passed as an argument. If it's defined within a function, ensure the function is called appropriately before line 136.

3. Missing Variable Definition:

• Problem: The most likely scenario is that you haven't defined the permem variable at all. Slurm doesn't automatically assign a default value; you must explicitly define it.
• Solution: Add a line defining permem before line 136, assigning it a suitable value. This value should reflect your desired memory allocation. For example: permem="10G" (for 10 gigabytes) or permem="4000M" (for 4000 megabytes). Remember to choose a memory allocation that's appropriate for your job's needs and your system's resources.

4. Incorrect Usage of srun or sbatch:

• Problem: If you're trying to use permem within a script launched via srun or sbatch, ensure you're using the --mem or --mem-per-cpu options correctly within the srun or sbatch command itself, rather than trying to define it within the script. permem is not a standard Slurm environment variable directly managed by the scheduler.
• Solution: Instead of defining permem within your script, use the appropriate Slurm options during job submission: sbatch --mem=10G my_script.sh or srun --mem-per-cpu=4G my_program.

5. Permission Issues (Less Likely):

• Problem: While less common, file permission issues could potentially prevent the script from being read or executed correctly.
• Solution: Check the permissions of your script file using ls -l your_script.sh. Ensure that you have read and execute permissions. If not, use chmod +x your_script.sh to add the necessary permissions.

Debugging Strategies

• Print Statements: Add echo "permem = $permem" just before line 136 to check if the variable is actually defined and its value.
• Error Logging: Implement proper error logging in your script to help pinpoint the exact location and cause of the issue.
• Simplified Testing: Create a minimal, reproducible example script to isolate the problem and avoid unnecessary complexity.

By carefully examining your script for these issues and utilizing the debugging strategies mentioned, you should be able to successfully resolve the "permem: unbound variable" error and successfully execute your Slurm job. Remember to always consult the official Slurm documentation for the most up-to-date information and best practices.