sbatch: error: invalid directive found in batch script: 16

Lemon

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03-02-2025

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The error message "sbatch: error: invalid directive found in batch script: 16" indicates a problem within your Slurm batch script. The number "16" points to a specific line (or around line 16) containing an invalid Slurm directive or syntax error. This isn't a general Slurm error; it's highly specific to the content of your script. Let's troubleshoot this effectively.

Understanding the sbatch Command and Slurm Directives

sbatch is the command used to submit batch scripts to the Slurm Workload Manager. These scripts contain directives that tell Slurm how to manage your job, including resource requests (CPUs, memory, time), job dependencies, and output handling. An "invalid directive" means you've used a Slurm keyword incorrectly or used a keyword that Slurm doesn't recognize.

Common Causes and Solutions

Here are the most frequent reasons for this error and how to address them:

1. Typos and Incorrect Syntax

• Problem: The most common cause is a simple typo in a Slurm directive. For example, misspelling #SBATCH (which must be at the beginning of each directive line) or misusing other keywords like --ntasks, --cpus-per-task, --mem, --time, etc.
• Solution: Carefully review line 16 (and the surrounding lines) of your script. Double-check the spelling of all Slurm directives and ensure they adhere to the correct syntax. Refer to your Slurm documentation for the exact format of each directive.

2. Missing or Extra Characters

• Problem: An extra space, a missing hyphen, or an incorrect character can invalidate a directive.
• Solution: Scrutinize line 16 for any extraneous characters. Make sure hyphens are used correctly in options (e.g., --time=00:30:00), and that there are no leading or trailing spaces.

3. Unsupported Directives

• Problem: You might be using a Slurm directive that isn't supported by your specific Slurm version or cluster configuration.
• Solution: Consult your system's Slurm documentation to determine which directives are available. Outdated examples or tutorials might use unsupported features.

4. Incorrect Variable Usage

• Problem: Incorrectly using environment variables within Slurm directives can lead to this error.
• Solution: Ensure that any variables used within the directives are correctly defined and expanded. Avoid directly embedding variable values within the directives; instead, use appropriate substitution methods.

5. Mixing Shell Commands and Slurm Directives

• Problem: Slurm directives (#SBATCH...) are different from shell commands. Make sure you're not mixing them inappropriately. Slurm directives go at the beginning of the script before any shell commands.
• Solution: Organize your script. Place all Slurm directives at the very beginning, followed by your shell commands.

Debugging Steps

1. Print the problematic script line: Use sed -n '16p' your_script.slurm to display only line 16 of your script. This isolates the problematic line for easier examination.
2. Check your Slurm version: Use scontrol show config to check the version of Slurm running on your system. Compare your directives to the documentation for that specific version.
3. Simplify your script: Create a minimal, reproducible example script. Start with only essential directives and gradually add complexity until you pinpoint the problematic line.
4. Consult your system administrator: If you're still stuck, contact your cluster's system administrator or support team. They have the most detailed knowledge of your cluster's specific Slurm configuration.

By systematically checking these points and using the debugging steps, you should be able to identify and resolve the "invalid directive" error in your Slurm batch script. Remember to always refer to your cluster's official Slurm documentation for the most accurate and up-to-date information.