Snakemake Executor Plugin SLURM

Oct 13, 2025 by pinkandtrash.com 75 views

Introduction

As a user of the Snakemake workflow management system, you may encounter issues when running your pipelines on a SLURM cluster. One such issue is the "SLURM account appears to be invalid" error, which can be frustrating and time-consuming to resolve. In this article, we will delve into the causes of this error, provide a step-by-step guide to troubleshooting, and offer potential solutions to get your pipeline running smoothly.

Software Versions

Before we dive into the troubleshooting process, let's take a look at the software versions used in this scenario:

Snakemake: 8.30.0
Snakemake Executor Plugin SLURM: 1.0.0
Snakemake Executor Plugin SLURM Jobstep: 0.3.0
SLURM: 24.05.3

Describe the Bug

When running a Snakemake pipeline with the SLURM plugin, you may encounter the following error:

No SLURM account given, trying to guess.
Guessed SLURM account: xyz
WorkflowError:
The given account xyz appears to be invalid. Available accounts:

The guessed account xyz is correct, but the error is thrown due to an issue with the command used to retrieve registered accounts.

Understanding the Issue

The reason for this error lies in the command used to retrieve registered accounts, which returns an empty list on your cluster. This is in contrast to the sshare command, which returns your accounts and could be used as an alternative.

Minimal Example

Unfortunately, a minimal example is not provided, as it is likely influenced by local SLURM configuration.

Troubleshooting Steps

To resolve the "SLURM account appears to be invalid" error, follow these steps:

Step 1: Verify SLURM Configuration

Ensure that your SLURM configuration is correct and up-to-date. Check the SLURM documentation for any changes or updates that may affect your pipeline.

Step 2: Check Account Availability

Verify that the guessed account xyz is indeed available on your cluster. You can do this by running the sacct command with the --format option to display the available accounts.

$ sacct --format=Account

Step 3: Use Sshare as an Alternative

As mentioned earlier, the sshare command can be used as an alternative to sacct to retrieve registered accounts. You can modify your pipeline to use sshare instead of sacct.

$ sshare -U

Step 4: Update Snakemake Executor Plugin SLURM

Ensure that you are using the latest version of the Snakemake Executor Plugin SLURM. You can update the plugin by running the following command:

$ mamba install -c conda-forge snakemake-executor-plugin-slurm

Step 5: Re-run the Pipeline

After making the necessary changes, re-run your pipeline to see if the error is resolved.

Conclusion

The "SLURM account appears to be invalid" error can be frustrating and time-consuming to resolve. By following the troubleshooting steps outlined in this article, you should be able to identify and fix the issue. Remember to verify your SLURM configuration, check account availability, use sshare as an alternative, update the Snakemake Executor Plugin SLURM, and re-run your pipeline. With these steps, you should be able to get your pipeline running smoothly on your SLURM cluster.

Additional Resources

For more information on Snakemake, SLURM, and the Snakemake Executor Plugin SLURM, refer to the following resources:

Snakemake Documentation
SLURM Documentation
Snakemake Executor Plugin SLURM Documentation
SLURM Account Appears to be Invalid: A Q&A Guide =====================================================

Introduction

In our previous article, we explored the "SLURM account appears to be invalid" error and provided a step-by-step guide to troubleshooting. In this article, we will answer some frequently asked questions (FAQs) related to this issue.

Q: What is the SLURM account appears to be invalid error?

A: The SLURM account appears to be invalid error is a message displayed by Snakemake when it is unable to validate a SLURM account. This error can occur due to various reasons, including incorrect SLURM configuration, unavailable accounts, or issues with the Snakemake Executor Plugin SLURM.

Q: Why is my SLURM account not being recognized?

A: There could be several reasons why your SLURM account is not being recognized. Some possible causes include:

Incorrect SLURM configuration
Unavailable accounts
Issues with the Snakemake Executor Plugin SLURM
Outdated Snakemake or SLURM versions

Q: How do I troubleshoot the SLURM account appears to be invalid error?

A: To troubleshoot the SLURM account appears to be invalid error, follow these steps:

Verify your SLURM configuration
Check account availability
Use sshare as an alternative to sacct
Update the Snakemake Executor Plugin SLURM
Re-run your pipeline

Q: What is the difference between `sacct` and `sshare`?

A: sacct and sshare are two different commands used to retrieve information about SLURM accounts. sacct is used to display information about completed jobs, while sshare is used to display information about available accounts.

Q: How do I update the Snakemake Executor Plugin SLURM?

A: To update the Snakemake Executor Plugin SLURM, run the following command:

$ mamba install -c conda-forge snakemake-executor-plugin-slurm

Q: What are some common issues that can cause the SLURM account appears to be invalid error?

A: Some common issues that can cause the SLURM account appears to be invalid error include:

Incorrect SLURM configuration
Unavailable accounts
Issues with the Snakemake Executor Plugin SLURM
Outdated Snakemake or SLURM versions
Conflicting account names or IDs

Q: How do I prevent the SLURM account appears to be invalid error in the future?

A: To prevent the SLURM account appears to be invalid error in the future, follow these best practices:

Regularly update your Snakemake and SLURM versions
Verify your SLURM configuration
Check account availability before running your pipeline
Use sshare as an alternative to sacct when necessary
Monitor your pipeline's output for any errors or warnings

Conclusion

The SLURM account appears to be invalid error can be frustrating and time-consuming to resolve. By understanding the causes of this error and following the troubleshooting steps outlined in this article, you can identify and fix the issue. Remember to verify your SLURM configuration, check account availability, use sshare as an alternative, update the Snakemake Executor Plugin SLURM, and re-run your pipeline. With these steps, you should be able to get your pipeline running smoothly on your SLURM cluster.

Additional Resources

For more information on Snakemake, SLURM, and the Snakemake Executor Plugin SLURM, refer to the following resources: