Questions on how to properly setup Snakemake LSF executor Job stderr and stdout logging

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Summary

The issue at hand is related to properly setting up Snakemake LSF executor job stderr and stdout logging. The user is experiencing difficulties in getting the job names changed and the stderr and stdout files to be written correctly when using Snakemake 9.+ with the LSF executor. The goal is to replicate the behavior achieved in Snakemake v7 using the --cluster-config and --cluster arguments.

Root Cause

The root cause of the issue lies in the incorrect configuration of the LSF executor. The user has attempted to add lsf_extra arguments to each rule, but this approach is not correct. The error message indicates that the jobs are not being properly accounted for in the LSF cluster, which suggests a misconfiguration of the job submission process. Key points to consider:

  • Incorrect use of lsf_extra arguments
  • Missing or incorrect configuration of job accounting in the LSF cluster
  • Inadequate linking of log files to the LSF executor

Why This Happens in Real Systems

This issue occurs in real systems due to:

  • Insufficient understanding of the LSF executor configuration: The user may not be familiar with the correct way to configure the LSF executor in Snakemake 9.+
  • Incompatible configuration between Snakemake versions: The user is trying to replicate a configuration that worked in Snakemake v7, but the configuration options and behavior may have changed in Snakemake 9.+
  • LSF cluster configuration issues: Problems with the LSF cluster configuration, such as incorrect job accounting settings, can prevent the jobs from being properly submitted and tracked

Real-World Impact

The impact of this issue is:

  • Inability to track job execution: The user is unable to monitor the execution of jobs, making it difficult to diagnose issues and optimize workflows
  • Loss of logging information: The stderr and stdout files are not being written correctly, resulting in lost logging information that could be useful for debugging and troubleshooting
  • Inefficient use of resources: The incorrect configuration may lead to inefficient use of resources, such as unnecessary job submissions or incorrect allocation of resources

Example or Code

rule annotate_variants:
    output:
        "results/annotate_variants.{PROJECT}.chr{CHR}.vcf"
    log:
        stderr="logs/lsf/annotate_variants.{PROJECT}.chr{CHR}.e",
        stdout="logs/lsf/annotate_variants.{PROJECT}.chr{CHR}.o"
    resources:
        lsf_queue="knmkln_normal",
        mem_mb=8000,
        threads=1
    shell:
        "annotate_variants --input {input} --output {output}"

Note that the log directive is used to specify the stderr and stdout files, and the resources directive is used to configure the LSF executor.

How Senior Engineers Fix It

Senior engineers would fix this issue by:

  • Carefully reviewing the LSF executor configuration: Ensuring that the configuration is correct and compatible with Snakemake 9.+
  • Verifying the LSF cluster configuration: Checking that the job accounting settings are correct and that the cluster is properly configured
  • Using the correct directives for logging: Using the log directive to specify the stderr and stdout files, rather than relying on lsf_extra arguments
  • Testing and validating the configuration: Thoroughly testing the configuration to ensure that it works as expected

Why Juniors Miss It

Juniors may miss this issue due to:

  • Lack of experience with Snakemake and LSF: Inadequate familiarity with the tools and their configuration options
  • Insufficient understanding of job submission and accounting: Limited knowledge of how jobs are submitted and tracked in the LSF cluster
  • Overreliance on outdated documentation or examples: Using outdated or incorrect information, which can lead to configuration errors and issues with job execution. Key takeaways for juniors include:
  • Carefully reviewing the documentation and configuration options for Snakemake and LSF
  • Seeking guidance from experienced engineers or mentors
  • Thoroughly testing and validating configurations to ensure correct behavior.

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