SLURM error and output files with custom variable name

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                          I'd like my log files to be named after a variable. Since this isn't possible:

    #SBATCH --output some_software.${var}.out
    #SBATCH --error  some_software.${var}.err

I came across this work around but not sure if it's ok, or if it's wrong or if there's a better way:

    #!/bin/bash
    #SBATCH --job-name my_job
    #SBATCH --partition some_partition
    #SBATCH --nodes 1
    #SBATCH --cpus-per-task 8
    #SBATCH --mem 50G
    #SBATCH --time 6:00:00
    #SBATCH --get-user-env=L
    #SBATCH --export=NONE
    
    var=$1
    
    # SLURM doesn't support variables in #SBATCH --output, so handle logs manually
    if [ -z "$SLURM_JOB_ID" ]; then
      log_dir="/data/logs"
      sbatch --output="${log_dir}/some_software.${var}.out" \
             --error="${log_dir}/some_software.${var}.err" \
             "$0" "$var"
      exit
    fi
    
        
    /data/software/nextflow run /data/software/some_software/main.nf
                        

Asked by Caterina (103 rep)

May 12, 2025, 10:46 PM
Last activity: May 13, 2025, 04:09 PM

SLURM error and output files with custom variable name

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