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Status Not under consideration
Workspace Spectrum LSF
Created by Guest
Created on Jan 4, 2019

prevent LSF docker jobs from failing with unuseful error message

When submitting docker jobs, using LSF (with the -app bsub option), the entire user's env is sent directly to the docker-current command (with the --env-file docker option), even though the docker-current command does not accept certain env variable formats (anything with whitespace). LSF is primarily(?) a batch job scheduler, which is commonly used in an HPC environment. Lmod, an implementation of "environment modules" is also very common in HPC environments. Lmod defines the "module" command (and the "ml" command) as a function in the user's environment. This function contains whitespace, so the job fails with "/usr/bin/docker-current: poorly formatted environment: variable '[ $? ' has white spaces.". It took a fair amount of effort to figure out what this error message was referring to. I think LSF should tell the user why the job is failing and automatically prevent the failure, or at the very least, print the workaround in the error message. My workaround is to add this bsub option:

#BSUB -env "all,~BASH_FUNC_module(),~BASH_FUNC_ml()"

  • Guest
    Apr 30, 2021

    It is impractical for LSF to check for anything and everything that will cause docker (or another container runtime to fail).