module envs are missing when using SlurmSpawner

[eddy16112]

Bug description

My sbatch script is:

[I 2022-06-02 22:44:23.718 JupyterHub batchspawner:292] Spawner submitted script:
    #!/bin/bash
    #SBATCH -t 00:30:00
    #SBATCH -N 1
    env
    module load PrgEnv/GCC+OpenMPI/2021-05-27 cuda gcc openmpi
    which mpirun
    batchspawner-singleuser jupyterhub-singleuser

I am getting an error in the slurm-xxxxx.out /var/spool/slurm/d/job242029/slurm_script: line 5: module: command not found Looks like it can not find the module.

However, if I manually submit the script using sbatch mytest.sub, and I do not see the error.

More details

I compared the env output from the slurm.out generated by SlurmSpawner and the one generated by manual submission, and I found out the following module related envs are missing from the slurm.out generated by the spawner.

MODULEPATH=/gpfs/fs1/SHARE/Modules/Latest:/gpfs/sw/modules/all:/gpfs/fs1/SHARE/Modules/Bundles:/gpfs/fs1/SHARE/Modules/PrgEnv/GCC+OpenMPI/2021-05-27
MODULEPATH_ROOT=/gpfs/fs1/SHARE/Utils/Lmod/8.1/GCC-BASE-7.4.0/modulefiles
MODULESHOME=/gpfs/fs1/SHARE/Utils/Lmod/8.1/GCC-BASE-7.4.0
BASH_FUNC_module%%=() {  eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
BASH_FUNC_ml%%=() {  eval $($LMOD_DIR/ml_cmd "$@")
}

Is it a bug or did I miss anything when using the SlurmSpawner?

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[mahendrapaipuri]

Hey, As you rightly figured out, this is problem of the environment not being complete when batchspawner submitting the job. Under the hood, batchspawner submits the job using command sudo -E -u <target_user> sbatch --parsable <script>. You can run test this command as same user as the JupyterHub running under to see why complete environment is not being sourced. But I do not think this has to do anything with batchspawner and more with your platform configuration.