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Using environment modules with SGE jobs and qlogin
qlogin
For qsub jobs, if you have not overridden the default SGE parameters then the entire environment is passed to the job. This is because the -V qsub flag is set in the default request. Since environment modules set up the environment then the environment set up by the modules will be passed. Since the list of the loaded modules is also part of the environment then the list of loaded modules will be passed as well. However, the above does not apply to qlogin sessions as that creates a fresh environment. See the Qlogin for Interactive Sessions - HPC Documentation - UIowa Wiki page for more information.However, the
standard qsub
The recommendation for "standard" qsub jobs is to include the module load statements in your job script and not depend on the environment passed in from the submit host. That way, setting up the needed environment is part of the job and is thus more reproducible. If depending on loading modules before qsub then you have to remember to get the environment set up before job submission. When loading modules in your job script, it is best to use module sets. If you would prefer to make sure that the module loads are more explicit then make sure to do a
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before any "module load ..." commands.
High Throughput Computing (HTC) and/or High Volume Computing (HVC)
If your jobs are High Throughput Computing (HTC) and/or High Volume Computing (HVC) jobs, it is advised to not load modules per job but rather use the submission environment. The reason is that many thousands of jobs will need to do a large number of module loads in relatively short time frames, which could cause failures. For HTC/HVC type jobs, carefully load the modules that you will need for the jobs prior to job submission. The loaded modules are part of the environment so they will get passed to the job, unless you have overridden the default. Do not load any modules or module sets in the job script, although you may want to have comments regarding what modules are in use. Do not load any modules or module sets in your ~/.bashrc file. Finally, disable the default module set if you have one.