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Appendix

This appendix details some specifities and helpful tips.

Useful Aliases

Setting some aliases may be useful in running the model. You can edit your bash settings file to add aliases. Run source on that file to start using your new aliases. Examples:

  • Chrysalis – source ~/.bashrc
  • Compy – source ~/.bash_profile
  • Perlmutter – source ~/.bash_profile.ext

Note that the specific file name may differ amongst machines. For example, it might be named ~/.bashrc.ext.

Batch Jobs

To check on all batch jobs, with the Slurm scheduler:

alias sqa='squeue -o "%8u %.7a %.4D %.9P %7i %.2t %.10r %.10M %.10l %.8Q %j" --sort=P,-t,-p'

To check on your batch jobs, with the Slurm scheduler:

alias sq='sqa -u $USER'

The output of sq uses several abbreviations: ST = Status, R = running, PD = pending, CG = completing.

Directories

You will likely be working in several directories. Here are some example values:

<run_scripts_dir>: ${HOME}/E3SM/scripts

<code_source_dir>: ${HOME}/E3SM/code

The path for <simulations_dir> will likely be machine-dependent. For example,:

  • Anvil/Chrysalis (LCRC): /lcrc/group/e3sm/<username>/E3SMv2
  • Compy (PNNL): /compyfs/<username>/E3SMv2
  • Perlmutter (NERSC): /global/cfs/cdirs/e3sm/<username>/E3SMv2

So, it may be useful to set the following aliases:

# Model running

alias run_scripts="cd <run_scripts_dir>"
alias code_source="cd <code_source_dir>"
alias simulations="cd <simulations_dir>"