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Frequently Asked Questions (FAQ)

  • How can I access CESM-Lab after the tutorial?

    • You can always find all the tutorial materials here.
    • Your access to AWS will be depracted after this tutorial but you can access CESM-Lab using an AWS account (check with your lab or university).
    • You can also run CTSM using dockers on your own laptops. Details on running CTSM using containers through our CTSM-NEON tutorial tool are available here.

  • How can I transfer my progress/data outside the cloud or on another machine?

    • You can transfer Jupyter notebooks, case directories, and other files you created or modified during the tutorial from CESM-Lab to your personal computer (or any other machine) using rsync.
      • Open a terminal window (or SSH into, for a machine like NCAR's Cheyenne) in the machine you would like the files transferred to. On Macs you can generally access a terminal via Applications > Utilities > Terminal. On Windows machines you may need to download a software like PuTTY.
      • Inside the terminal, navigate to the location you would like the files downloaded to and type: rsync -avz <username>@ctsmworkshop2022.cesm.cloud:<full_path_of_file> .
      • Your computer may say it cannot "recognize the authenticity of the host", but you can enter yes
      • Then you will be prompted to enter your CTSM Tutorial 2022 password (the password you used to log into CESM-Lab)
    • Alternatively on CESM-Lab you can directly download any individual files by right clicking on them in the left-hand file navigation pane and clicking Download. Directories can be downloaded by first tar-ing them (e.g. tar -zcvf my_files.tar.gz clm_tutorial_cases). Then right click on the tarred file in the file navigation pane to download it as you would a file.

  • I messed up the notebooks. How can I find what it should be??

    You can look at the notebooks on GitHub and correct small mistakes, or you can do the following:

    • Open up terminal window
    • Navigate to CTSM-Tutorial-2022 directory (cd ~/CTSM-Tutorial-2022)
    • Run git status to check the status of your notebooks and which branch you are on.
    • If you are on the main branch, run git stash which stashes your progress and whatever you saved in your notebooks.
    • Next, run git pull to get a clean version of the tutorial notebooks from the original repository.

  • How do I see what jobs are running on AWS?

    • You can either use qstat or squeue in terminal to list all your jobs and their status.

    • Below is the list of acronyms in the ST column and their meanings:

      Status Code Description
      Completed C Job just successfully completed.
      Running R The Job is currently running.
      Queued/Waiting Q / PD The job is waiting for allocation in the queue.

  • How do I kill a job that’s running?

    • You can either use qdel JOBID or scancel JOBID. You should replace JOBID with the job ids that you'd want to stop. Please note that you can get your JOBID by using qstat or squeue.

  • I get a message saying that there is an existing directory and cannot run my code. What do I do??

    • Remove the existing directory, which was likely created for an earlier failed case. Alternatively, if this error occurs when using the run_neon script, you can use the --overwrite option.

  • Which parameters need to have a re-build after changing them?

    • You only need to rebuild if you've changed something in env_build.xml or env_mach_pes.xml. You can change env_run.xml or user_nl_* files without rebuilding. The only exception to that is if you are restarting and trying to change the years you are running over for DATM. For more information on when a rebuild is necessary, please see section 4.2 on this website.