Logging-in to Derecho

Tutorial practice exercises are tailored to work on the NSF NCAR's Derecho HPC - an HPC cluster that includes the libraries needed by WRF and its pre- and post-processing tools through modules.

Note that WRF Tutorial instructors are not able to help with this process. If you cannot obtain help from a systems administrator at your institution, you will need to contact NCAR'S CISL HPC User Support

1. Open a teminal window on your local system.
   
   

   Note: If you are using a Windows system and don't know how to do this, See the Notes for Windows Users (note that this page is titled to be specific for running on an AWS cloud platform, but they can be generally helpful for this purpose, as well). Otherwise, if you have access to a systems administrator (or IT staff) at your institution, they should be able to help.

   
   


2. Type in the following command, but USE YOUR OWN USER NAME instead of "user".

   >ssh -Y user@derecho.hpc.ucar.edu

   then hit the "enter/return" key.



3. You should then see

   >(user@derecho.hpc.ucar.edu) ncar-two-factor:




4. Type your password here (the password you set up using the emailed instructions from NSF NCAR/CISL).
   *Note* - your password will not display as you type it. This is normal. After you type it in, just hit the "enter/return" key.



5. If you have the DUO app installed on your phone, you should get a DUO notification like this.

   
   
   




6. Tap on the notification and you should see a screen that looks like the following.

   
   
   




7. Tap the "Approve" button and then you should be let in to the Derecho system.

Setting–up Your Environment

When you first log–in to Derecho, you will be placed in your home directory (/glade/u/home/$USER, where "$USER" is your CISL log-in name).

Before going through any of the exercises in subsequent sections, several environmental settings will need to be in place. To make this easier, we have placed them all into a .bash script you can simply copy to your home directory. From your home direcotry, issue the following:

cp -r /glade/campaign/mmm/wmr/wrf_tutorial/practice_exercises/.bashrc .

and then source the .bashrc script to implement the environment settings.

source .bashrc

Note Now that you have the .bashrc file in your home directory, next time you log-in to Derecho, it will automatically apply the settings, so you will not need to do this step at any point after this.

Setting up Your Practical Exercises

• During this tutorial, you will run all your exercises in the scratch directory (/glade/derecho/scratch/$USER). Go ahead and move into that directory.

  > cd /glade/derecho/scratch/$USER

  Note Although you each have a user name assigned specifically to you, using the syntax $USER will also take you to your specific directory. Anywhere in these exercises that you see $USER, you can choose to replace it with your specific user name.

  
  
  


• The entire preconfigured directory structure is available. You just need to copy that folder to your /glade/derecho/scratch/$USER directory. Don't forget the dot (".") at the end of the command.
  
  NOTE that you will likely see errors indicating a lack of permissions to copy some of the .git–related files over. This is okay, as you shouldn't need those files, so you can ignore those errors.
  

  > cp -r /glade/campaign/mmm/wmr/wrf_tutorial/practice_exercises .
  

  This will take several minutes. Once it completes, you will be given the command line prompt again in your terminal window, and at that time, you can move into the practice_exercises directory.

  > cd practice_exercises

Running Jobs on Derecho

Running jobs on Derecho requires the submission of a job script to a batch queueing system, which allocates requested computing resources to your job when they become available. In general, it's best to avoid running any compute-intensive jobs on the login nodes. The practice instructions throughout this tutorial will guide you in the process of submitting jobs when necessary.

As a first introduction to running jobs on Derecho, there are several key commands worth noting:

• qsub - This command submits a job script, which describes a job to be run on one or more batch nodes.


• qstat -u $USER - This command tells you the status of your pending and running jobs. Note that you may need to wait 30 seconds to 1 minute for a recently submitted job to show up.


• qdel - This command deletes a queued or running job.

At various points in the practical exercises, you'll need to submit jobs to Derecho's queueing system using the qsub command, and after doing so, you may opt to check on the status of the job with the qstat command, and then monitor the log files produced by the job once you see that the job has begun to run.

You are now ready to begin running the practice exercises!

You will find all case studies here. Make sure to start with the Initial Exercise, and then do the Single Domain case before trying other cases.