MSI Runtime

Important

Prior to executing these steps you should have:

1. Already successfully completed the MSI Setup steps. If not–shoo! Go do that first.

Workflow

1. Read the documentation for SLURM scripts and MSI job submission to a partition on your chosen cluster:

   • https://www.msi.umn.edu/partitions https://www.msi.umn.edu/content/job-submission-and-scheduling-slurm

   Seriously–READ THEM.

2. Now that you have read the MSI docs, copy and modify scripts/example.sh script in the TITERRA repo for your experiment/batch experiment, and modify as needed:

   SLURM parameters you DO need to change:

   • The email (I don’t want to get emails about YOUR jobs).

   SLURM parameters you MIGHT need to change:

   • The number of requested nodes.

   Other things you MIGHT need to change:

   • The location of the FORDYCA and SIERRA repos in the script, if you did not clone them to the same location as specified earlier in these steps.

3. Have your jobs script reviewed before submission (will likely save you a LOTS of time fighting with the job submission system).

4. Submit your job via:

   sbatch your-script.sh
   

   Note the job number that the job submission will print when you run this command–it is important to track job progress and to figure out what happened when (not if) things go wrong.

   It is also generally a good idea to get in the habit of giving your PBS scripts (fairly) unique and descriptive names when submitting, in order to make tracking down what stderr/stdout file belongs to what job when once you’ve run a few dozen jobs.

   You will get an email when your job starts, aborts because of error, and finishes. To view the in-progress stdout of the job, look in your home directory for output/error files:

   • $HOME/R-your-jobname.1234.out where 1234 is the job number of your job. MSI will create this file in the directory you submit the job from, and direct your job’s stdout to it.

   • $HOME/R-your-jobname.1234.err where 1234 is the job number of your job. MSI will create this file in the directory you submit the job from, and direct your job’s stderr to it.

5. Reap the rewards of research!