This repo is created as a part of the CSDE Workshop on Introduction to the UNIX/Linux Shell.
It includes a sample script for working with UW HYAK -- on-campus high-performance computing platform for scalable scientific computing.

Object: Running a simple regression model and calculating Bootstrap Confidence Intervals.

1. First we need to log-in to our HYAK instance. Open a terminal instance and paste the following:

ssh [UW-NetID]@mox.hyak.uw.edu

2. Enter your password. Then, you will be directed to 2-Factor Authentication via Duo Mobile.

3. Once you are successfully logged in, navigate to your project directory. (Hint: ls, cd, pwd commands are your best friends.)

4. We can use sftp or git (recommended) for file transfer between local and HYAK. (Hint: You can use lcd, lls, lpwd to navigate through local files.)

sftp [UW-NetID]@mox.hyak.uw.edu
put -r [PATH-TO-LOCAL-FILE]

5. Then, you can submit your job via this command:

sbatch submit.slurm

6. If successfuly, you should receive a message with your job id:
   Submitted batch job [JOBID]

7. You can track the progress of your currents job via:

squeue -u [UW-NetID]

or including past jobs:

sacct 

8. Once finished, you can do quickly check the output in command line:

cat slurm-*

9. To export final output into our local machines, we can use sftp or git (recommended) again:

get -r [PATH-TO-REMOTE-FILE]

• example.R: Demonstration of the task, interactively.
• bootstrap.R: Bootstrapping script designed to be used with a slurm script.
• submit.slurm: Slurm script for a single batch submission.
• slurm-[JOBID].out: Once our job is finished, the console output is stored in here.
• output/: The resulting data.frames with bootstrap estimates.
• plots/: Plots that show the distribution of bootstrap estimates.
• bootstrapArray.R: Bootstrapping script modified for array batch submission
• submitArray.slurm: Slurm script modified for array batch submission.
• slurm-[JOBID]_N.out: Outputs of array batches stored in this format.