aebratt/qermserver-hyak-tutorial

Materials for QERM 597, Feb 5 2020

QERM Server and Hyak Tutorial

This repository contains all necessary materials for QERM 597, Feb 5 2020

Authors: Abby Bratt, Maria Kuruvilla, Connie Okasaki

EDIT May 18, 2022

Updated by Abby Bratt, Emily Sellinger, Kelly Mistry, and Anne Polyakov

Prerequisites

Here is your homework for QERM 597 on Feb 5—Hyak/SEFS/QERM Servers. It requires getting access to Hyak from the Research Computing Club and the SEFS/QERM servers from SEFSIT. Both processes can take up to a week depending on how busy the IT folks are so we recommend you begin thinking about this as soon as possible so you are ready to go on the 5th.

For the Hyak portion:

Read the page on getting started with the Research Computing Club. The club owns a bunch of Hyak nodes purchased with the Student Technology Fee so all students can access Hyak, after jumping through a few hoops. The hoops are:

1. Join the Research Computing Club

2. Fill out the Hyak quiz

3. Get added to the STF group on Hyak

4. Set up two-factor authentication

5. Add Hyak and Lolo as services

Details of how to do each of these are at the link above. If you are feeling adventurous you can also read this page on the Hyak wiki and this tutorial on Slurm, which is the resource manager Hyak uses to submit jobs. We will spend time going over this, so don't fret.

Make sure you pay attention to any emails from the HPC list. They contain helpful Hyak updates as well as notifications about club meetings. Everyone is required to attend at least one club meeting a year to stay on the STF partition.

Bonus homework for Windows users: Check that you have SSH enabled as that's how we'll log in to Hyak. This should be default if you are running a recentish version of Windows 10+. If you're old school, you might check out puTTY.

For the QERM/SEFS Servers portion:

Please take a look at the QERM wiki simulation servers page. Here are the basic steps you should have completed before class on Feb 5:

1. Contact SEFSIT to gain access to the servers. In you email, include which specific server(s) you would like access to (e.g. Snoqualmie). This should be done well in advance to give them a chance to respond.

2. Mac and Linux users need to install some software. Mac users need Microsoft Remote Desktop. Linux users need to find your favorite Remote Desktop client -- Remmina seems to be the good option for Ubuntu which comes preinstalled. I'll trust Linux users to figure out whatever fiddling needs to be done ahead of time. Linux users will also need to make sure they have a SFTP program as outlined in the UDrive instructions. Mac and Windows users have built-in programs to do this. Note that the QERM/SEFS servers will are down approximately 1day/month for maintenance.

Resources

QERM/SEFS Servers

• QERM wiki simulation servers page

• UDrive instructions

Hyak

We find the Hyak wiki really difficult to navigate. In our opinion the most useful pages for getting started are:

• Managing your files

• Mox overview

• Scheduling jobs

• Slurm tutorial

• Batch script examples

• Research Computing Club

• R Programming on Hyak

If you don't find what you need there and you have hunted around for a bit, the Research Computing Club officers hold office hours in the eScience Institute. Find out when.

General

• eScience Institute office hours

• How to add a new SSH key to your GitHub account. Stop typing your GitHub password every time you do something!