Setting up Farm

High Performance Computing (HPC) refers to computers that have more capability than a typical personal computer (i.e. most desktops and laptops). Many research problems we encounter when analyzing sequencing data require more resources than we have available on our laptops. For this, we use large, remote compute systems that have more resources available.

Most universities have access to an HPC (or cluster) that has a large amount of hard drive space to store files, RAM for computing tasks, and CPUs for processing. Other options for accessing large computers include NSF XSEDE services like Jetstream and paid services like Amazon Web Services or Google Cloud. We will use the UC Davis Farm Cluster during this rotation.

Getting an account on Farm

To be able to use Farm, you need to sign up for an account. Farm requires key file authentication. Key files come in pairs like the locks and keys on doors. The private key file is the first file, and it is like the key to a door. This file is private and should never be shared with anyone (do not post this file on GitHub, slack, etc.). The public key file is the second file, and it is like the lock on a door. It is publicly viewable, but cannot be "unlocked" without the private key file.

We need to generate a key file pair in order to create a farm account.

Open the Terminal application or the Terminal emulator you installed in the first_lesson.

Change directories into the .ssh folder. This folder is where key file pairs are typically stored.

cd ~/.ssh

If this command does not work, create your own ssh folder and cd into it:

mkdir -p ~/.ssh
cd ~/.ssh

Then, generate the keyfile pair by running:

ssh-keygen

Follow the prompts on the screen. If prompted for a password, you can hit Enter on your keyboard to avoid setting one.

Two files will be created by this command. These files should have the same prefix. The file that ends in .pub is the public key.

The account request form

Next, navigate to this page. From the first drop down menu (Which cluster are you applying for an account on?), select vetmed. Then, upload your public key file to the page. Submit the form. Once Titus approves your account, you will have farm access!

Don't lose the key file pair you just made. You will need the private key file each time you log into farm.

Connecting to a remote computer

Once you have a farm account, we will use the command ssh to connect to farm. ssh stands for "secure shell".

To connect to your account on farm, type:

ssh -i ~/.ssh/your_keyfile_name username@farm.cse.ucdavis.edu

If you are successful, you will see a message that looks something like this: * Your Farm user name might be different than your e-mail username; if your e-mail username does not work, try using your UC Davis computing account user name (aka your Kerberos username or CAS LoginID).

Welcome to Ubuntu 18.04.3 LTS (GNU/Linux 4.15.0-70-generic x86_64)

1 updates could not be installed automatically. For more details,
see /var/log/unattended-upgrades/unattended-upgrades.log

*** System restart required ***
A transfer node, c11-42, is available for rsync, scp, gzip
From outside the Farm cluster use port 2022 to access the transfer node.
 ssh -p 2022 username@farm.cse.ucdavis.edu
 scp -P 2022 src username@farm.cse.ucdavis.edu:/destination

   REMINDER: Farm does not back up user data. Please ensure your data is backed up offsite.

 *** Dec 04 2019:
 * 2:10pm - Service restored. Please report any issues to help@cse.ucdavis.edu.


   Email help@cse.ucdavis.edu for help with Farm.

Downtime scheduled for the first Wednesday of Oct and April.  The next downtime is Wednesday April 1st at 11:59pm.

If interested in contributing to farm, the rates for 5 years are:
  $ 1,000 per 10TB, served from redundant servers with compression
  $ 8,800 per parallel node (256GB ram, 32 cores/64 threads, 2TB /scratch)
  $17,500 per GPU node (Nvidia Telsa V100, dual Xeon 4114, 2TB /scratch)
  $22,700 per bigmem node (1TB ram, 48 cores/96 threads, 2TB /scratch)

Last login: Thu Jan  2 17:01:36 2020 from 76.105.143.194
Module slurm/19.05.3 loaded
Module openmpi/4.0.1 loaded
username@farm:~$

When you first login to farm, you will be in your home directory. This is where you will write your files and run the majority of your commands.

When you are done using farm, you can exit your ssh connection with the exit command.

exit