This repo contains auxiliary teaching resources for Digital Biology, a grad/undergrad bioinformatics course taught at Indiana University.

Common HPC error messages

• Killed: with no other info could be multiple things, but most commonly you need more memory.
• OOM: "out of memory"
• Disk quota exceeded: ran out of storage space. Need to make space or move over to scratch/.

Troubleshooting Notes

Here we will compile topics flagged in class as confusing, challenging, or that lead to computer errors.

CTRL + f on Windows

To search for some text inside your git bash window, if CTRL-F doesn't work try right clicking and then click "Search".

File paths

File paths are a little tricky at first.

• Assignment 2 "Part I" is designed for practicing file paths. You can do it again for practice.
• The online Hendrix text (link under Module 1 on canvas) provides further reading.
• If you still have trouble come to office hours.

GitHub Classroom account setup

Check your email from GH, that link tends to work instead of the auto-generated one.

Keyboard doesn't communicate with shell as expected

• Research Desktop. The keyboard shortcuts we use don't work in Research Desktop. And in general we want to wean off the Research Desktop and use a basic shell.
• Non-US computer. We may or may not be able to troubleshoot this. First, come to office hours and we can try changing your settings. Alternatively, email biocomp@iu.edu to borrow a computer.

nano

• How to undo? EST + u (at least with macbook).
• How to ctrl-F on Windows? ctrl-W should do it.
• How to pause nano so you can test a script while editing?
  • bigred: CTRL+T+CTRL+Z to pause; then fg on the command line to return (don't forget to save, still)
  • quartz: if you want this capability ask the instructor to help you set it up.

HPC login without username and full address

On your laptop run mkdir -p ~/.ssh; touch .ssh/config. And then copy this code block into the terminal, replacing "chriscs" with your username:

cat <<'EOF' >> ~/.ssh/config
Host bigred
     HostName bigred200.uits.iu.edu
     User chriscs
Host quartz
     HostName quartz.uits.iu.edu
     User chriscs
EOF

Now you should be able to SSH with ssh quartz instead of the full command (not certain if this works on Windows.)

HPC login without password

1. Submit the SSH Key Agreement Form, in which you agree to set a passphrase on your private key when you generate your key pair. Note: it can take several days before this is reviewed; but you should do the below steps in the meantime.
2. On your laptop run: ssh-keygen -t rsa. Press ENTER to accept default file path. When prompted for a password type in the new password you want to use to login; if you press ENTER without typing anything, this means no password.
3. Next copy your "key" to Quartz (or BigRed): scp ~/.ssh/id_rsa.pub <username>@quartz.uits.iu.edu:~/
4. Log into Quartz (or BigRed).
5. Run mkdir -p ~/.ssh; touch ~/.ssh/authorized_keys; cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
6. Finally, run rm ~/id_rsa.pub

That should do it for macbook (not certain if this works on Windows). More info here: https://servicenow.iu.edu/kb?id=kb_article_view&sysparm_article=KB0023919

SCP

Most often the trick is to give correct file paths on both ends. Resources:

• see description in Assignment 2, Part I, Step 7.
• see failure modes in the posted slides from class.
• see more examples and edge cases here.

Where to store my data on Quartz/BigRed?

Class project? -> /N/slate/ (long term storage for intermediate-sized files)

Assignments? -> /N/slate/ is fine. Scratch is also fine if your run out of space, but it gets deleted after 30 days.

Temporary files? -> /N/scratch/