Frequently Asked Questions

Find solutions to common problems below

Cannot login to Jetstream VM

If you try to ssh to mbs-337 and it gives any sort of error or if it asks you for a password, it is likely that you removed some necessary lines from your ~/.ssh/config on student-login. Contact one of the course instructors and we will restore it for you.

How do I copy data from my local laptop to mbs-337?

Assuming you have a file like ‘data.csv’ on your local laptop and you want to copy it to mbs-337. It will require two hops: first copy from laptop to student-login, then from student-login to mbs-337:

[local]$ ls
data.csv
[local]$ scp data.csv username@student-login.tacc.utexas.edu:~/
Password:
TACC_Token:

The file ‘data.csv’ is now copied to your home directory on student-login, so ssh to student-login and from there copy it to mbs-337:

[local]$ ssh username@student-login.tacc.utexas.edu
Password:
TACC_Token:
[student-login]$ ls
data.csv
[student-login]$ scp data.csv mbs-337:~/
# no password or token prompt

How do I copy an image from mbs-337 to my local laptop?

Assuming you have a file like ‘output.png’ on mbs-337 that you want to copy to your local laptop. It will require two hops: first copy from mbs-337 to student-login, then from student-login to your laptop:

[mbs-337]$ pwd
/path/where/data/is
[mbs-337]$ ls
output.png
[mbs-337]$ logout

[student-login]$ pwd
/home/username
[student-login]$ scp mbs-337:/path/where/data/is/output.png ./

This will copy ‘output.png’ from mbs-337 to your home directory on student-login. Next, logout of student-login and copy the file to your local laptop:

[student-login]$ logout
[local]$ scp username@student-login.tacc.utexas.edu:~/output.png ./
Password:
TACC_Token:

ERROR: Corrupted MAC on input.

If logging in from a windows machine and you encounter the ‘Corrupted MAC on input.’ error, then add the following line to your local laptop ssh config:

Host student-login-jump
    HostName student-login.tacc.utexas.edu
    User your_tacc_username
    IdentityFile ~/.ssh/id_ed25519
    ForwardAgent yes
    MACs hmac-sha2-512

I don’t know how to format my README.md.

README.md files use Markdown syntax, hence the .md file ending. Markdown is great because it provides a simple way to format text (such as documentation) in an intuitive, organized structure. There’s a great general-use example README.md template here. For your homework assignments, you can use the following Markdown template as a guide:

# Project Title

Simple overview of use/purpose.

## Setup Instructions

Describe any necessary setup that someone would need to reproduce what you did: E.g.,:

I ran these exercises in a virtual environment with the **pydantic** and **biopython** packages installed:
```bash
source myenv/bin/activate
pip3 install pydantic
pip3 install biopython
```

## Exercise Descriptions

### Exercise 1
***Requires pydantic package***

Description of the exercise and what you did. Optionally describe any functions/classes defined within your code:
1. **find_total_mass**: description
2. **find_large_proteins**: description

## Note on AI Usage (if applicable)

Describe which/how AI tools were used to complete your homework exercises.