Tutorial 3: Linux Survival Guide

Objective: Master the command-line skills required to navigate Anvil, manage simulation data, and troubleshoot runs.

In HPC, there is no “File Explorer.” Everything is text-based. Mastering these commands is the difference between a 5-minute task and a 5-hour struggle.

1. Navigating the File System¶

• pwd (Print Working Directory): Shows your current “address.”

• ls (List): Shows files in the current folder.

  • ls -l: Shows detailed info (permissions, size, date).

  • ls -h: Makes file sizes readable (e.g., 2G instead of 2147483648).

• cd <folder> (Change Directory): Move into a folder.

  • cd .. : Go up one level.

  • cd ~ : Jump to Home.

  • cd $SCRATCH : Jump to your high-speed work area.

2. The Power of Wildcards (*)¶

You will often have 100s of files (e.g., frame_1.pdb, frame_2.pdb). You don’t want to move them one by one.

• ls *.pdb : Lists only files ending in .pdb.

• rm frame_*.log : Deletes every log file starting with “frame_”.

• cp *.in ../backup/ : Copies all input files to another folder.

3. Searching and Inspecting Files¶

Molecular dynamics logs can be millions of lines long. Do not use cat on them!

• grep "ENERGY" production.log : Searches for the word “ENERGY” in a file and prints those lines.

• less production.log : Opens the file for scrolling.

  • Use Arrow Keys to move.

  • Press / to search for a word.

  • Press q to quit.

• tail -f production.log : “Follow” a file. This shows you the simulation progress in real-time as the software writes to the log.

4. File Permissions (chmod)¶

If you see an “Access Denied” error, check your permissions.

• chmod +x script.sh : Makes a script “executable” so you can run it.

• chmod 700 private_folder : Makes a folder invisible to everyone but you.

5. Anvil Specifics: Modules¶

Software on Anvil is “hidden” until you ask for it. This prevents version conflicts.

• module list : See what is currently active.

• module spider gromacs : Search for GROMACS versions.

• module load gromacs/2023.2 : Load a specific version.

• module purge : Clear everything (useful if your environment gets messy).

6. Pro-Tips for Speed¶

1. Tab Completion: Type cd Sc and hit Tab. It will auto-fill cd Scratch/. This prevents typos!

2. Command History: Use the Up/Down arrows to scroll through previous commands.

3. The Manual: Not sure what a command does? Type man ls to see the manual.

📚 External Learning Resources¶

If you want to dive deeper into Linux, these are the best free resources available:

• Linux Journey: Probably the best site for beginners. It’s organized by level (Grasshopper to Wizard).

• The Missing Semester of Your CS Education: A fantastic course by MIT that covers the “shell” tools that most classes skip.

• Software Carpentry: The Unix Shell: A classic guide designed specifically for researchers and scientists.

• Ryans Tutorials: Very easy-to-follow practical examples.

Practice Exercise¶

1. Go to your scratch space: cd $SCRATCH

2. Create a “Lab1” folder: mkdir Lab1

3. Enter it: cd Lab1

4. Create three dummy files: touch test1.txt test2.txt log.pdb

5. List only the .txt files: ls *.txt

6. Check your storage usage: myquota