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  • Research Computing and Data Workshops

Introductory Sequence

  • Introduction to Linux
    • Workshop Outline
    • What is Linux?
    • Shell Specifics
    • Accessing the Palmetto Cluster
    • Navigating Files and Directories
    • Working With Files and Directories
    • File Permissions and Attributes
    • Pipes and Redirection
    • Environment Variables
    • .bashrc and Environment Customization
    • Finding Things
    • Utilities and Useful Information
    • Workshop Conclusion
  • Introduction to Palmetto
    • Introduction
    • Accessing the Palmetto Cluster
    • The structure of the Palmetto Cluster
    • Storage on Palmetto
    • Running an interactive job on Palmetto
    • Transferring files to and from Palmetto
    • Web-based access to the Palmetto Cluster
    • Running a batch job

R

  • Introduction to R
    • Introduction to R
    • Basics of R
    • Data Structures
    • Vectors, Matrices, Lists and Data Frames
    • Control Structure
    • Functions
    • Parallel Computing in R
    • Basic plotting with R
    • Ploting with ggplot
    • R in Palmetto
  • Machine Learning using R
    • Introduction to Machine Learning
    • Introduction to Caret
    • Data Partition with caret
    • Evaluation Metrics with caret
    • Training Machine Learning model using Regression Method
    • Classification with decision boundaries
    • Nearest Neighbours Classification
    • Training Machine Learning model using Tree-based model
    • Training Machine Learning model using Ensemble approach
    • Unsupervised Learning
    • Neural Network

Python

  • Introduction to Python Programming
    • Introduction to Python I
    • Introduction to Python II
    • Introduction to Python III
    • Matplotlib
  • Machine Learning using Python
    • Machine Learning in Python using Clemson High Performance Computing
    • Introduction to Python for Machine Learning
    • Introduction to ML Concepts
    • Unsupervised Learning Algorithms
    • Supervised Learning Model Evaluation Metrics
    • Data Preparation
    • Scripting Your Code
  • Deep Learning in Python
    • Introduction to Deep Learning
    • Deep Learning Library Framework
    • Recap on ANN
    • Introduction to Keras
    • Training Deep Learning Regression model with Keras
    • Training Deep Learning Classification model with Keras
    • Convolution Neural Network for image classification
    • Recurrent Neural Network for Timeseries forecasting
  • Big Data Analytics in Python
    • Introduction to Apache Spark
    • Launching the Spark cluster
  • HPC Python on Palmetto 2
    • Introduction to Polars
    • GPU Acceleration with Python
    • Multi-node Parallelism and Dask
    • Debugging and Performance Tuning

Deep Learning

  • Deep Learning in Pytorch
    • PyTorch Quickstart
    • PyTorch Basics
    • Pytorch GPU support
    • Regression and Classification with Fully Connected Neural Networks
    • High Dimensional Data
    • Datasets and data loading
    • Building the network
    • Computer Vision and Convolutional Neural Networks
    • Intro to Natural Language Processing
  • Advanced Deep Learning in Pytorch
    • EMNIST Baseline
    • Move reused code into python script files
    • Model fine-tuning
    • Pytorch Lightning
    • Training Techniques

Large language models (LLMs)

  • Attention, Transformers, and LLMs: a hands-on introduction in Pytorch
    • Preparing data for LLM training
    • Small Language Models: an introduction to autoregressive language modeling
    • Attention is all you need
    • Other LLM Topics
  • Running LLMs on Palmetto
    • Running LLMs on Palmetto
    • Minimum working example, and what it’s missing
    • Batching, multi-gpu, and multi-node for large data and large models
  • Fine-tuning LLMs on Palmetto
    • Alternatives to fine-tuning
    • Data preparation
    • Full fine-tune
    • Parameter-efficient Fine-tuning (PEFT)
    • Project Logging with Weights and Biases (WandB)
    • Efficiency and using multiple GPUs

Advanced Palmetto Usage

  • Containerization on Palmetto (under development)
    • Introduction to CloudLab
    • Docker Containers on CloudLab
    • Singularity/Apptainers on Palmetto
  • Advanced Scheduling (under development)

Software Development Life Cycle

  • Introduction to Version Control with Git and GitLab
    • Version Control Overview
    • Git Version Control
    • Git Commands
    • Installing Git
    • Practice With a Local Repository
    • GitLab
    • Collaboration and Conflicts
    • More Resources
  • .md

Navigating Files and Directories

Contents

  • Slashes
  • Listing files and directories
  • Creating and Changing Directories
    • Other Hidden Files
    • One More Shortcut

Navigating Files and Directories#

The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called “folders”), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories. The first command that we will look at is called pwd (print working directory). Let’s type it in:

$ pwd
/home/<your Palmetto username>

To understand what a “home directory” is, let’s have a look at how the file system as a whole is organized. On Palmetto, the filesystem looks something like this:

The File System

At the top is the root directory that holds everything else. We refer to it using a slash character / on its own.

Inside that directory are several other directories: home (where users’ personal directories are located), bin (which is where some built-in programs are stored), tmp (for temporary files that don’t need to be stored long-term), etc (for miscellaneous data files), and so on.

Slashes#

There are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. This is called an absolute path. When it appears inside a name, it’s a relative path.

Underneath /home, we find one directory for each user with an account on Palmetto.

Listing files and directories#

The command ls will list the contents of the working directory.

$ ls
Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

Your results might be completely different, depending on the contents of your home directory.

ls prints the names of the files and directories in the current directory in alphabetical order, arranged neatly into columns.

We can also use ls to see the contents of a specified directory. Let’s list the directories of all the Palmetto users (note that you cannot actually see inside other people’s directories):

$ ls /home

We can make its output more comprehensible by using the flag -F, which tells ls to add a trailing / to the names of directories:

$ ls -F
Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

And note that there is a space between ls and -F: without it, the shell thinks we’re trying to run a command called ls-F, which doesn’t exist.

ls has lots of other options. To find out what they are, we can type:

$ ls --help
Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      scale sizes by SIZE before printing them; e.g.,
                               '--block-size=M' prints sizes in units of
                               1,048,576 bytes; see SIZE format below
  -B, --ignore-backups       do not list implied entries ending with ~
  -c                         with -lt: sort by, and show, ctime (time of last
                               modification of file status information);
                               with -l: show ctime and sort by name;
                               otherwise: sort by ctime, newest first
  -C                         list entries by columns
      --color[=WHEN]         colorize the output; WHEN can be 'always' (default
                               if omitted), 'auto', or 'never'; more info below
  -d, --directory            list directories themselves, not their contents
  -D, --dired                generate output designed for Emacs' dired mode
  -f                         do not sort, enable -aU, disable -ls --color
  -F, --classify             append indicator (one of */=>@|) to entries
      --file-type            likewise, except do not append '*'
      --format=WORD          across -x, commas -m, horizontal -x, long -l,
                               single-column -1, verbose -l, vertical -C
      --full-time            like -l --time-style=full-iso
  -g                         like -l, but do not list owner
      --group-directories-first
                             group directories before files;
                               can be augmented with a --sort option, but any
                               use of --sort=none (-U) disables grouping
  -G, --no-group             in a long listing, don't print group names
  -h, --human-readable       with -l and/or -s, print human readable sizes
                               (e.g., 1K 234M 2G)
      --si                   likewise, but use powers of 1000 not 1024
  -H, --dereference-command-line
                             follow symbolic links listed on the command line
      --dereference-command-line-symlink-to-dir
                             follow each command line symbolic link
                               that points to a directory
      --hide=PATTERN         do not list implied entries matching shell PATTERN
                               (overridden by -a or -A)
      --indicator-style=WORD  append indicator with style WORD to entry names:
                               none (default), slash (-p),
                               file-type (--file-type), classify (-F)
  -i, --inode                print the index number of each file
  -I, --ignore=PATTERN       do not list implied entries matching shell PATTERN
  -k, --kibibytes            default to 1024-byte blocks for disk usage
  -l                         use a long listing format
  -L, --dereference          when showing file information for a symbolic
                               link, show information for the file the link
                               references rather than for the link itself
  -m                         fill width with a comma separated list of entries
  -n, --numeric-uid-gid      like -l, but list numeric user and group IDs
  -N, --literal              print raw entry names (don't treat e.g. control
                               characters specially)
  -o                         like -l, but do not list group information
  -p, --indicator-style=slash
                             append / indicator to directories
  -q, --hide-control-chars   print ? instead of nongraphic characters
      --show-control-chars   show nongraphic characters as-is (the default,
                               unless program is 'ls' and output is a terminal)
  -Q, --quote-name           enclose entry names in double quotes
      --quoting-style=WORD   use quoting style WORD for entry names:
                               literal, locale, shell, shell-always,
                               shell-escape, shell-escape-always, c, escape
  -r, --reverse              reverse order while sorting
  -R, --recursive            list subdirectories recursively
  -s, --size                 print the allocated size of each file, in blocks
  -S                         sort by file size, largest first
      --sort=WORD            sort by WORD instead of name: none (-U), size (-S),
                               time (-t), version (-v), extension (-X)
      --time=WORD            with -l, show time as WORD instead of default
                               modification time: atime or access or use (-u);
                               ctime or status (-c); also use specified time
                               as sort key if --sort=time (newest first)
      --time-style=STYLE     with -l, show times using style STYLE:
                               full-iso, long-iso, iso, locale, or +FORMAT;
                               FORMAT is interpreted like in 'date'; if FORMAT
                               is FORMAT1<newline>FORMAT2, then FORMAT1 applies
                               to non-recent files and FORMAT2 to recent files;
                               if STYLE is prefixed with 'posix-', STYLE
                               takes effect only outside the POSIX locale
  -t                         sort by modification time, newest first
  -T, --tabsize=COLS         assume tab stops at each COLS instead of 8
  -u                         with -lt: sort by, and show, access time;
                               with -l: show access time and sort by name;
                               otherwise: sort by access time, newest first
  -U                         do not sort; list entries in directory order
  -v                         natural sort of (version) numbers within text
  -w, --width=COLS           set output width to COLS.  0 means no limit
  -x                         list entries by lines instead of by columns
  -X                         sort alphabetically by entry extension
  -Z, --context              print any security context of each file
  -1                         list one file per line.  Avoid '\n' with -q or -b
      --help     display this help and exit
      --version  output version information and exit

The SIZE argument is an integer and optional unit (example: 10K is 10*1024).
Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,... (powers of 1000).

Using color to distinguish file types is disabled both by default and
with --color=never.  With --color=auto, ls emits color codes only when
standard output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

Exit status:
 0  if OK,
 1  if minor problems (e.g., cannot access subdirectory),
 2  if serious trouble (e.g., cannot access command-line argument).

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'

Many Linux commands, and programs that people have written that can be run from within the shell, support a --help flag to display more information on how to use the commands or programs.

For more information on how to use ls we can type man ls. man is the Unix “manual” command: it prints a description of a command and its options, and (if you’re lucky) provides a few examples of how to use it.

To navigate through the man pages, you may use the up and down arrow keys to move line-by-line, or try the “b” and spacebar keys to skip up and down by full page. Quit the man pages by typing “q”.

Creating and Changing Directories#

The next command we will discuss is mkdir, which creates a new directory. Let’s create a directory with the name linux_workshop:

$ mkdir linux_workshop

Now, if you type ls, you should see linux_workshop listed among the contents of your home directory.

The next command that we will discuss is cd (“change directory”), which changes our location to a different directory. Let’s enter the directory we have just created:

$ cd linux_workshop

Now, our current directory is linux_workshop:

$ pwd
/home/<your Palmetto username>/linux_workshop

If you type ls, you won’t see anything, because we have just created this directory and it is empty.

To go back to your home directory, you need to go one level up on the directory tree. There is a shortcut in the shell to move up one directory level that looks like this:

$ cd ..

Path Shortcuts:

  • .. parent directory

  • . current directory

  • ~ home directory

$ pwd
/home/<your Palmetto username>

Directories starting with . are hidden from ls by default. The -a flag to ls will list all files and directories.

$ ls -F -a

Other Hidden Files#

Many common configuration files will begin with .. You may see a .bash_profile or .bashrc file in your home directory which you can edit to alias certain commands or add variables to use later.

One More Shortcut#

Another shortcut is the - (dash) character. cd will translate - into *the previous working directory *. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back.

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Accessing the Palmetto Cluster

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Working With Files and Directories

Contents
  • Slashes
  • Listing files and directories
  • Creating and Changing Directories
    • Other Hidden Files
    • One More Shortcut

By Linh Ngo

Research Computing and Data Workshops is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.