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The Terminal window
- Macs and Linux have a Terminal programs program built-in – find it now on your computer
- Windows 10 or later has ssh and scp in Command Prompt or PowerShell (may require latest Windows updates)
- Open the Start menu → Search for Command
- Open the Start menu → Search for Command
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If your Windows version does not have ssh in Command Prompt or PowerShell:
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More advanced options for those who want a full Linux environment on their Windows system:
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From now on, when we refer to "Terminal", it is either the Mac/Linux Terminal program, Windows Command Prompt or PowerShell, or the PuTTY program.
- terminal plus minimal Linux environment
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SSH
ssh is an executable program that runs on your local computer and allows you to connect securely to a remote computer.
On Macs, Linux and Windows Git-bash or Cygwin, you run it from a Terminal window. Answer yes to the SSH security question prompt.
We're going to use ssh to access the Lonestar6 compute cluster at TACC (Texas Advanced Computing Center), where the remote host name is ls6.tacc.utexas.edu.
In your local Terminal window:
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ssh your<your_TACC_userID@stampedeuserID>@ls6.tacc.utexas.edu # For example: ssh abattenh@ls6.tacc.utexas.edu |
- Answer yes to the SSH security question prompt
- this will only be asked the 1st time you access ls6
- Enter the password associated with your TACC account
- for security reasons, your password characters will not be echoed to the screen
- Get your 2-factor authentication code from your phone's TACC Token app, and type it in
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If you're using |
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PuTTY as your Terminal from Windows:
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The bash shell
You're now at a command line! It looks as if you're running directly on the remote computer, but really there are two programs communicating:
- your local Terminal
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- the remote shell
Shell. There are many shell programs available in Linux, but the default is bash (Bourne-again shellBourne-again shell).
The Terminal is pretty "dumb" – just sending your typing what you type over its secure sockets layer (SSL) connection to TACC, then displaying the text sent back by the shell. The real work is being done on the remote computer, by executable programs called by the bash shell .(also called commands, since you call them on the command line).
About the command line
Read more about the command line and commands on our Linux fundamentals page:
- The bash shell REPL and commands
- Getting help
- Literal characters and metacharacters
- About command line input
Setting up your environment
First create a few directories and links we will use (more on these later).
Setup your login profile (~/.bashrc)
Now execute the lines below to set up a login script, called ~/.bashrc. [ Note the tilde ( ~ ) is shorthand for "my Home directory". See Linux fundamentals: pathname syntax ]
When you login via an interactive shell, a well-known script is executed to establish your favorite environment settings. The well-known filename is ~/.bashrc (or ~/.profile on some systems), which is specific to the bash shell.
We've pre-created a common login script for you that will help you know where you are in the file system and make it easier to access some of our shared resources. To set it up, perform the steps below:
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You can copy and paste these lines from the code block below into your Terminal window. Just make sure you hit "Enter" after the last line. |
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If you already have a .bashrc set up, make a backup copy first.
You can restore your original login script after this class is over. |
If your Terminal has a dark background (e.g. black), copy this file:
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cpln -s -f $SCRATCH scratch ln -s -f $WORK work ln -s -f /corral-repl/utexas/BioITeam mkdir -p $HOME/local/bin cd $HOME/local/bin ln -s -f /corral-repl/utexas/BioITeam/bin/launcher_creator.py |
Now execute the lines below to set up a login script, called .profile_user. This script will be executed whenever you login to stampede.
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cd
cp /work/01063/abattenh/seq/code/script/tacc/stampede_dircolors .dircolors
cp /work/01063/abattenh/seq/code/script/tacc/stampede_corengs_profile .profile_user
chmod 600 .profile_user |
Finally, log off and log back in to stampede.tacc.utexas.edu. You should see a new command prompt:
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stamp:~$ |
And nice directory colors when you list your home directory:
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ls |
/core_ngs_tools/login/bashrc.corengs.ls6.dark_bg ~/.bashrc
chmod 600 ~/.bashrc |
If your Terminal has a light background (e.g. white), copy this file:
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cp /corral-repl/utexas/BioITeam/core_ngs_tools/login/bashrc.corengs.ls6.light_bg ~/.bashrc
chmod 600 ~/.bashrc |
So why don't you see the .
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bashrc file you
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just copied when you do ls? Because all files starting with a period (
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dot files
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all)
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options to ls:
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# show a long listing of all files in the current directory, including "dot files" that start with a period ls -la |
File systems at TACC
Local file systems
There are 3 local file systems available on any TACC cluster (stampede, lonestar, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).
On stampede these local file systems have the following characteristics:
$HOME | $WORK | $SCRATCH | |
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quota | 5 GB | 400 GB | 12+ PB (basically infinite) |
policy | backed up | not backed up, not purged | not backed up, purged if not accessed recently (~10 days) |
access command | cd | cdw | cds |
root file system | /home | /work | /scratch |
Notice when you login, the system gives you information about disk quota and your compute allocation quota:
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--------------------- Project balances for user abattenh ----------------------
| Name Avail SUs Expires | Name Avail SUs Expires |
| CancerGenetics 10627 2014-09-30 | genomeAnalysis 94284 2015-03-31 |
------------------------ Disk quotas for user abattenh ------------------------
| Disk Usage (GB) Limit %Used File Usage Limit %Used |
| /home1 0.0 1.1 0.29 463 1001000 0.05 |
| /work 42.1 250.0 16.85 16281 500000 3.26 |
------------------------------------------------------------------------------- |
(Read more about File attributes)
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What's going on with chmod? The chmod 600 ~/.bashrc command marks the file as readable and writable only by you. |
Since your ~/.bashrc is executed when you login, to ensure it is set up properly you should first log off Lonestar6 like this:
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exit |
Your Terminal has logged off of Lonestar6 and is back on your local computer.
Now log back in to ls6.tacc.utexas.edu. This time your ~/.bashrc will be executed to establish your environment:
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Your new ~/.bashrc file defines a ll alias command, so when you type ll it is short for ls -la. |
You should see a new command line prompt:
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ls6:~$ |
The great thing about this prompt is that it always tells you where you are, which avoids you having to execute the pwd (present working directory) command every time you want to know what the current directory is. Execute these commands to see how the prompt reflects your current directory.
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# mkdir -p says to create all parent directories in the specified path
mkdir -p ~/tmp/a/b/c
cd ~/tmp/a/b/c
# Your prompt should look like this:
ls6:~/tmp/a/b/c$ |
The prompt now tells you you are in the c sub-directory of the b sub-directory of the a sub-directory of the tmp sub-directory of your Home directory ( ~ ).
Your login script has configured this command prompt behavior, along with a number of other things.
Create some symbolic links and directories
Create some symbolic links that will come in handy later:
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cd # makes your Home directory the "current directory"
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -sf /work/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS
ls # you'll see the 3 symbolic links you just created
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Symbolic links (a.k.a. symlinks) are "pointers" to files or directories elsewhere in the file system hierarchy. You can almost always treat a symlink as if it is the actual file or directory.
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$WORK and $SCRATCH are TACC environment variables that refer to your Work and Scratch file system areas – more on these file system areas soon. (Read more about Environment variables) |
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The ln -s command creates a symbolic link, a shortcut to the linked file or directory.
Want to know where a link points to? Use ls with the -l (long listing) option.
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Set up a ~/local/bin directory and link a script there that we will use in the class.
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mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_creator.py
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Since our ~/.bashrc login script added ~/local/bin to our $PATH, we can call any script or command in that directory with just its file name. And Tab completion works on program names too:
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cd
# hit Tab once after typing "laun"
# This will expand to launcher_creator.py
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Details about your login script
Let's take a look at the contents of your ~/.bashrc login script, using the cat (concatenate files) command. cat simply reads a file and writes each line of content to standard output (here, your Terminal):
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cd
cat .bashrc
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The cat command just displays the entire file's content, line by line, without pausing, so should not be used to display large files. Instead, use a pager like more or less. For example: more ~/.bashrc This will display one "page" (Terminal screen) of text at a time, then pause. Press space to advance to the next page, or Ctrl-c to exit more. |
You'll see the following (you may need to scroll up a bit to see the beginning):
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#!/bin/bash
# TACC startup script: ~/.bashrc version 2.1 -- 12/17/2013
# This file is NOT automatically sourced for login shells.
# Your ~/.profile can and should "source" this file.
# Note neither ~/.profile nor ~/.bashrc are sourced automatically
# by bash scripts.
# In a parallel mpi job, this file (~/.bashrc) is sourced on every
# node so it is important that actions here not tax the file system.
# Each nodes' environment during an MPI job has ENVIRONMENT set to
# "BATCH" and the prompt variable PS1 empty.
#################################################################
# Optional Startup Script tracking. Normally DBG_ECHO does nothing
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}~/.bashrc{"; fi
##########
# SECTION 1 -- modules
if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
export __BASHRC_SOURCED__=1
module load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONAL_PATH__" ]; then
export __PERSONAL_PATH__=1
export PATH=.:$HOME/local/bin:$PATH
fi
# For better colors using a dark background terminal, un-comment this line:
#export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'
# For better colors using a white background terminal, un-comment this line:
#export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'
export LANG="C" # avoid the annoying Perl locale warnings
export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export BI=/corral-repl/utexas/BioITeam
export ALLOCATION=OTH21164 # For ls6 Group is G-824651
##export ALLOCATION=UT-2015-05-18 # For stampede2 Group is G-816696
##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='ls6:\w$ '; fi
##########
# SECTION 4 -- Umask and aliases
#alias ls="ls --color=always"
alias ll="ls -la"
alias lah="ls -lah"
alias lc="wc -l"
alias hexdump='od -A x -t x1z -v'
umask 002
##########
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi |
There's a lot of stuff here; let's look at just a few things.
Environment variables
The login script sets several environment variables.
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export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
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Environment variables are like variables in other programming languages like python or perl (in fact bash is a complete programming language).
They have a name (like BIWORK above) and a value (the value of $BIWORK is the pathname of the shared /work/projects/BioITeam directory).
To see the value of an environment variable, use the echo command, then the variable name after a dollar sign ( $ ):
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echo $CORENGS
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We'll use the $CORENGS environment variable to avoid typing out a long pathname:
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ls $CORENGS
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(Read more about Environment variables)
Shell completion with Tab
You can use these environment variables to shorten typing, for example, to look at the contents of the shared /work/projects/BioITeam directory as shown below, using the magic Tab key to perform shell completion.
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The Tab key is one of your best friends in Linux. Hitting it invokes shell completion, which is as close to magic as it gets!
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Follow along with this:
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# hit Tab once to expand the environment variable name
ls $BIW
# hit Tab again to expand the environment variable
ls $BIWORK/
# now hit Tab twice to see the contents of the directory
ls /work/projects/BioITeam/
# type "pr" and hit Tab again
ls /work/projects/BioITeam/pr
# type "co" and hit Tab again
ls /work/projects/BioITeam/projects/co
# type "Co" and hit Tab again
ls /work/projects/BioITeam/projects/courses/Co
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/
# now type "mi" and one Tab
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/mi
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/
# now hit Tab once
# There is no unambiguous match, so hit Tab again
# After hitting Tab twice you should see several filenames:
# fastqc/ small.bam small.fq small2.fq
# now type "sm" and one Tab
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# type a period (".") then hit Tab twice again
# You're narrowing down the choices -- you should see two filenames
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# small.bam small.fq
# finally, type "f" then hit Tab again. It should complete to this:
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq |
Extending the $PATH
When you type a command name the shell has to have some way of finding what program to run. The list of places (directories) where the shell looks is stored in the $PATH environment variable. You can see the entire list of locations by doing this:
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echo $PATH
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As you can see, there are a lot of locations on the $PATH.
Here's how the common login script adds the ~/local/bin directory you created above, to the location list, along with a special dot character ( . ) that means "here", or "whatever the current directory is". In the statement below, colon ( : ) separates directories in the list. (Read more about pathname syntax)
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export PATH=.:$HOME/local/bin:$PATH
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Setting up the friendly command prompt
The complicated looking if statement in SECTION 3 of your .bashrc sets up a friendly shell prompt that shows the current working directory. This is done by setting the special PS1 environment variable and including a special \w directive that the shell knows means "current directory".
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# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='ls6:\w$ '; fi
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