ssh is an executable program that runs on your local computer and allows you to connect securely to a remote computer. We're going to use ssh to access the lonestar6 compute cluster at TACC, where the remote host name is ls6.tacc.utexas.edu.
In your local Terminal window:
ssh <your_TACC_userID>@ls6.tacc.utexas.edu |
If you're using Putty as your Terminal from Windows:
SSHYou'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:
There are many shell programs available in Linux, but the default is bash (Bourne-again shell).
The Terminal is pretty "dumb" – just sending your typing 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 programs called by the bash shell.
The bash command-line environment is extremely powerful, but also complex and unforgiving – a one-character mistake can make all the difference between a command that works and one that doesn't! In spite of the hurdles, learning to get around the Linux command line will pay substantial dividends. A good place to start is with our Linux fundamentals wiki page. |
First create a few directories and links we will use (more on these later).
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. |
Create some symbolic links that will come in handy later:
cd ln -s -f $SCRATCH scratch ln -s -f $WORK2 work2 ln -s -f /work2/projects/BioITeam ln -s -f /work2/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS |
$WORK2 and $SCRATCH are TACC environment variables that refer to your Work2 and Scratch file system areas. To see the value of an environment variable, use the echo command:
|
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.
|
Set up a $HOME/local/bin directory and link several scripts there that we will use in the class.
mkdir -p ~/local/bin cd ~/local/bin ln -s -f /work2/projects/BioITeam/common/bin/launcher_creator.py ln -s -f /work2/projects/BioITeam/common/bin/launcher_maker.py |
The tilde character ( ~ ) is a pathname shortcut that means "home directory". We'll see more of it later. $HOME is an environment variable set by TACC that also refers to your home directory. |
Now execute the lines below to set up a login script, called .bashrc
When you login via an interactive shell as you did above, a well-known script is executed by the shell to establish your favorite environment settings. We've set up a common login script for you to start with that will help you know where you are in the file system and make it easier to access some of our shared resources. To set it up, do the steps below:
If you already have a .bashrc set up, make a backup copy first.
You can restore your original login script after this class is over. |
cd cp /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.stampede2 .bashrc chmod 600 .bashrc |
What's going on with chmod?
|
Since .bashrc is executed when you login, to ensure it is set up properly you should first log off stampede2 like this:
exit |
Then log back in to stampede2.tacc.utexas.edu. This time your .bashrc will be executed and you should see a new shell prompt:
stamp2:~$ |
The great thing about this prompt is that it always tells you where you are, which avoids having to issue the pwd (present working directory) command all the time. Execute these commands to see how the prompt reflects your current directory.
mkdir -p ~/tmp/a/b/c cd ~/tmp/a/b/c # Your prompt should look like this: stamp2:~/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 ( ~ ).
So why don't you see the .bashrc file you copied to your home directory? Because all files starting with a period (dot files) are hidden by default. To see them add the -a (all) option to ls:
cd ls -a |
To see even more detail, including file type and permissions and symbolic link targets, add the -l (long listing) switch:
ls -la |
Your new ~/.bashrc files defines a ll alias command, so when you type ll it is short for ls -la. |
We list the contents of your .bashrc login script to the Terminal with the cat (concatenate files) command. cat simply reads a file and writes each line of content to standard output (here, your Terminal):
cd cat .bashrc # or for larger files... more .bashrc |
| 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) or look at parts of the file with head or tail. |
You'll see the following (you may need to scroll up a bit to see the beginning):
#!/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. However, a script inherits the environment variables
# from its parent shell. Both of these are standard bash behavior.
# 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
# There are 3 independent, safe ways to modify the standard module setup:
# 1) Use "module save" (see "module help" for details).
# 2) Place module commands in ~/.modules
# 3) Place module commands in this file inside the if block below.
if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
export __BASHRC_SOURCED__=1
module load launcher
module load git
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONAL_PATH__" ]; then
export __PERSONAL_PATH__=1
# for NGS course
export LANG="C" # avoid the annoying Perl warnings on cds, etc.
export PATH=.:$HOME/local/bin:$PATH
export ALLOCATION=UT-2015-05-18 # Group is G-816696
export BIWORK=/work2/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export BI=/corral-repl/utexas/BioITeam
export PATH=.:$HOME/local/bin:$PATH
# 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:'
fi
########################
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='stamp2:\w$ '; fi
########################
# SECTION 4 -- aliases and umask
alias ll='ls -la'
alias lh='ls -lh'
umask 002
###################################
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi |
So what does the common login script do? A lot! Let's look at just a few of them.
The first line is the she-bang. Even though the expression is inside a shell comment (denoted by the # character), it tells the shell what program should execute this file – in this case, bash itself.
#!/bin/bash |
The login script also sets an environment variable $BIWORK to point to the shared directory /work2/projects/BioITeam, and another environment variable $CORENGS to point to the specific sub-directory for our class.
export BIWORK=/work2/projects/BioITeam export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools |
Environment variables are like variables in a programming language like python or perl (in fact bash is a complete programming language). They have a name (like BIWORK above) and a value (the value for BIWORK is the pathname /work/projects/BioITeam). Read more about environment variables here: More on environment variables.
You can use these environment variables to shorten typing, for example, to look at the contents of the shared /work2/projects/BioITeam directory as shown below, using the magic Tab key to perform shell completion.
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!
|
# hit Tab once after typing $BIWORK/ to expand the environment variable
ls $BIWORK/
# now hit Tab twice to see the contents of the directory
ls /work2/projects/BioITeam/
# type "pr" and hit Tab again
ls /work2/projects/BioITeam/pr
# type "co" and hit Tab again
ls /work2/projects/BioITeam/projects/co
# type "Co" and hit Tab again
ls /work2/projects/BioITeam/projects/courses/Co
# your command line should now look like this
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/
# now type "mi" and one Tab
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/mi
# your command line should now look like this
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/
# now hit Tab once
# the shell expands as far as it can unambiguously,
# so your command line should look like this
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# now hit Tab twice
# You should see 3 filenames, all starting with "small"
# type a period (".") then hit Tab twice again
# You're narrowing down the choices -- you should see two filenames
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# finally, type "f" then hit Tab again. It should complete to this:
ls /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq |
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:
echo $PATH |
As you can see, there are a lot of locations on the $PATH. That's because when you load modules at TACC (such as the module load lines in the common login script), that makes the programs available to you by putting their installation directories on your $PATH. We'll learn more about modules later.
Here's how the common login script adds your $HOME/local/bin directory to the location list – recall that's where we linked several useful scripts – along with a special dot character ( . ) that means "here", or "whatever the current directory is". In the statment below, colon ( : ) separates directories in the list.
export PATH=.:$HOME/local/bin:$PATH |
The complicated looking if statement in SECTION 3 of your .bashrc sets up a friendly shell prompt that shows the current working directory. This is done by setting the special PS1 environment variable and including a special \w directive that the shell knows means "current directory".
########## # SECTION 3 -- controlling the prompt if [ -n "$PS1" ]; then PS1='stamp2:\w$ '; fi |