Getting started at TACC

Getting to a remote computer

The Terminal window

Macs and Linux have Terminal programs built-in – find it now on your computer
Windows needs help
- Putty – http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
  - simple Terminal and file copy programs
  - download either the Putty installer (https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.70-installer.msi)
    - or putty.exe (terminal) and pscp.exe (secure copy client)
- Windows Subsystem for Linux – Windows 10 Professional includes a Ubuntu-like bash shells
  - See https://docs.microsoft.com/en-us/windows/wsl/install-win10
  - We recommend the Ubuntu Linux distribution, but any Linux distribution will have an SSH client
- Cygwin – http://www.cygwin.com/
  - A full Linux environment, including X-windows for running GUI programs remotely
  - Complicated to install

SSH

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 Lonestar5 compute cluster at TACC, where the remote host name is ls5.tacc.utexas.edu.

On Macs or Linux, you run ssh from a Terminal window. To invoke a Linux Terminal window if you have the Windows subsystem for Linux installed, double-click on the icon for the Linux distribution you installed (e.g. Ubuntu).

In your local Terminal window:

SSH to access lonestar5 at TACC

ssh <your_TACC_userID>@ls5.tacc.utexas.edu

Answer yes to the SSH security question prompt
Enter the password associated with your TACC account
Wait for your 2-factor authentication code to arrive via SMS or app, then type it in

If you're using Putty as your Terminal from Windows:

Double-click the Putty icon
In the PuTTY Configuration window
- make sure the Connection type is SSH
- enter ls5.tacc.utexas.edu for Host Name
- click Open button
- answer Yes to the SSH security question
In the PuTTY terminal
- enter your TACC user id after the "login as:" prompt, then Enter
- enter the password associated with your TACC account
- wait for your 2-factor authentication code to arrive via SMS or app, then type it in

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
the remote Shell

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.

Setting up your environment

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:

Create symbolic directory links

cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -s -f /work/projects/BioITeam

$WORK and $SCRATCH are TACC environment variables that refer to your work and scratch file system areas. To see the value of an environment variable, use the echo command:

echo $SCRATCH

What is "ln -s" doing?

The ln -s command creates a symbolic link, a shortcut to the linked file or directory.

Here the link targets are your work and scratch file system areas
Having these link shortcuts will help when you want to copy files to your work or scratch, and when you navigate the TACC file system using a remote SFTP client
Always change directory (cd) to the directory where we want the links created before executing ln -s
- Here we want the links under your home directory (cd with no arguments)

Want to know where a link points to? Use ls with the -l (long listing) option.

ls -l shows where links go

ls -l

Set up a $HOME/local/bin directory and link several scripts there that we will use in the class.

Set up $HOME/local/bin directory

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_creator.py
ln -s -f /work/projects/BioITeam/ls5/opt/cutadapt-1.10/bin/cutadapt
ln -s -f /work/projects/BioITeam/ls5/opt/multiqc-1.0/multiqc
ln -s -f /work/projects/BioITeam/ls5/opt/samstat-1.09/samstat

The tilde ( ~ ) character

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.

cd
cp .bashrc .bashrc.beforeNGS

You can restore your original login script after this class is over.

Copy a pre-configured login script

cd
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5  .bashrc
chmod 600 .bashrc

What is chmod doing?

What's going on with chmod?

The chmod 600 .bashrc command marks the file as readable and writable only by you.
The .bashrc script file will not be executed unless it has these exact permissions settings.
The well-known filename is .bashrc (or .profile on some systems), which is specific to the bash shell.

Since .bashrc is executed when you login, to ensure it is set up properly you should first log off ls5 like this:

Log off Lonestar5

exit

Then log back in to ls5.tacc.utexas.edu. This time your .bashrc will be executed and you should see a new shell prompt:

ls5:~$

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:
ls5:~/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:

How to see hidden files

cd
ls -a

To see even more detail, including file type and permissions and symbolic link targets, add the -l (long listing) switch:

Long listing form of ls

ls -la

Details about your login script

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):

List .bashrc file contents without pausing

cd
cat .bashrc

# or for larger files...
more .bashrc

Don't use cat for large files

The cat command just echos 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):

Contents of your .bashrc file

#!/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 python
  module load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONAL_PATH__" ]; then
  export __PERSONAL_PATH__=1

# For CCBB summer school courses
  export ALLOCATION=UT-2015-05-18
  export BI=/corral-repl/utexas/BioITeam
  export BIWORK=/work/projects/BioITeam
  export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
  export PATH=.:$HOME/local/bin:$PATH
  # For cutadapt support:
  export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH
  # For MultiQC support:
  export PYTHONPATH=$BIWORK/ls5/lib/python2.7/annab-packages:$PYTHONPATH

# Turn on coloring by file type in the shell
  export LS_OPTIONS='-N --color=auto -T 0'
  # For better colors using a white background terminal, un-comment this line:
  #export LS_COLORS=$LS_COLORS:'di=1;33:'
  # For better colors using a white background terminal, un-comment this line:
  #export LS_COLORS=$LS_COLORS:'di=1;34:'
fi
##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then
  PS1='ls5:\w$ '
fi
##########
# SECTION 4 -- Umask and aliases
umask 002
alias ll="ls -la"
alias lah="ls -lah"
alias hexdump='od -A x -t x1z -v'
##########
# 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 "she-bang"

The first line is the she-bang. It tells the shell what program should execute this file – in this case, bash itself – even though the expression is inside a shell comment (denoted by the # character).

The "she-bang" line

#!/bin/bash

environment variables

The login script also sets an environment variable $BIWORK to point to the shared directory /work/projects/BioITeam, and another environment variable $CORENGS to point to the specific sub-directory for our class.

Setting environment variables to useful locations

export BIWORK=/work/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 environemt variables here: More on environment variables.

shell completion

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.

Important Tip -- the Tab key is your BFF!

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!

Tab once will expand the current command line contents as far as it can unambiguously.
- if nothing shows up, there is no unambiguous match
Tab twice will give you a list of everything the shell finds matching the current command line.
- you then decide where to go next

Shell completion exercise

# 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 /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 "m" and one Tab
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/m

# your command line should now look like this
ls /work/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 /work/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 /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small

# 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:

See where the bash shell looks for programs

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.

Adding directories to PATH

export PATH=.:$HOME/local/bin:$PATH

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".

Setting up the friendly shell prompt for stampede

##########
# SECTION 3 -- controlling the prompt
# for NGS course
if [ -n "$PS1" ]; then
  PS1='ls5:\w$ '
fi

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