Versions Compared

Old Version 156

changes.mady.by.user Anna M Battenhouse

Saved on

compared with

New Version 164

changes.mady.by.user Anna M Battenhouse

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

The Terminal window

  • Macs and Linux have a Terminal programs program built-in – find it now on your computer
  • Windows optons:Windows 10Command shell 10 or later has ssh and scp in Command Prompt or PowerShell (may require latest Windows updates)
    • Open the Start menu → Search for Command
Expand
title

...

...

Other Windows ssh/Terminal options

If your Windows version does not have ssh in Command Prompt or PowerShell:

...

...

...

    • Terminal) and pscp.exe (secure copy client)

...

More advanced options for those who want a full Linux environment on their Windows system:

  • Windows Subsystem for Linux – Windows 10 Professional includes a Ubuntu-like bash shells

...

...

...

...

  • A full Linux environment, including X-windows for running GUI programs remotely
  • Complicated to install

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.

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 stampede2 Lonestar6 compute cluster at TACC, where the remote host name is stampede2ls6.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:

Code Block
languagebash
titleSSH to access lonestar5 Lonestar6 at TACC
ssh <your_TACC_userID>@stampede2userID>@ls6.tacc.utexas.edu

# For example:
ssh abattenh@ls6.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
Expand
titleLoggin in with PuTTY

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

...

...

        • Lonestar6 into the Saved Sessions text box, then click Save
        • Next time select

...

        • Lonestar6 from the Saved Sessions list and click Load.
    • 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
    • provide your 2-factor authentication code

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:

  1. your local Terminal
  2. 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 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 programs called by the bash shell.

...

Setting up your environment

Create some

...

symbolic links and directories

First we will create a few directories and links we will use (more on these later).

...

Code Block
languagebash
titleCreate symbolic directory linkssymbolic directory links
cd  # makes your Home directory the "current directory"cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK2$WORK work2work
ln -s -f /work2work/projects/BioITeam
ln -s -f /work2/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS
/projects/courses/Core_NGS_Tools CoreNGS

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.

Tip

$WORK

Tip

$WORK2 and $SCRATCH are TACC environment variables that refer to your Work2 and Scratch file system areas. Work and Scratch file system areas. They are like variables in other programming languages, in that they have a name (WORK, SCRATCH) and hold a value ($WORK, $SCRATCH) To see the value of an environment variable, use the echo command:

Code Block
languagebash
echo $SCRATCH


...

Expand
titleWhat 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 Work2 Work and Scratch file system areas
  • Having these link shortcuts will help when you want to copy files to your Work2 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.

Code Block
languagebash
titlels -l shows where links go
ls -l


...

Code Block
languagebash
titleSet up $HOME/local/bin directory
mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work2work/projects/BioITeam/common/bin/launcher_creator.py
ln -s -f /work2/projects/BioITeam/common/bin/launcher_maker.py


Tip
titleThe tilde ( ~ ) character

The tilde character ( ~ ) is a pathname shortcut that means "home Home directory". We'll see more of it later.

$HOME is an environment variable set by TACC that also refers to your home Home area directory.

Setup your login profile (~/.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 perform the steps below:

Warning

If you already have a .bashrc set up, make a backup copy first.

Code Block
languagebash
cd
cp .bashrc .bashrc.beforeNGS

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

...

Code Block
languagebash
titleCopy a pre-configured login script
cd
cp /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.stampede2ls6 .bashrc
chmod 600 .bashrc

...

Since .bashrc is executed when you login, to ensure it is set up properly you should first log off stampede2 ls6 like this:

Code Block
languagebash
titleLog off Lonestar5Lonestar6
exit

Then log back in to stampede2ls6.tacc.utexas.edu. This time your .bashrc will be executed and you should see a new shell prompt:

Code Block
stamp2ls6:~$

The great thing about this prompt is that it always tells you where you are, which avoids you having to issue the execute the pwd (present working directory) command all the timeevery time you want to know where you are. Execute these commands to see how the prompt reflects your current directory.

Code Block
languagebash
mkdir -p ~/tmp/a/b/c
cd ~/tmp/a/b/c

# Your prompt should look like this:
stamp2ls6:~/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 (allall) option to ls:

Code Block
languagebash
titleHow 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) switchoption:

Code Block
titleLong listing form of ls
ls -la


Tip
titlell alias

Your new ~/.bashrc files bashrc file defines a ll alias command, so when you type ll it is short for ls -la.

...

Code Block
languagebash
titleContents 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. However, a script inherits the environment variables
# from its parent shell. Both of these are standard bash behavior
# 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
# 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. modules
if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
  export __BASHRC_SOURCED__=1
  module load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__BASHRCPERSONAL_SOURCEDPATH__" -a "$ENVIRONMENT" != BATCH ]; then
  export __BASHRCPERSONAL_SOURCEDPATH__=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:$PATH
  export ALLOCATION=UT-2015-05-18    # Group is G-816696
  export BIWORK=/work2/projects/BioITeam
  export PATH=.:$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 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
########################/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 "$PS1" ]; then PS1='stamp2ls6:\w$ '; fi
##################################
# SECTION 4 -- Umask and aliases and umask
#alias ls="ls --color=always"
alias ll='"ls -la'"
alias lah="ls -lah"
alias lc="wc -l"
alias lhhexdump='lsod -A x -t x1z -lhv'
umask 002
#############################################
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi

So what does the common this 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 (bash) what program should execute this file – in this case, bash itself.

...

The login script also sets an environment variable $BIWORK to point to the shared directory /work2work/projects/BioITeam, and another environment variable $CORENGS to point to the specific sub-directory for our class.

Code Block
languagebash
titleSetting environment variables to useful locations
export BIWORK=/work2work/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 of $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 /work2work/projects/BioITeam directory as shown below, using the magic Tab key to perform shell completion.

...

Code Block
languagebash
titleShell 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 /work2work/projects/BioITeam/

# type "pr" and hit Tab again
ls /work2work/projects/BioITeam/pr

# type "co" and hit Tab again
ls /work2work/projects/BioITeam/projects/co

# type "Co" and hit Tab again
ls /work2work/projects/BioITeam/projects/courses/Co

# your command line should now look like this
ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/

# now type "mi" and one Tab
ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/mi

# your command line should now look like this
ls /work2work/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 /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small

# now hit Tab twice
# You should see 3 filenames, all starting with "small"
# small.bam  small.fq   small2.fq

# type a period (".") then hit Tab twice again
# You're narrowing down the choices -- you should see two filenames
ls /work2work/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 /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq

...

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 statement below, colon ( : ) separates directories in the list.

...

Code Block
languagebash
titleSetting up the friendly shell prompt for stampede
##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='stamp2ls6:\w$ '; fi