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 putty.exe (terminal) and pscp.exe (secure copy client)
  • Git-bash – http://msysgit.github.io/
    • terminal plus minimal Linux environment
  • 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.

On Macs, Linux and Windows Git-bash or Cygwin, you run it from a Terminal window. Answer yes to the SSH security question prompt.

ssh your_TACC_userID@stampede.tacc.utexas.edu

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

• Double-click the Putty.exe icon
• In the PuTTY Configuration window
  • make sure the Connection type is SSH
  • enter stampede.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

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 and 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.

Setting up your environment

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

cd 
ln -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.

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:

stamp:~$

And nice directory colors when you list your home directory:

ls

So why don't you see the .profile_user 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:

ls -la

.profile_user

Let's take a quick look at what is being done by the .profile_user login script, using cat (concatenate):

cat .profile_user

#!/bin/bash
# Change the command line prompt to contain the current directory name
PS1='stamp:\w$ '

# Ensure all created files can be read/written by group members
umask 002

# Use yellow for directories, not that horrible blue
dircolors .dircolors > /dev/null

# Make common useful software available
module load python
module load launcher

# Environment variables for useful locations
export BI=/corral-repl/utexas/BioITeam/
export CLASSDIR="$BI/core_ngs_tools"

# Add current directory and $HOME/local/bin to PATH
export PATH=.:$HOME/local/bin:$PATH