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
- Putty – http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
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
- make sure the Connection type is
- 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).
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.
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