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 to access Lonestar at TACC

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).

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

File systems at TACC

Local file systems

There are 3 local file systems available on any TACC cluster (stampede, lonestar, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).

On stampede these local file systems have the following characteristics:

	Home	Work	Scratch
quota	5 GB	400 GB	12+ PB (basically infinite)
policy	backed up	not backed up, not purged	not backed up, purged if not accessed recently (~10 days)
access command	`cd`	`cdw`	`cds`
environment variable	$HOME	$WORK	$SCRATCH
root file system	/home	/work	/scratch
use for	Small files such as scripts that you don't want to lose.	Medium-sized artifacts you don't want to copy over all the time. For example, custom programs you install (these can get large), or annotation file used for analysis.	Large files accessed from batch jobs. Your starting files will be copied here from somewhere else, and your results files will be copied back to your home system.

When you login, the system gives you information about disk quota and your compute allocation quota:

--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires | Name           Avail SUs     Expires |
| CancerGenetics     10627  2014-09-30 | genomeAnalysis     94284  2015-03-31 |
------------------------ Disk quotas for user abattenh ------------------------
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1              0.0       1.1     0.29          463     1001000    0.05 |
| /work              42.1     250.0    16.85        16281      500000    3.26 |
-------------------------------------------------------------------------------

Exercise

When you first login, you start in your home directory. Use these commands to change to your other file systems, and see how your command prompt changes to show your location.

cdw
cds
cd

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