Step 1: Connecting to and establishing a profile on Lonestar (GVA14)

Logging in

Start SSH Secure Shell or Putty and connect to a login node of the lonestar compute cluster (lonestar.tacc.utexas.edu) at TACC using your TACC user name.

ssh <username>@lonestar.tacc.utexas.edu

Settup up a profile

There are many flavors of Linux/Unix shells. The default for TACC's Linux (and most other Linuxes) is bash (bourne again shell), which we will use throughout.

Whenever 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 profile 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 up this profile, do the following steps after logging in:

Copy a preconfigured "profile" to use with your account

cdh
cp /corral-repl/utexas/BioITeam/scripts/ngsc_profile_user .profile
chmod 600 .profile

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

Notice that when you do a normal ls to list the contents of your home directory, this file doesn't appear. That's because it's a hidden "dot file" – a file that has no filename, only an extension. To see these hidden files use the -a (all) switch for ls:

How to see hidden and not hidden files in linux

ls -a

To see even more detail, including file permissions, add the -l (long listing) switch:

How to see details about hidden and not hidden files in linux

ls -la

Since .profile is executed when you login, to ensure it is set up properly you should first logout:

How to leave Lonestar by logging out

exit

then log back in:

Go log back in to Lonestar

ssh <username>@lonestar.tacc.utexas.edu

If everything is working correctly you should now see a prompt like this:

tacc:~$

What your .profile does Let's look at what your .profile profile actually does: Print the contents of your .profile file lstar:~$ cat .profile #!/bin/bash # include common settings for the NGS course . /corral-repl/utexas/BioITeam/bin/profile_ngs_course.bash All this does is "import" some settings in the common /corral-repl/utexas/BioITeam/bin/profile_ngs_course.bash file into your environment, and all its descendents. The "import" operator is the period ( . ). This is also known as "sourcing a script". So what does the common profile file do? For one thing, it sets an environment variable BI to point to the /corral-repl/utexas/BioITeam directory. So you can look at the file as shown below. Notice that if you hit TAB after typing cat $BI/ the shell expands the BI environment variable. Print the contents of the NGS course common profile lstar:~$ cat $BI/bin/profile_ngs_course.bash #!/bin/bash PS1='tacc:\w$ ' umask 002 export BI=/corral-repl/utexas/BioITeam export PATH=$BI/bin:$HOME/local/bin:$PATH module load launcher module load python module load samtools module load R The first line – the "she-bang" – tells the shell what program should execute this file – in this case, bash itself. The PS1='tacc:\w$ ' line is a special setting that tells the shell to display the current directory as part of its prompt. It saves you typing pwd all the time to see where you are in the directory hierarchy. Try this: See how your prompt reflects your current directory lstar:~$ mkdir tmp lstar:~$ cd tmp lstar:~/tmp$ Your prompt now tells you you are in the tmp subdirectory of your home directory (~). To return to top-level of your home directory, just type How to return to your home directory cd The export profile lines define the two shell variables BI and PATH. You've already seen how using $BI can come in handy accessing our shared course directory. As for PATH, that is a well-known environment variable that defines a set of directories where the shell will look when you type in a program's name. Our shared profile adds the common course /corral-repl/utexas/BioITeam/bin directory and your local ~/local/bin directory (which does not exist yet) to the location list. You can see the entire list of locations by doing this: How to 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 profile), that mechanism makes the programs available to you by putting their installation directories on your $PATH. We'll learn more about modules shortly.

Now let's go on to editing files on Lonestar.