Computational Techniques for Life Sciences

Network and File Transfers

In order to login or transfer files to a remote Linux file system, you must know the hostname (unique network identifier) and the username. If you are already on a Linux file system, those are easy to determine using the following commands:

$ whoami
wallen
$ hostname -f
login1.ls5.tacc.utexas.edu

Given that information, a user would remotely login to this Linux machine using the Terminal command:

$ ssh wallen@ls5.tacc.utexas.edu
(enter password)
(enter token)

Windows users would typically use the program “PuTTY” to perform this operation. Logging out of a remote system is done using the logout command, or the shortcut <Ctrl+d>:

  [ls5]$ logout
[local]$ 

Copying files from your local computer to Lonestar5 would require the scp command (Windows users use the program “WinSCP”):

[local]$ scp my_file wallen@ls5.tacc.utexas.edu:~/
(enter password)
(enter token)

In this command, you specify the name of the file you want to transfer (my_file), the username (wallen), the hostname (ls5.tacc.utexas.edu), and the path you want to put the file (~/). Take careful notice of the seperators including spaces, the @ symbol and the colon. Copy files from Lonestar5 to your local computer using ths following:

[local]$ scp wallen@ls5.tacc.utexas.edu:~/my_file ./
(enter password)
(enter token)

Instead of files, full directories can be copied using the “recursive” flag (scp -r ...). The rsync tool is an advanced copy tool that is useful for synching data between two sites. Although we will not go into depth here, example rsync usage is as follows:

$ rsync -azv local remote
$ rsync -azv remote local

This is just the basics of copying files. See example scp usage here and example rsync usage here.

Exercise

1. Identify which Lonestar5 login node you are on (login1, login2, login3)
2. Remotely login to a different Lonestar5 login node and list what files are available.
3. Logout until you are back to your original login node.
4. Copy the file chr21.fa to your local computer.

Click here for solution

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