File transfer using scp

Learning outcomes

• Practice using the documentation of your favorite HPC cluster
• Can transfer files using scp

For teachers

Teaching goals are:

• Learners have practiced using the documentation of their favorite HPC cluster
• Learners have transferred files using scp

Prior questions:

• Who has heard of scp?
• Who has already used scp?

Info

• We start with a transferring tool in the command line.
• Let's focus on the easiest.
• Next session we try a tool with a graphical interface!

Overview of terminal transfer tools

Info

• Terminal transfer tools are handy when you are already working in the terminal and can sometimes be superior to Graphical tools.

  • No switching applications
  • Your hands stay on the keyboard, you dont need to grab the mouse
  • Tab completion can make finding files faster
  • If you work on servers or over ssh you might not have a gui

• scp has the similar arguments as for the linux copy function cp.
• sftp is more versatile with more file management capabilities. Optional lesson

• rsync is perfect for syncing and have many capabilities. Optional lesson

• All are considered secure.

But what is wget and curl?

• These tools are used to download files from websites or ftp servers

• wget saves downloaded contents to local files, like

  • wget ftp://ftp.sunet.se/mirror/archive/ftp.sunet.se/pub/pictures/space/*
  • wget https://upload.wikimedia.org/wikipedia/commons/3/37/Grace_Hopper_and_UNIVAC.jpg -O grace_hopper.jpg
  • typical usecases:
    • download data from a service
    • download a program or compressed source code
  • supports HTTP, HTTPS, and FTP
  • user-friendly for basic tasks
  • good for mirroring websites
    • downloading entire directories recursively for offline viewing or backups.
  • most popular from Unix-based systems, like Linux

• curl outputs the content to the terminal by default.

  • add -O to download as file.
  • supports a wide range of protocols: HTTP, HTTPS, FTP, FTPS, SCP, SFTP, TFTP...
  • often preferred for scripting and automation due to its versatility
  • interacting with APIs, handling complex web requests
  • often available by default on Windows and MacOS.

SCP is an abbreviation for Secure Copy Protocol

Pros

• Simple
• One-line command
• Secure
• Use cases
  • copy just a file
  • copy just a specific directory (with sub-directories).

When not to use

• When needing several one-line commands
  • requires credentials every time
• When looking to do more than a basic file transfer, SCP falls short.
• Transfers that are interrupted you have to restart the entire transfer.
• A file with the same name in the same directory is transferred, will be overwritten.

Risk of overwriting files

• There is no warning if a file is about to be overwritten.
  • There is no scp -i ... as for rm -i that asks if you really want to remove the file.
• rsync may be a better tool if you want to sync existing content.

Procedure

• Run the scp commands on YOUR computer, since you probably do not have a server address to your computer!

• In the terminal (from local, not server session)

  scp <from> <to>
  

• Where <from> is the file(s) you want to copy, and <to> is the destination.

Syntax for command arguments

• We use <content> to tell that this should be replaced by applicable names or paths etcetera...
• We use [content] to tell that this argument is not necessary

More detailed general procedure

Copy a file from your local computer to the cluster:

scp <local_file/folder> <username>@<cluster adress>:<path-to-folder/>

• where <username> is your cluster username,
• where <local_folder> is your local folder, for example:

Copy a file from the cluster to your local computer, do the command above in reverse order:

scp <username>@<cluster adress>:<path-to-folder/file> <local_folder or "." for _present_ folder>

If asked, give your center's password. You can get rid of this prompt if you have setup SSH keys

Example for Tetralith

This is how you copy a file from your local computer directly to your HOME folder (~/):

scp my_file.txt x_nisse@tetralith.nsc.liu.se:~/

To copy a file from Tetralith to your local computer (and present folder), do the command above in reverse order:

scp x_nisse@tetralith.nsc.liu.se:/home/x_nisse/remote_file.txt .

If asked, give your center's password. You can get rid of this prompt if you have setup SSH keys

Cheat sheet for scp

• scp followed by none or any of the following option flags and the files and servers involved

• scp provides a number of options that control every aspect of its behavior. The most widely used options are:

• -P - Specifies the remote host ssh port.

• -p - Preserves file modification and access times.
• -q - Use this option if you want to suppress the progress meter and non-error messages.
• -C - This option forces scp to compress the data as it is sent to the destination machine.
• -r - This option tells scp to copy directories recursively.

Exercises

Exercise 0: Use the documentation of your HPC cluster

• Search for how to transfer files to/from your HPC cluster using scp. At which URL is it described?

  • Tip: not all HPC centers have documented this, so you should give up searching after a while.

    • If the center maintaining you HPC cluster has not documented how to use scp, follow the Rackham documentation.

Where is that documentation?

HPC Cluster	Documentation
Alvis	Documentation.
Berzelius	Documentation
Bianca	Available for download via the transit server, see documentation
COSMOS	Documented on UPPMAX page.
Dardel	Documentation
Kebnekaise	Documentation
LUMI	Documentation
Pelle	Documentation
Rackham	Documentation
Tetralith	Documentation
Vera	Documentation.

Exercise 1: Upload a file from your computer, using scp

Tips

• Useful terminal commands (both locally and remotely)

  • pwd - which folder am I in?
  • cd [path] - change folder (go up in hierarchy with cd ..)
  • ls - list content of folder
  • mkdir - make a new folder
  • touch - create empty file

• (If you want to create a file in local terminal: $ touch local_file)

• (You can check the file structure in an ssh session)
• Send it to an existing folder (e.g. transfer) on Tetralith
  • use mkdir <folder name> if it is not there
• Check on server that it is there

Answer (Tetralith example)

Locally

• (If you want to create a file in local terminal: $ touch local_file)

• Send it to an existing folder (e.g. transfer) on Tetralith:

• $ scp local_file <username>@tetralith.nsc.liu.se:~/transfer/

Check on server that it is there

• $ ls ~/transfer

• Video for Tetralith

Exercise 2: Download a file from the server to your computer, using scp

Tips

• (If you want to create a file in remote ssh terminal: $ touch remote_file)
• Send it to an existing local folder
• Check locally that it is there

Answer (Tetralith example)

On Server

• (If you want to create a remote file first, in an SSH session, do: $ touch remote_file)
• Get it the present local folder: $ scp <username>@tetralith.nsc.liu.se:~/transfer/remote_file .

Check locally that it is there

• $ ls

• (or in the File explorer)

• Video for Tetralith