Transferring files

Instructor note

Total: 45min (Teaching:30Min | Discussion:0min | Breaks:0min | Exercises:10Min)

Objectives

• Questions

  • How do I upload/download files to the cluster?

• Objectives

  • Be able to transfer files to and from a computing cluster.

• Keypoints

  • wget downloads a file from the internet.

  • scp transfer files to and from your computer.

  • You can use an SFTP client like FileZilla to transfer files through a GUI.

Computing with a remote computer offers very limited use if we cannot get files to or from the cluster. There are several options for transferring data between computing resources, from command line options to GUI programs, which we will cover here.

Downloading from the internet

Download files from the internet using wget

One of the most straightforward ways to download files is to use wget. Any file that can be downloaded in your web browser with an accessible link can be downloaded using wget. This is a quick way to download datasets or source code.

The syntax is: wget https://some/link/to/a/file.tar.gz. For example, download the lesson sample files using the following command:

# To find the value of <URL> refer to the downloads section of tutorial

[MY_USER_NAME@CLUSTER_NAME ~]$ wget <URL>

Downloading GitHub repositories

Sometimes the data, pipeline or software you need is stored in a repository on GitHub or GitLab. In this case you either download individual (“raw”) files using wget or the whole repository with git clone.

We can download for example this test repository, with:

[MY_USER_NAME@CLUSTER_NAME ~]$ git clone https://github.com/test/HelloWorld.git

It will be saved into the current directory with the new folder having the name of the repository, so “HelloWorld” in this case.

Transferring files

Transferring single files and folders with scp

To upload a single file to or from the cluster, we can use scp (“secure copy”). The syntax can be a little complex for new users, but we’ll break it down.

To create and upload a file:

SAGA/Fram/BetzyFOX

[user@laptop ~]$ echo $(date) > from_laptop.txt
[user@laptop ~]$ scp from_laptop.txt MY_USER_NAME@saga.sigma2.no:

# Login to SAGA and check the file in the HOME folder

To download from the cluster:

SAGA/Fram/BetzyFOX

# Create a file on SAGA
[MY_USER_NAME@login-5.SAGA~]$ echo $(hostname) > from_saga.txt
[MY_USER_NAME@login-5.SAGA~]$ echo $(date) >> from_saga.txt

# From the laptop download it
[user@laptop ~]$ scp MY_USER_NAME@saga.sigma2.no:from_saga.txt .
Password: 

from_fox.txt   100%   63     5.4KB/s   00:00

[user@laptop ~]$ cat from_saga.txt
login-5.saga
ma. 14. mars 19:14:53 +0100 2022

To recursively copy a directory, we just add the -r (recursive) flag:

[user@laptop ~]$ scp -r some-local-folder MY_USER_NAME@CLUSTER_NAME:

This will create the directory ‘some-local-folder’ on the remote system, and recursively copy all the content from the local to the remote system. Existing files on the remote system will not be modified, unless there are files from the local system with the same name, in which case the remote files will be overwritten.

A trailing slash on the target directory is optional, and has no effect for scp -r, but it can be important in other commands.

Transferring files using a graphical user interface

While scp is an efficient way of transferring files between your computer and the cluster, it can be quite intimidating and overwhelming in the beginning. Luckily we can also use programs with a GUI (Graphical User Interface) to make it easier for us to browse through remote folders on the cluster and upload or download files.

FileZilla is available for all popular operating systems and can be downloaded here. After installing it, you only have to enter the host (e.g. saga.sigma2.no), your username, password and port 22, like shown here:

You can upload and download files by dragging them from the local (left side) to the remote (right side) pane or vice versa.

Archiving files

One of the biggest challenges we often face when transferring data between remote HPC systems is that of large numbers of files. There is an overhead to transferring each individual file and when we are transferring large numbers of files these overheads combine to slow down our transfers to a large degree.

The solution to this problem is to archive multiple files into smaller numbers of larger files before we transfer the data to improve our transfer efficiency. Sometimes we will combine archiving with compression to reduce the amount of data we have to transfer and so speed up the transfer.

The most common archiving command you will use on a (Linux) HPC cluster is tar. tar can be used to combine files into a single archive file and, optionally, compress. For example, to collect all files contained inside output_data into an archive file called output_data.tar we would use:

[user@laptop ~]$ tar -cvf output_data.tar output_data/

The options we used for tar are:

• -c - Create new archive

• -v - Verbose (print what you are doing!)

• -f mydata.tar - Create the archive in file output_data.tar

The tar command allows users to concatenate flags. Instead of typing tar -c -v -f, we can use tar -cvf.

The tar command can also be used to interrogate and unpack archive files. The -t argument (”table of contents”) lists the contents of the referred-to file without unpacking it.
The -x (“extract”) flag unpacks the referred-to file. To unpack the file after we have transferred it:

[user@laptop ~]$ tar -xvf output_data.tar

This will put the data into a directory called output_data. Be careful, it will overwrite data there if this directory already exists!

Sometimes you may also want to compress the archive to save space and speed up the transfer. However, you should be aware that for large amounts of data compressing and un-compressing can take longer than transferring the un-compressed data so you may not want to transfer. To create a compressed archive using tar we add the -z option and add the .gz extension to the file to indicate it is gzip-compressed, e.g.:

[user@laptop ~]$ tar -czvf output_data.tar.gz output_data/

The tar command is used to extract the files from the archive in exactly the same way as for uncompressed data. The tar command recognizes that the data is compressed, and automatically selects the correct decompression algorithm at the time of extraction:

[user@laptop ~]$  tar -xvf output_data.tar.gz

Working with Windows

When you transfer files to from a Windows system to a Unix system (Mac, Linux, BSD, Solaris, etc.) this can cause problems. Windows encodes its files slightly different than Unix, and adds an extra character to every line.

On a Unix system, every line in a file ends with a \n (newline). On Windows, every line in a file ends with a \r\n (carriage return + newline). This causes problems sometimes.

Though most modern programming languages and software handles this correctly, in some rare instances, you may run into an issue. The solution is to convert a file from Windows to Unix encoding with the dos2unix command.

You can identify if a file has Windows line endings with cat -A filename. A file with Windows line endings will have ^M$ at the end of every line. A file with Unix line endings will have $ at the end of a line.

To convert the file, just run dos2unix filename. (Conversely, to convert back to Windows format, you can run unix2dos filename.)

 [MY_USER_NAME@CLUSTER_NAME ~]$ dos2unix File-created-on-windows.txt

A note on ports

All file transfers using the above methods use encrypted communication over port 22. This is the same connection method used by SSH. In fact, all file transfers using these methods occur through an SSH connection. If you can connect via SSH over the normal port, you will be able to transfer files.

How to use backup

The files in your home (/cluster/home) and project folder (/cluster/projects) are regularly backed up to either NIRD or one of the other clusters, as described in the documentation. So if you ever accidentally delete or overwrite a file in one of those folder, you can get your data back.