Transferring files

Last updated on 2025-10-15 | Edit this page

Overview

Questions

  • How do I transfer files to and from an HPC cluster?

Objectives

  • Copy files from your laptop onto the cluster (and vice-versa)
  • Download files directly onto the cluster

Performing work on a remote computer is not very useful if we cannot get files to or from the cluster. There are several options for transferring data between computing resources using CLI and GUI utilities, a few of which we will cover.

Download Lesson Files From the Internet Onto Your Laptop

One of the most straightforward ways to download files is to use either curl or wget. One of these is usually installed in most Linux shells, on Mac OS terminal and in GitBash. Any file that can be downloaded in your web browser through a direct link can be downloaded using curl or wget. This is a quick way to download datasets or source code. The syntax for these commands is

BASH 

wget [-O new_name] https://some/link/to/a/file
curl [-o new_name] -L https://some/link/to/a/file

By default, curl and wget download files to the same name as the file on the remote file server. The -O option to wget and the -o option to curl allow you to specify a new name for the file that you download.

Note that curl needs the -L option to follow links that redirect, whereas wget follows follows by default.

Challenge

Download the “tarball””

Try it out by downloading some material we’ll use later on, from a terminal on your local machine, using the URL of the current codebase:

https://github.com/hpc-carpentry/amdahl/tarball/main

The word “tarball” in the above URL refers to a compressed archive format commonly used on Linux, which is the operating system the majority of HPC cluster machines run. A tarball is a lot like a .zip file. The actual file extension is .tar.gz, which reflects the two-stage process used to create the file: the files or folders are merged into a single file using tar, which is then compressed using gzip, so the file extension is “tar-dot-g-z.” That’s a mouthful, so people often say “the xyz tarball” instead.

You may also see the extension .tgz, which is just an abbreviation of .tar.gz.

Use one of the above commands to save the tarball as amdahl.tar.gz, rather than using the same name as on the server

[you@laptop:~]$ wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
# or
[you@laptop:~]$ curl -o amdahl.tar.gz -L https://github.com/hpc-carpentry/amdahl/tarball/main

After downloading the file, use ls to see it in your working directory:

BASH 

[you@laptop:~]$ ls

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 and folders into a single archive file and optionally compress the result. Let’s look at the file we downloaded from the lesson site, amdahl.tar.gz.

The .gz part stands for gzip, which is a compression library. It’s common (but not necessary!) that this kind of file can be interpreted by reading its name: it appears somebody took files and folders relating to something called “amdahl,” wrapped them all up into a single file with tar, then compressed that archive with gzip to save space.

Let’s see if that is the case, without unpacking the file. tar prints the “table of contents” with the -t flag, for the file specified with the -f flag followed by the filename. Note that you can concatenate the two flags: writing -t -f is interchangeable with writing -tf together. However, the argument following -f must be a filename, so writing -ft will not work.

BASH 

[you@laptop:~]$ tar -tf amdahl.tar.gz
hpc-carpentry-amdahl-46c9b4b/
hpc-carpentry-amdahl-46c9b4b/.github/
hpc-carpentry-amdahl-46c9b4b/.github/workflows/
hpc-carpentry-amdahl-46c9b4b/.github/workflows/python-publish.yml
hpc-carpentry-amdahl-46c9b4b/.gitignore
hpc-carpentry-amdahl-46c9b4b/LICENSE
hpc-carpentry-amdahl-46c9b4b/README.md
hpc-carpentry-amdahl-46c9b4b/amdahl/
hpc-carpentry-amdahl-46c9b4b/amdahl/__init__.py
hpc-carpentry-amdahl-46c9b4b/amdahl/__main__.py
hpc-carpentry-amdahl-46c9b4b/amdahl/amdahl.py
hpc-carpentry-amdahl-46c9b4b/requirements.txt
hpc-carpentry-amdahl-46c9b4b/setup.py

This example output shows a folder which contains a few files, where 46c9b4b is an 8-character git commit hash that will change when the source material is updated.

Now let’s unpack the archive. We’ll run tar with a few common flags:

  • -x to extract the archive
  • -v for verbose output
  • -z for gzip compression
  • -f TARBALL for the file to be unpacked
Discussion

Challenge

Using the flags above, unpack the source code tarball using tar.

BASH 

[you@laptop:~]$ tar -xvzf amdahl.tar.gz

OUTPUT 

hpc-carpentry-amdahl-46c9b4b/
hpc-carpentry-amdahl-46c9b4b/.github/
hpc-carpentry-amdahl-46c9b4b/.github/workflows/
hpc-carpentry-amdahl-46c9b4b/.github/workflows/python-publish.yml
hpc-carpentry-amdahl-46c9b4b/.gitignore
hpc-carpentry-amdahl-46c9b4b/LICENSE
hpc-carpentry-amdahl-46c9b4b/README.md
hpc-carpentry-amdahl-46c9b4b/amdahl/
hpc-carpentry-amdahl-46c9b4b/amdahl/__init__.py
hpc-carpentry-amdahl-46c9b4b/amdahl/__main__.py
hpc-carpentry-amdahl-46c9b4b/amdahl/amdahl.py
hpc-carpentry-amdahl-46c9b4b/requirements.txt
hpc-carpentry-amdahl-46c9b4b/setup.py

Note that we did not need to type out -x -v -z -f, thanks to flag concatenation, though the command works identically either way – so long as the concatenated list ends with f, because the next string must specify the name of the file to extract.

The folder has an unwieldly name, so let’s change that to something more convenient. For this tasks we’ll use the mv command. This can be used to move files and directories, or rename them in place, and has this syntax:

BASH 

mv SOURCE DEST

We rename the directory using:

BASH 

[you@laptop:~]$ mv hpc-carpentry-amdahl-46c9b4b amdahl

Now let’s check the size of the extracted directory and compare to the compressed file size, using the du command for “disk usage”. We’ll use the -s option to summarise the total space used, and -h to present it in a human-readable format.

BASH 

[you@laptop:~]$ du -sh amdahl.tar.gz
8.0K     amdahl.tar.gz
[you@laptop:~]$ du -sh amdahl
48K    amdahl

Text files (including Python source code) compress nicely: the “tarball” is one-sixth the total size of the raw data!

If you want to reverse the process – compressing raw data instead of extracting it – set a c flag instead of x, set the archive filename, then provide a directory to compress:

BASH 

[you@laptop:~]$ tar -cvzf compressed_code.tar.gz amdahl

OUTPUT 

amdahl/
amdahl/.github/
amdahl/.github/workflows/
amdahl/.github/workflows/python-publish.yml
amdahl/.gitignore
amdahl/LICENSE
amdahl/README.md
amdahl/amdahl/
amdahl/amdahl/__init__.py
amdahl/amdahl/__main__.py
amdahl/amdahl/amdahl.py
amdahl/requirements.txt
amdahl/setup.py

If you give amdahl.tar.gz as the filename in the above command, tar will update the existing tarball with any changes you made to the files. That would mean adding the new amdahl folder to the existing folder (hpc-carpentry-amdahl-46c9b4b) inside the tarball, doubling the size of the archive!

So don’t do that!

Transferring Single Files and Folders With scp

To copy 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. The scp command is a relative of the ssh command we used to access the system, and can use the same authentication mechanism as we used before.

To upload to another computer, the template command is

[you@laptop:~]$ scp local_file yourUsername@cluster_url:remote_destination

in which @ and : are field separators and remote_destination is a path relative to your remote home directory, or a new filename if you wish to change it, or both a relative path and a new filename. If you don’t have a specific folder in mind you can omit the remote_destination and the file will be copied to your home directory on the remote computer (with its original name). If you do include a remote_destination, note that scp interprets this as follows: if it exists and is a folder, the file is copied inside the folder; if it exists and is a file, the file is overwritten with the contents of local_file; if it does not exist, it is assumed to be a destination filename for local_file.

Upload the lesson material to your remote home directory like so:

BASH 

[you@laptop:~]$ scp compressed_code.tar.gz yourUsername@hpc-training.digitalmaterials-cdt.ac.uk:
Challenge

Why Not Download the files directly to HPC?

Most computer clusters are protected from the open internet by a firewall. For enhanced security, some are configured to allow traffic inbound, but not outbound. This means that an authenticated user can send a file to a cluster machine, but a cluster machine cannot retrieve files from a user’s machine or the open Internet.

Try downloading the file directly! This can be done on the login node - no need for a batch job submission.

BASH 

[you@laptop:~]$ ssh yourUsername@hpc-training.digitalmaterials-cdt.ac.uk
yourUsername@login:~$ wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
# or
yourUsername@login:~$ curl -o amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
Challenge

Copy a file from the HPC cluster to your laptop

So far we’ve copied files from a laptop to HPC, but how about the other way round?

The syntax is very similar, and the transfer is once again initiated from your laptop rather than from the HPC prompt. The command we will use swaps the order of the arguments such that it looks like this:

BASH 

[you@laptop:~]$ scp yourUsername@hpc-training.digitalmaterials-cdt.ac.uk:remote_directory/remote_file local_destination

Using this as a guide, copy your hostname.sh script from the HPC cluster to your laptop.

BASH 

[you@laptop:~]$ scp yourUsername@hpc-training.digitalmaterials-cdt.ac.uk:hostname.sh .

Note the final .. This is a shorthand way to refer to the current directory. An alternative would have been

BASH 

[you@laptop:~]$ scp yourUsername@hpc-training.digitalmaterials-cdt.ac.uk:hostname.sh hostname.sh

Verify that the transfer was complete by listing the file using ls.

Key Points
  • Use wget to download files onto HPC
  • Use scp for copying files between laptop and HPC
  • Use tar for creating and unpacking archives