Transferring files with remote computers

Last updated on 2026-08-20 | Edit this page

Overview

Questions

  • How do I transfer files to (and from) the cluster?
  • What tools do HPC systems provide to manage software dependencies?

Objectives

  • Transfer files to and from a computing cluster.
  • Install an executable from source
  • Use modules to meet software dependencies

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

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

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

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

Challenge

Download the “Tarball”

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.

By default, curl and wget download files to the same name as the URL: in this case, main. Use one of the above commands to save the tarball as amdahl.tar.gz.

BASH 

[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

The -L option to curl tells it to follow URL redirects (which wget does by default).

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-710cf57/
hpc-carpentry-amdahl-710cf57/.github/
hpc-carpentry-amdahl-710cf57/.github/workflows/
hpc-carpentry-amdahl-710cf57/.github/workflows/python-publish.yml
hpc-carpentry-amdahl-710cf57/.github/workflows/test.yml
hpc-carpentry-amdahl-710cf57/.gitignore
hpc-carpentry-amdahl-710cf57/LICENSE
hpc-carpentry-amdahl-710cf57/README.md
hpc-carpentry-amdahl-710cf57/amdahl/
hpc-carpentry-amdahl-710cf57/amdahl/__init__.py
hpc-carpentry-amdahl-710cf57/amdahl/__main__.py
hpc-carpentry-amdahl-710cf57/amdahl/amdahl.py
hpc-carpentry-amdahl-710cf57/pyproject.toml

This example output shows a folder that contains several files. Here, 710cf57 is an 8-character [git][git-swc] commit hash that changes whenever the [amdahl][amdahl-git-repo] source code 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

Extract the Archive

Using the flags above, unpack the source code tarball into a new directory named “amdahl” using tar.

BASH 

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

OUTPUT 

hpc-carpentry-amdahl-710cf57/
hpc-carpentry-amdahl-710cf57/.github/
hpc-carpentry-amdahl-710cf57/.github/workflows/
hpc-carpentry-amdahl-710cf57/.github/workflows/python-publish.yml
hpc-carpentry-amdahl-710cf57/.github/workflows/test.yml
hpc-carpentry-amdahl-710cf57/.gitignore
hpc-carpentry-amdahl-710cf57/LICENSE
hpc-carpentry-amdahl-710cf57/README.md
hpc-carpentry-amdahl-710cf57/amdahl/
hpc-carpentry-amdahl-710cf57/amdahl/__init__.py
hpc-carpentry-amdahl-710cf57/amdahl/__main__.py
hpc-carpentry-amdahl-710cf57/amdahl/amdahl.py
hpc-carpentry-amdahl-710cf57/pyproject.toml

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 unfortunate name, so let’s change that to something more convenient.

BASH 

[you@laptop:~]$ mv hpc-carpentry-amdahl-710cf57 amdahl

Check the size of the extracted directory and compare to the compressed file size, using du for “disk usage”.

BASH 

[you@laptop:~]$ du -sh amdahl.tar.gz
8.0K    amdahl.tar.gz
[you@laptop:~]$ du -sh amdahl
27K     amdahl

Text files (including Python source code) compress nicely: the “tarball” is approximately one-third of 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/.github/workflows/test.yml
amdahl/.gitignore
amdahl/LICENSE
amdahl/README.md
amdahl/amdahl/
amdahl/amdahl/__init__.py
amdahl/amdahl/__main__.py
amdahl/amdahl/amdahl.py
amdahl/pyproject.toml

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-710cf57) inside the tarball, doubling the size of the archive!

Callout

Working with Windows

When you transfer text files 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.)

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 public-key authentication mechanism.

To upload to another computer, the template command is

BASH 

[you@laptop:~]$ scp local_file yourUsername@cluster.hpc-carpentry.org: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 include a remote_destination, note that scp interprets this the same way cp does when making local copies: 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 amdahl.tar.gz yourUsername@cluster.hpc-carpentry.org:
Challenge

Why Not Download on HPC Carpentry’s Cloud Cluster Directly?

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. Note that it may well fail, and that’s OK!

BASH 

[you@laptop:~]$ ssh yourUsername@cluster.hpc-carpentry.org
[yourUsername@login1 ~]$ wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
# or
[yourUsername@login1 ~]$ curl -o amdahl.tar.gz -L https://github.com/hpc-carpentry/amdahl/tarball/main
Discussion

Why Not Download on HPC Carpentry’s Cloud Cluster Directly? (continued)

Did it work? If not, what does the terminal output tell you about what happened?

Transferring a Directory

To transfer an entire directory, we add the -r flag for “recursive”: This copies the item specified, and every item below it, and every item below those, and so on, until it reaches the bottom of the directory tree rooted at the folder name you provided.

BASH 

[you@laptop:~]$ scp -r amdahl yourUsername@cluster.hpc-carpentry.org:
Callout

Caution

For a large directory – either in size or number of files – copying with -r can take a long time to complete.

When using scp, you may have noticed that a : always follows the remote computer name. A string after the : specifies the remote directory you wish to transfer the file or folder to, including a new name if you wish to rename the remote material. If you leave this field blank, scp defaults to your home directory and the name of the local material to be transferred.

On Linux computers, / is the separator in file or directory paths. A path starting with a / is called absolute, since there can be nothing above the root /. A path that does not start with / is called relative, since it is not anchored to the root.

If you want to upload a file to a location inside your home directory – which is often the case – then you don’t need a leading /. After the :, you can type the destination path relative to your home directory. If your home directory is the destination, you can leave the destination field blank, or type ~ – the shorthand for your home directory – for completeness.

With scp, a trailing slash on the target directory is optional, and has no effect. A trailing slash on a source directory is important for other commands, like rsync.

Callout

A Note on rsync

As you gain experience with transferring files, you may find the scp command limiting. The [rsync] utility provides advanced features for file transfer and is typically faster compared to both scp and sftp (see below). It is especially useful for transferring large and/or many files and for synchronizing folder contents between computers.

The syntax is similar to scp. To transfer to another computer with commonly used options:

BASH 

[you@laptop:~]$ rsync -avP amdahl.tar.gz yourUsername@cluster.hpc-carpentry.org:

The options are:

  • -a (archive) to preserve file timestamps, permissions, and folders, among other things; implies recursion
  • -v (verbose) to get verbose output to help monitor the transfer
  • -P (partial/progress) to preserve partially transferred files in case of an interruption and also displays the progress of the transfer.

To recursively copy a directory, we can use the same options:

BASH 

[you@laptop:~]$ rsync -avP amdahl yourUsername@cluster.hpc-carpentry.org:~/

As written, this will place the local directory and its contents under your home directory on the remote system. If a trailing slash is added to the source, a new directory corresponding to the transferred directory will not be created, and the contents of the source directory will be copied directly into the destination directory.

To download a file, we simply change the source and destination:

BASH 

[you@laptop:~]$ rsync -avP yourUsername@cluster.hpc-carpentry.org:amdahl ./

File transfers using both scp and rsync use SSH to encrypt data sent through the network. So, if you can connect via SSH, you will be able to transfer files. By default, SSH uses network port 22. If a custom SSH port is in use, you will have to specify it using the appropriate flag, often -p, -P, or --port. Check --help or the man page if you’re unsure.

Challenge

Change the Rsync Port

Say we have to connect rsync through port 768 instead of 22. How would we modify this command?

BASH 

[you@laptop:~]$ rsync amdahl.tar.gz yourUsername@cluster.hpc-carpentry.org:

Hint: check the man page or “help” for rsync.

BASH 

[you@laptop:~]$ man rsync
[you@laptop:~]$ rsync --help | grep port
     --port=PORT             specify double-colon alternate port number
See http://rsync.samba.org/ for updates, bug reports, and answers
[you@laptop:~]$ rsync --port=768 amdahl.tar.gz yourUsername@cluster.hpc-carpentry.org:

(Note that this command will fail, as the correct port in this case is the default: 22.)

Install the amdahl executable

Downloading the software is only part of the process. Before we can run it, we need to install it. Advanced software, including simple examples like amdahl, have dependencies – additional software that the software uses when it runs, and which is not included as part of the software itself, because many pieces of software may have the same dependency.

In our case, our software depends on both a compatible Python executable environment, and a set of communications libraries called MPI, and their corresponding Python implementation.

If you have disconnected, log back in to the cluster:

[you@laptop:~]$ ssh yourUsername@cluster.hpc-carpentry.org

Then go to the re-named amdahl source tree. Ensure that the appropriate Python and MPI modules are loaded, and install the executable using the Python pip installation command:

BASH 

[yourUsername@login1 ~]$ cd amdahl
[yourUsername@login1 ~]$ python3 -m pip install --user .
Callout

Amdahl is Python Code

The Amdahl program is written in Python, and installing or using it requires locating the python3 executable on the login node. If it can’t be found, try listing available modules using module avail, load the appropriate one, and try the command again.

MPI for Python

The Amdahl code has one dependency: mpi4py. If it hasn’t already been installed on the cluster, pip will attempt to collect mpi4py from the Internet and install it for you. If this fails due to a one-way firewall, you must retrieve mpi4py on your local machine and upload it, just as we did for Amdahl.

Discussion

Retrieve and Upload mpi4py

If installing Amdahl failed because mpi4py could not be installed, retrieve the tarball from https://github.com/mpi4py/mpi4py/tarball/master then rsync it to the cluster, extract, and install:

BASH 

[you@laptop:~]$ wget -O mpi4py.tar.gz https://github.com/mpi4py/mpi4py/tarball/master
[you@laptop:~]$ scp mpi4py.tar.gz yourUsername@cluster.hpc-carpentry.org:
# or
[you@laptop:~]$ rsync -avP mpi4py.tar.gz yourUsername@cluster.hpc-carpentry.org:

BASH 

[you@laptop:~]$ ssh yourUsername@cluster.hpc-carpentry.org
[yourUsername@login1 ~]$ tar -xvzf mpi4py.tar.gz  # extract the archive
[yourUsername@login1 ~]$ mv mpi4py* mpi4py        # rename the directory
[yourUsername@login1 ~]$ cd mpi4py
[yourUsername@login1 ~]$ python3 -m pip install --user .
[yourUsername@login1 ~]$ cd ../amdahl
[yourUsername@login1 ~]$ python3 -m pip install --user .
Discussion

If pip Raises a Warning…

pip may warn that your user package binaries are not in your PATH.

WARNING 

WARNING: The script amdahl is installed in "${HOME}/.local/bin" which is
not on PATH. Consider adding this directory to PATH or, if you prefer to
suppress this warning, use --no-warn-script-location.

To check whether this warning is a problem, use which to search for the amdahl program:

BASH 

[yourUsername@login1 ~]$ which amdahl

If the command returns no output, displaying a new prompt, it means the file amdahl has not been found. You must update the environment variable named PATH to include the missing folder. Edit your shell configuration file as follows, then log off the cluster and back on again so it takes effect.

BASH 

[yourUsername@login1 ~]$ nano ~/.bashrc
[yourUsername@login1 ~]$ tail ~/.bashrc

OUTPUT 

export PATH=${PATH}:${HOME}/.local/bin

After logging back in to cluster.hpc-carpentry.org, which should be able to find amdahl without difficulties. If you had to load a Python module, load it again.

Help!

Many command-line programs include a “help” message. Try it with amdahl:

BASH 

[yourUsername@login1 ~]$ amdahl --help

OUTPUT 

usage: amdahl [-h] [-p [PARALLEL_PROPORTION]] [-w [WORK_SECONDS]] [-t] [-e] [-j [JITTER_PROPORTION]]

options:
  -h, --help            show this help message and exit
  -p, --parallel-proportion [PARALLEL_PROPORTION]
                        Parallel proportion: a float between 0 and 1
  -w, --work-seconds [WORK_SECONDS]
                        Total seconds of workload: an integer greater than 0
  -t, --terse           Format output as a machine-readable object for easier analysis
  -e, --exact           Exactly match requested timing by disabling random jitter
  -j, --jitter-proportion [JITTER_PROPORTION]
                        Random jitter: a float between -1 and +1

This message doesn’t tell us much about what the program does, but it does tell us the important flags we might want to use when launching it.

Key Points
  • wget -O and curl -o download a file from the internet.
  • scp and rsync transfer files to and from your computer.
  • Users can install custom software on their accounts.
  • The system can help meet software dependencies.