Transferring files with remote computers
OverviewTeaching: 15 min
Exercises: 15 minQuestions
How do I transfer files to (and from) the cluster?Objectives
Be able to transfer files to and from a computing cluster.
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.
Download files from the Internet
One of the most straightforward ways to download files is to use
wget. Any file that can be
downloaded in your web browser through a direct 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. Try it out by downloading some material
we’ll use later on, from a terminal on your local machine.
[[email protected] ~]$ wget https://learnhpc.github.io/2021-02-hpc-intro/files/hpc-intro-data.tar.gz
This is an archive file format, just like
.zip, commonly used and supported by default on Linux, which is the operating system the majority of HPC cluster machines run. You may also see the extension
.tgz, which is exactly the same. We’ll talk more about “tarballs,” since “tar-dot-g-z” is a mouthful, later on.
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.
To upload to another computer:
To download from another computer:
Note that everything after the
: is relative to our home directory on the remote computer. We can
leave it at that if we don’t care where the file goes.
Upload a file
Copy the file you just downloaded from the Internet to your home directory on custom.learnhpc.eu.
Why not download on custom.learnhpc.eu directly?
Some computer clusters are behind firewalls set to only allow transfers initiated from the outside. This means that the
wgetcommand will fail, as an address outside the firewall is unreachable from the inside. To get around this, run the
wgetcommand from your local machine to download the file, then use the
scpcommand (just below here) to upload it to the cluster.
Try downloading the file directly. Note that it may well fail, and that’s OK!
Did it work? If not, what does the terminal output tell you about what happened?
To copy a whole directory, we add the
-r flag, for “recursive”: copy the item
specified, and every item below it, and every item below those… until it reaches the
bottom of the directory tree rooted at the folder name you provided.
For a large directory — either in size or number of files — copying with
-rcan take a long time to complete.
What’s in a
scp, you may have noticed that a
: always follows the remote computer name;
/ follows that, and sometimes not, and sometimes there’s a final
/. On Linux
/ is the root directory, the location where the entire filesystem (and others
attached to it) is anchored. 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
:, start writing the
sequence of folders that lead to the final storage location for the file or, as mentioned
above, provide nothing if your home directory is the destination.
A trailing slash on the target directory is optional, and has no effect for
scp -r, but is
important in other commands, like
A note on
As you gain experience with transferring files, you may find the
scpcommand limiting. The rsync utility provides advanced features for file transfer and is typically faster compared to both
sftp(see below). It is especially useful for transferring large and/or many files and creating synced backup folders.
The syntax is similar to
scp. To transfer to another computer with commonly used options:
a(archive) option preserves file timestamps and permissions among other things; the
v(verbose) option gives verbose output to help monitor the transfer; the
z(compression) option compresses the file during transit to reduce size and transfer time; and the
P(partial/progress) option preserves 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:
As written, this will place the local directory and its contents under the specified directory on the remote system. If the trailing slash is omitted on the destination, a new directory corresponding to the transferred directory (‘dir’ in the example) will not be created, and the contents of the source directory will be copied directly into the destination directory.
a(archive) option implies recursion.
To download a file, we simply change the source and destination:
A note on ports
All file transfers using the above methods 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
- If a custom SSH port is in use, you will have to specify it using the appropriate flag, often
manpage if you’re unsure.
Say we have to connect
rsyncthrough port 768 instead of 22. How would we modify this command?
Transferring files interactively with FileZilla
FileZilla is a cross-platform client for downloading and uploading files to and from a remote
computer. It is absolutely fool-proof and always works quite well. It uses the
sftp protocol. You
can read more about using the
sftp protocol in the command line here.
Download and install the FileZilla client from https://filezilla-project.org. After installing and opening the program, you should end up with a window with a file browser of your local system on the left hand side of the screen. When you connect to the cluster, your cluster files will appear on the right hand side.
To connect to the cluster, we’ll just need to enter our credentials at the top of the screen:
- User: Your cluster username
- Password: Your cluster password
- Port: (leave blank to use the default port)
Hit “Quickconnect” to connect. You should see your remote files appear on the right hand side of the screen. You can drag-and-drop files between the left (local) and right (remote) sides of the screen to transfer files.
Finally, if you need to move large files (typically larger than a gigabyte) from one remote computer
to another remote computer, SSH in to the computer hosting the files and use
transfer over to the other. This will be more efficient than using FileZilla (or related
applications) that would copy from the source to your local machine, then to the destination
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 can be used
to combine files into a single archive file and, optionally, compress it.
Let’s start with the file we downloaded from the lesson site,
hpc-lesson-data.tar.gz. The “gz”
part stands for gzip, which is a compression library. Reading this file name, it appears somebody
took a folder named “hpc-lesson-data,” wrapped up all its contents in a single file with
compressed that archive with
gzip to save space. Let’s check using
tar with the
-t flag, which
prints the “table of contents” without unpacking the file, specified by
-f <filename>, on the
remote computer. Note that you can concatenate the two flags, instead of writing
-t -f separately.
[[email protected] ~]$ ssh [email protected] [[email protected] ~]$ tar -tf hpc-lesson-data.tar.gz hpc-intro-data/ hpc-intro-data/north-pacific-gyre/ hpc-intro-data/north-pacific-gyre/NENE01971Z.txt hpc-intro-data/north-pacific-gyre/goostats hpc-intro-data/north-pacific-gyre/goodiff hpc-intro-data/north-pacific-gyre/NENE02040B.txt hpc-intro-data/north-pacific-gyre/NENE01978B.txt hpc-intro-data/north-pacific-gyre/NENE02043B.txt hpc-intro-data/north-pacific-gyre/NENE02018B.txt hpc-intro-data/north-pacific-gyre/NENE01843A.txt hpc-intro-data/north-pacific-gyre/NENE01978A.txt hpc-intro-data/north-pacific-gyre/NENE01751B.txt hpc-intro-data/north-pacific-gyre/NENE01736A.txt hpc-intro-data/north-pacific-gyre/NENE01812A.txt hpc-intro-data/north-pacific-gyre/NENE02043A.txt hpc-intro-data/north-pacific-gyre/NENE01729B.txt hpc-intro-data/north-pacific-gyre/NENE02040A.txt hpc-intro-data/north-pacific-gyre/NENE01843B.txt hpc-intro-data/north-pacific-gyre/NENE01751A.txt hpc-intro-data/north-pacific-gyre/NENE01729A.txt hpc-intro-data/north-pacific-gyre/NENE02040Z.txt
This shows a folder containing another folder, which contains a bunch of files. If you’ve taken The
Carpentries’ Shell lesson recently, these might look familiar. Let’s see about that compression,
du for “disk usage”.
[[email protected] ~]$ du -sh hpc-lesson-data.tar.gz 36K hpc-intro-data.tar.gz
If the filesystem block size is larger than 36 KB, you’ll see a larger number: files cannot be smaller than one block.
Now let’s unpack the archive. We’ll run
tar with a few common flags:
-xto extract the archive
-vfor verbose output
-zfor gzip compression
-ffor the file to be unpacked
When it’s done, check the directory size with
du and compare.
Extract the Archive
Using the four flags above, unpack the lesson data using
tar. Then, check the size of the whole unpacked directory using
tarlets you concatenate flags.
[[email protected] ~]$ tar -xvzf hpc-lesson-data.tar.gz
hpc-intro-data/ hpc-intro-data/north-pacific-gyre/ hpc-intro-data/north-pacific-gyre/NENE01971Z.txt hpc-intro-data/north-pacific-gyre/goostats hpc-intro-data/north-pacific-gyre/goodiff hpc-intro-data/north-pacific-gyre/NENE02040B.txt hpc-intro-data/north-pacific-gyre/NENE01978B.txt hpc-intro-data/north-pacific-gyre/NENE02043B.txt hpc-intro-data/north-pacific-gyre/NENE02018B.txt hpc-intro-data/north-pacific-gyre/NENE01843A.txt hpc-intro-data/north-pacific-gyre/NENE01978A.txt hpc-intro-data/north-pacific-gyre/NENE01751B.txt hpc-intro-data/north-pacific-gyre/NENE01736A.txt hpc-intro-data/north-pacific-gyre/NENE01812A.txt hpc-intro-data/north-pacific-gyre/NENE02043A.txt hpc-intro-data/north-pacific-gyre/NENE01729B.txt hpc-intro-data/north-pacific-gyre/NENE02040A.txt hpc-intro-data/north-pacific-gyre/NENE01843B.txt hpc-intro-data/north-pacific-gyre/NENE01751A.txt hpc-intro-data/north-pacific-gyre/NENE01729A.txt hpc-intro-data/north-pacific-gyre/NENE02040Z.txt
Note that we did not type out
-x -v -z -f, thanks to the flag concatenation, though the command works identically either way.
[[email protected] ~]$ du -sh hpc-lesson-data 144K hpc-intro-data
Was the data compressed?
Text files compress nicely: the “tarball” is one-quarter the total size of the raw data!
If you want to reverse the process — compressing raw data instead of extracting it —
c flag instead of
x, set the archive filename, then provide a directory to compress:
[[email protected] ~]$ tar -cvzf compressed_data.tar.gz hpc-intro-data
Working with Windows
When you transfer text 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
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
wgetdownloads a file from the internet.
scptransfer files to and from your computer.
You can use an SFTP client like FileZilla to transfer files through a GUI.