Transferring files with remote computers

Overview

Teaching: 15 min
Exercises: 15 min

Questions

• How do I transfer files to (and from) the cluster?

Objectives

• Transfer files to and from a computing 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 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 -O or wget. This is a quick way to download datasets or source code.

The syntax for these commands is: curl -O https://some/link/to/a/file and 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.

[user@laptop ~]$ curl -O https://baskerville-hpc.github.io/hpc-intro/files/hpc-intro-data.tar.gz

or

[user@laptop ~]$ wget https://baskerville-hpc.github.io/hpc-intro/files/hpc-intro-data.tar.gz

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. 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:

[user@laptop ~]$ scp path/to/local/file.txt yourUsername@login.baskerville.ac.uk:/path/on/Baskerville

To download from another computer:

[user@laptop ~]$ scp yourUsername@login.baskerville.ac.uk:/path/on/Baskerville/file.txt path/to/local/

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.

[user@laptop ~]$ scp local-file.txt yourUsername@login.baskerville.ac.uk:

Upload a File

Copy the file you just downloaded from the Internet to your home directory on Baskerville.

Solution

[user@laptop ~]$ scp hpc-intro-data.tar.gz yourUsername@login.baskerville.ac.uk:~/

Most computer clusters are protected from the open internet by a firewall. This means that the curl command will fail, as an address outside the firewall is unreachable from the inside. To get around this, run the curl or wget command from your local machine to download the file, then use the scp command to upload it to the cluster.

Why Not Download on Baskerville Directly?

Try downloading the file directly. Note that it may well fail, and that’s OK!

Commands

[user@laptop ~]$ ssh yourUsername@login.baskerville.ac.uk
[yourUsername@bask-pg0310u18a ~]$ curl -O https://baskerville-hpc.github.io/hpc-intro/files/hpc-intro-data.tar.gz
or
[yourUsername@bask-pg0310u18a ~]$ wget https://baskerville-hpc.github.io/hpc-intro/files/hpc-intro-data.tar.gz

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.

[user@laptop ~]$ scp -r some-local-folder yourUsername@login.baskerville.ac.uk:target-directory/

Caution

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

What’s in a /?

When using scp, you may have noticed that a : always follows the remote computer name; sometimes a / follows that, and sometimes not, and sometimes there’s a final /. On Linux computers, / 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 rsync.

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 creating synced backup folders.

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

[user@laptop ~]$ rsync -avzP path/to/local/file.txt yourUsername@login.baskerville.ac.uk:directory/path/on/Baskerville/

The options are:

• a (archive) to preserve file timestamps and permissions among other things
• v (verbose) to get verbose output to help monitor the transfer
• z (compression) to compress the file during transit to reduce size and transfer time
• 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:

[user@laptop ~]$ rsync -avzP path/to/local/dir yourUsername@login.baskerville.ac.uk:directory/path/on/Baskerville/

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.

The a (archive) option implies recursion.

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

[user@laptop ~]$ rsync -avzP yourUsername@login.baskerville.ac.uk:path/on/Baskerville/file.txt path/to/local/

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 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.

Change the Rsync Port

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

[user@laptop ~]$ rsync test.txt yourUsername@login.baskerville.ac.uk:

Solution

[user@laptop ~]$ rsync --help | grep port
     --port=PORT             specify double-colon alternate port number
See http://rsync.samba.org/ for updates, bug reports, and answers
[user@laptop ~]$ rsync --port=768 test.txt yourUsername@login.baskerville.ac.uk:

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 in the lesson discussion.

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:

• Host: sftp://login.baskerville.ac.uk
• 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 scp or rsync to 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 machine.

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 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 tar, then 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.

[user@laptop ~]$ ssh yourUsername@login.baskerville.ac.uk
[yourUsername@bask-pg0310u18a ~]$ 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, using du for “disk usage”.

[yourUsername@bask-pg0310u18a ~]$ du -sh hpc-lesson-data.tar.gz
36K     hpc-intro-data.tar.gz

Files Occupy at Least One “Block”

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:

• -x to extract the archive
• -v for verbose output
• -z for gzip compression
• -f for 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 du.

Hint: tar lets you concatenate flags.

Commands

[yourUsername@bask-pg0310u18a ~]$ 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.

[yourUsername@bask-pg0310u18a ~]$ 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 – set a c flag instead of x, set the archive filename, then provide a directory to compress:

[user@laptop ~]$ 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 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.)

Key Points

• wget and curl -O download a file from the internet.

• scp and rsync transfer files to and from your computer.

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