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 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

• curl -O https://some/link/to/a/file
• 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://hpc-workshops.github.io/ctcms-hpc-intro/files/hpc-intro-code.tar.gz

or

[user@laptop ~]$ wget https://hpc-workshops.github.io/ctcms-hpc-intro/files/hpc-intro-code.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” later, since “tar-dot-g-z” is a mouthful.

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 local_file yourUsername@ruth.nist.gov:remote_path

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 have a more specific destination in mind.

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

[user@laptop ~]$ scp hpc-intro-code.tar.gz yourUsername@ruth.nist.gov:

Why Not Download on ruth Directly?

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.

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

Commands

[user@laptop ~]$ ssh yourUsername@ruth.nist.gov
501 ruth% curl -O https://hpc-workshops.github.io/ctcms-hpc-intro/files/hpc-intro-code.tar.gz
# or
501 ruth% wget https://hpc-workshops.github.io/ctcms-hpc-intro/files/hpc-intro-code.tar.gz

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

Transferring a Directory

If you went ahead and extracted the tarball, don’t worry! scp can handle entire directories as well as individual files.

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 hpc-intro-code yourUsername@ruth.nist.gov:~/

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 hpc-intro-code.tar.gz yourUsername@ruth.nist.gov:

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
• 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 hpc-intro-code yourUsername@ruth.nist.gov:~/

As written, this will place the local directory and its contents under your home directory on the remote system. If the trailing slash is omitted on the destination, 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:

[user@laptop ~]$ rsync -avzP yourUsername@ruth.nist.gov:hpc-intro-code ./

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.

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 hpc-intro-code.tar.gz yourUsername@ruth.nist.gov:

Solution

[user@laptop ~]$ man rsync
[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 hpc-intro-code.tar.gz yourUsername@ruth.nist.gov:

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-intro-code.tar.gz. The “gz” part stands for gzip, which is a compression library. This kind of file can usually be interpreted by reading its name: it appears somebody took a folder named “hpc-intro-code,” 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@ruth.nist.gov
501 ruth% tar -tf hpc-intro-code.tar.gz
hpc-intro-code/
hpc-intro-code/amdahl
hpc-intro-code/README.md
hpc-intro-code/LICENSE.txt

This shows a folder which contains a few files. Let’s see about that compression, using du for “disk usage”.

501 ruth% du -sh hpc-intro-code.tar.gz
3.4K     hpc-intro-code.tar.gz

Files Occupy at Least One “Block”

If the filesystem block size is larger than 3.4 KB, you’ll see a larger number: files cannot be smaller than one block. You can use the --apparent-size flag to see the exact size, although the unoccupied space in that filesystem block can’t be used for anything else.

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

501 ruth% tar -xvzf hpc-intro-code.tar.gz

hpc-intro-code/
hpc-intro-code/amdahl
hpc-intro-code/README.md
hpc-intro-code/LICENSE.txt

Note that we did not type out -x -v -z -f, thanks to the 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.

501 ruth% du -sh hpc-intro-code
16K    hpc-intro-code

Was the Data Compressed?

Text files (including Python source code) 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_code.tar.gz hpc-intro-code

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.)

Key Points

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

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