Managing data

Instructor note

  • teaching: 15

  • exercises: 15

Questions

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

Objectives

  • Transfer files to and from a computing cluster.

Keypoints

  • 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.

This LUMI-self-learning chapter to be about transferring files, where to put your data on LUMI and the storage options, including LUMI-O.

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

Exercise

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.

wget and curl Commands

{{ site.local.prompt }} wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main or {{ site.local.prompt }} curl -o amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main


{: .solution}

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

{{ site.local.prompt }} 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.

{{ site.local.prompt }} 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

Extract the Archive

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

{{ site.local.prompt }} tar -xvzf 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



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.

{{ site.local.prompt }} mv hpc-carpentry-amdahl-46c9b4b amdahl

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

{{ site.local.prompt }} du -sh amdahl.tar.gz
8.0K     amdahl.tar.gz
{{ site.local.prompt }} 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:

{{ site.local.prompt }} tar -cvzf compressed_code.tar.gz amdahl

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!

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

{{ site.local.prompt }} scp local_file {{ site.remote.user }}@{{ site.remote.login }}: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:

{{ site.local.prompt }} scp amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:

Exercise

Why Not Download on {{ site.remote.name }} 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!

Commands

{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }} {{ site.remote.prompt }} wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main or {{ site.remote.prompt }} curl -o amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main


{: .solution}

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”: 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.

{{ site.local.prompt }} scp -r amdahl {{ site.remote.user }}@{{ site.remote.login }}:

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. It 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:

{{ site.local.prompt }} rsync -avP amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:



The options are:

* `-a` (**a**rchive) to preserve file timestamps, permissions, and folders,
   among other things; implies recursion
* `-v` (**v**erbose) 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:

{{ site.local.prompt }} rsync -avP amdahl {{ site.remote.user }}@{{ site.remote.login }}:~/



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:

{{ site.local.prompt }} rsync -avP {{ site.remote.user }}@{{ site.remote.login }}: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.

Exercise

Change the Rsync Port

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

{{ site.local.prompt }} rsync amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:



_Hint:_ check the `man` page or "help" for `rsync`.

 Solution

{{ site.local.prompt }} man rsync {{ site.local.prompt }} rsync –help | grep port –port=PORT specify double-colon alternate port number See http://rsync.samba.org/ for updates, bug reports, and answers {{ site.local.prompt }} rsync –port=768 amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:



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

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]({{ site.baseurl }}{% link _extras/discuss.md %}).

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://{{ site.remote.login }}

  • 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.

{% include links.md %}