Transferring files with remote computers
Last updated on 2024-12-03 | Edit this page
Overview
Questions
- How do I transfer files to (and from) the cluster?
Objectives
-
wgetandcurl -Odownload a file from the internet. -
scptransfers files to and from your computer.
Required Files
The program used in this example can be retrieved using wget or a browser and copied to the remote.
Using wget:
BASH
userid@ln03:~> wget https://epcced.github.io/2024-11-06-archer2-hpc-intro/files/hpc-intro-data.tar.gzUsing a web browser:
https://epcced.github.io/2024-11-06-archer2-hpc-intro/files/hpc-intro-data.tar.gz
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
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.
BASH
[user@laptop ~]$ curl -O https://epcced.github.io/2024-11-06-archer2-hpc-intro/files/hpc-intro-data.tar.gzor
BASH
[user@laptop ~]$ wget https://epcced.github.io/2024-11-06-archer2-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.
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 ARCHER2.
Why Not Download on ARCHER2 Directly?
Some computer clusters are behind firewalls set to only allow
transfers initiated from the outside. 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 (just below
here) to upload it to the cluster.
Can you download from the server directly?
Try downloading the file directly using curl or
wget. Do the commands understand file locations on your
local machine over SSH? Note that it may well fail, and that’s OK!
Using curl or wget commands like the
following:
BASH
[user@laptop ~]$ ssh userid@login.archer2.ac.uk
userid@ln03:~> curl -O https://epcced.github.io/2024-11-06-archer2-hpc-intro/files/hpc-intro-data.tar.gz
or
userid@ln03:~> wget https://epcced.github.io/2024-11-06-archer2-hpc-intro/files/hpc-intro-data.tar.gzDid 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.
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:
BASH
[user@laptop ~]$ rsync -avzP path/to/local/file.txt userid@login.archer2.ac.uk:directory/path/on/ARCHER2/The 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:
BASH
[user@laptop ~]$ rsync -avzP path/to/local/dir userid@login.archer2.ac.uk:directory/path/on/ARCHER2/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:
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 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.
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.
BASH
[user@laptop ~]$ ssh userid@login.archer2.ac.uk
userid@ln03:~> 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.txtThis 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”.
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:
-
-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 du. Hint: tar lets you concatenate
flags.
OUTPUT
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.txtNote that we did not type out -x -v -z -f, thanks to the
flag concatenation, though the command works identically either way.
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:
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
- “
wgetandcurl -Odownload a file from the internet.” - “
scptransfers files to and from your computer.”