OverviewTeaching: 20 min
Exercises: 10 minQuestions
How do I upload/download files to/from a remote HPC system?Objectives
Be able to tranfer files to and from a remote HPC system.
One thing people very frequently struggle with is transferring files to and from a remote system. We’ll cover several methods of doing this from the command line, then cover how to do this using the GUI program FileZilla. The method you choose will be decided by what is most covenient for your workflow.
To download files from the internet,
the easiest tool to use is
The syntax is relatively straightforward:
[remote]$ wget https://epcced.github.io/hpc-intro/files/cfd.tar.gz
--2018-07-17 11:44:44-- https://epcced.github.io/hpc-intro/files/cfd.tar.gz Resolving epcced.github.io (epcced.github.io)... 184.108.40.206, 220.127.116.11, 18.104.22.168, ... Connecting to epcced.github.io (epcced.github.io)|22.214.171.124|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 20480 (20K) [application/gzip] Saving to: ‘cfd.tar.gz’ 100%[===========================================================================================================>] 20,480 --.-K/s in 0.01s 2018-07-17 11:44:44 (2.05 MB/s) - ‘cfd.tar.gz’ saved [20480/20480]
To copy a single file to or from the remote system, we can use
The syntax can be a little complex for new users,
but we’ll break it down here:
To transfer to another computer:
[local]$ scp /path/to/local/file.txt yourUsername@remote.computer.address:/path/on/remote/computer
To download from another computer:
[local]$ scp yourUsername@remote.computer.address:/path/on/remote/computer/file.txt /path/to/local/copy
Note that we can simplify doing this by shortening our paths.
On the remote computer, everything after the
: is relative to our home directory.
We can simply just add a
: and leave it at that if we don’t care where the file goes.
[local]$ scp local-file.txt yourUsername@remote.computer.address:
To recursively copy a directory, we just add the
-r (recursive) flag:
[local]$ scp -r some-local-folder/ yourUsername@remote.computer.address:target-directory/
scp is useful, but what if we don’t know the exact location of what we want to transfer?
Or perhaps we’re simply not sure which files we want to tranfer yet.
sftp is an interactive way of downloading and uploading files.
Let’s connect to a remote system using
sftp, you’ll notice it works the same way as SSH:
[local]$ sftp yourUsername@login.cirrus.ac.uk
This will start what appears to be a bash shell (though our prompt says
However we only have access to a limited number of commands.
We can see which commands are available with
Available commands: bye Quit sftp cd path Change remote directory to 'path' chgrp grp path Change group of file 'path' to 'grp' chmod mode path Change permissions of file 'path' to 'mode' chown own path Change owner of file 'path' to 'own' df [-hi] [path] Display statistics for current directory or filesystem containing 'path' exit Quit sftp get [-afPpRr] remote [local] Download file reget [-fPpRr] remote [local] Resume download file reput [-fPpRr] [local] remote Resume upload file help Display this help text lcd path Change local directory to 'path' lls [ls-options [path]] Display local directory listing lmkdir path Create local directory ln [-s] oldpath newpath Link remote file (-s for symlink) lpwd Print local working directory ls [-1afhlnrSt] [path] Display remote directory listing # omitted further output for clarity
Notice the presence of multiple commands that make mention of local and remote. We are actually connected to two computers at once (with two working directories!).
To show our remote working directory:
Remote working directory: /lustre/home/y15/yourUsername
To show our local working directory, we add an
l in front of the command:
Local working directory: /Users/auser/carpentry
The same pattern follows for all other commands:
lsshows the contents of our remote directory, while
llsshows our local directory contents.
cdchanges the remote directory,
lcdchanges the local one.
To upload a file, we type
sftp> put input.dat
Uploading input.dat to /lustre/home/y15/yourUsername/input.dat input.dat 100% 2000KB 11.0MB/s 00:00
To download a file we type
sftp> get input.dat
Fetching /lustre/home/y15/yourUsername/input.dat to input.dat /lustre/home/y15/yourUsername/input.dat 100% 2000KB 11.0MB/s 00:00
And we can recursively put/get files by just adding
Note that the directory needs to be present beforehand.
sftp> mkdir data sftp> put -r data/
Uploading content/ to /lustre/home/y15/yourUsername/data Entering content/ ntering data/ data/data11.dat 100% 100KB 8.4MB/s 00:00 data/data10.dat 100% 100KB 8.8MB/s 00:00 data/data12.dat 100% 100KB 8.5MB/s 00:00 data/data13.dat 100% 100KB 8.7MB/s 00:00 data/data17.dat 100% 100KB 8.8MB/s 00:00 data/data16.dat 100% 100KB 8.4MB/s 00:00 data/data28.dat 100% 100KB 8.7MB/s 00:00 data/data14.dat 100% 100KB 8.5MB/s 00:00 data/data15.dat 100% 100KB 8.7MB/s 00:00 data/data29.dat 100% 100KB 4.7MB/s 00:00 data/data9.dat 100% 100KB 8.2MB/s 00:00 data/data8.dat 100% 100KB 8.6MB/s 00:00 data/data6.dat 100% 100KB 8.8MB/s 00:00 data/data7.dat 100% 100KB 8.8MB/s 00:00 data/data5.dat 100% 100KB 8.6MB/s 00:00 data/data4.dat 100% 100KB 8.5MB/s 00:00 data/data0.dat 100% 100KB 8.6MB/s 00:00 data/data1.dat 100% 100KB 8.6MB/s 00:00 data/data3.dat 100% 100KB 8.7MB/s 00:00 data/data2.dat 100% 100KB 8.6MB/s 00:00 data/data24.dat 100% 100KB 8.5MB/s 00:00 data/data18.dat 100% 100KB 8.4MB/s 00:00 data/data19.dat 100% 100KB 6.2MB/s 00:00 data/data25.dat 100% 100KB 7.3MB/s 00:00 data/data27.dat 100% 100KB 8.7MB/s 00:00 data/data26.dat 100% 100KB 6.2MB/s 00:00 data/data22.dat 100% 100KB 6.3MB/s 00:00 data/data23.dat 100% 100KB 7.9MB/s 00:00 data/data21.dat 100% 100KB 8.0MB/s 00:00 data/data20.dat 100% 100KB 7.8MB/s 00:00
To quit, we type
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.
In fact, it uses the exact same protocol as
sftp under the hood.
sftp works, so will FileZilla!
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:
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.
Using the above methods, try transferring files to and from the cluster. Which method do you like the best and why? Can you think of any potential issues with your preferred method?
If we are transferring large amounts of data then there are some additional things we have to take into account in terms of performance and being considerate to other users on the system. We will talk about these later in the lesson…
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 text 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 handle this correctly, in some 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
A note on ports
All file tranfers using the above methods use encrypted communication over port 22. This is the same connection method used by SSH. In fact, all file transfers using these methods occur through an SSH connection. If you can connect via SSH over the normal port, you will be able to transfer files.
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.