Using rsync for data transfer and synchronization

SSH keys are required to connect to Puhti and Mahti over SSH

Since April 14th 2025, connecting to Puhti and Mahti over SSH only works using SSH keys added in MyCSC. Password authentication and public keys stored in users' personal ~/.ssh/authorized_keys file on the supercomputer no longer works.

Read the detailed instructions on setting up and using SSH keys.

Rsync is a data transfer tool that can be used much like the scp command. When transferring data, rsync checks the difference between the source and target files and only transfers the parts that have changed. This makes rsync suitable for:

1. Synchronizing folders. Using scp or cp would copy and transfer everything, while rsync will only copy and transfer the modifications.
2. Transferring large files. rsync can be set to save progress, so if the transfer is interrupted, it can be resumed at the same point.

The basic command syntax of rsync is:

rsync -options source target

If the data source or target location is a remote site, it is defined with the syntax:

username@server:/path/on/server

However, both the target and source can also be located on the same machine. In that case you can just give directory paths to source and target sites.

The table below lists the most commonly used options:

Option	Argument	Description
-r		Recurse into directories
-a		Use archive mode: copy files and directories recursively and preserve access permissions and timestamps
-v		Verbose mode
-z		Compress
-e	ssh	Specify the remote shell to use
-n		Show what files would be transferred
--partial		Keep partially transferred files
--progress		Show progress during transfer
-P		Same as --partial --progress
-u		Skip files that are newer on the receiver

Warning

rsync will by default overwrite any changes made to the target, even if they are newer than the source! Use option -u to avoid this.

Using rsync to transfer data between your local computer and Puhti

The command for transferring a local folder to Puhti, while showing the progress and keeping partially transferred files, would for example be:

rsync -rP /path/to/local/folder <username>@puhti.csc.fi:/path/to/target

This would either:

1. Create a folder on Puhti at /path/to/target/folder if the folder was not present before. In this case, everything in the local folder will be transferred.
2. Synchronize the source and target folders if the folder already exists on Puhti. In this case, only changes we have made will be transferred.

And the same thing in reverse:

rsync -rP <username>@puhti.csc.fi:/path/to/target/folder /path/to/local

Note

If you have stored your SSH key file with a non-default name or in a non-default location (somewhere else than ~/.ssh/id_<algorithm>), you can specify where rsync should look for the key using the -e option. For example:

rsync -rP -e "ssh -i /path/to/private/key" /path/to/local/folder <username>@puhti.csc.fi:/path/to/target

Using rsync to transfer data directly between CSC supercomputers

To transfer data directly between CSC supercomputers, you must be able to access the SSH keys you've set up on your local workstation for authenticating to CSC supercomputers. This is accomplished by forwarding your SSH agent to the supercomputer you're first connecting to.

• SSH agent forwarding instructions for Linux/macOS
• SSH agent forwarding instructions for Windows

After this, rsync can be used to transfer data directly between CSC supercomputers using same syntax as above. For example, to copy a directory /scratch/project_2001234/myfiles on Puhti to the corresponding path on Mahti:

rsync -rP /scratch/project_2001234/myfiles <username>@mahti.csc.fi:/scratch/project_2001234

See also the final section of this tutorial.

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