Using Tar over SSH to move many files
SSH certificates are required to connect to Roihu over SSH
To connect to Roihu, users must sign their public key in MyCSC to obtain a time-based SSH certificate. Each certificate is valid for 24 hours, and once it expires, a new one must be generated by signing the public key again.
Linux tools such as scp and rsync are commonly used to transfer files
between a remote server and a local machine. However, these tools are not
very practical for moving many small files.
A simple, much faster solution is to write a (compressed) tar package
containing your data directly to the target system. This is accomplished by
piping the output of tar over an ssh connection. Writing the archive
directly to the destination helps also to conserve disk space on the source
system.
For general information about tar, see Packing and compression tools.
Examples
Transferring data between your local computer and Puhti
All following commands are executed on a local workstation, which is assumed to
have the required tools (tar, ssh and, optionally, gzip/bzip2) installed.
Puhti is used as the example remote server.
The general syntax is:
For example, the command to copy a directory myfiles from your local machine
to the directory /scratch/project_2001234 on Puhti would be:
Note
If you have stored your SSH key or certificate file with a non-default name
or in a non-default location (somewhere else than ~/.ssh/id_<algorithm>
and ~/.ssh/id_<algorithm>-cert.pub), you must specify where ssh should
look for the files using the -i option, e.g:
tar c myfiles | ssh -i <path_to_private_key> -i <path_to_certificate> <username>@<host> 'cat > /scratch/project_2001234/myfiles.tar'
The rest of this page assumes the key and certificate are stored in a
default location using standard naming, so the -i flag is omitted. Note
that SSH certificates are required for connecting to Roihu only.
To extract the tar archive at the same time, replace the cat command as:
Conversely, you could also copy data located on the remote server to your local machine using a command like:
ssh <username>@puhti.csc.fi 'tar c -C <parent_directory_on_puhti> <directory_to_transfer>' > <archive_on_local_machine>
For example, the command to copy a folder myfiles located in
/scratch/project_2001234 to your local machine would be:
To extract the archive at the same time:
Enable compression
The above commands did not use compression. Replace tar c (tar x) with
tar cz or tar cj (tar xz or tar xj) to enable gzip or bzip2
compression (decompression). Note that some files do not benefit from
compression (e.g. binary files or files that are already compressed), in
which case it is faster to transfer without compressing.
Avoid verbose output
Adding v option (e.g. tar czv) will produce verbose output, i.e. list
the processed files in the console. This slows down the transfer process
when moving many small files, so it is recommended to avoid using it.
Transferring 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. For Roihu, a valid SSH certificate is also needed. This is accomplished by forwarding your SSH agent including your SSH keys (and certificate) to the supercomputer you're first connecting to.
After this, data can be transferred directly between CSC supercomputers using
same syntax as above. For example, the command to transfer a directory
/scratch/project_2001234/myfiles on Puhti to the corresponding location on
Mahti would be:
tar c -C /scratch/project_2001234 myfiles | ssh <username>@mahti.csc.fi 'cat > /scratch/project_2001234/myfiles.tar'
The same could be accomplished while working on Mahti as follows:
ssh <username>@puhti.csc.fi 'tar c -C /scratch/project_2001234 myfiles' > /scratch/project_2001234/myfiles.tar
Performance comparison
Below is a rough comparison of the time taken to transfer a directory with many small files to Puhti. Each file is 100 KiB in size and no compression is applied.
| Number of files | tar + ssh |
scp |
|---|---|---|
| 100 | 0.5 s | 2.4 s |
| 1000 | 1.3 s | 20.5 s |
| 10000 | 9.4 s | 201.2 s |