No filesystems from other platforms are cross-mounted, so you will need to copy over what you need.
First of all, make sure you have set up password-less authentication as described in HPC2020: How to connect before proceeding.
For transfers, we recommend using rsync which will transfer the files over an ssh connection.
All examples are done with the generic HPCF login node hpc-login, but you should use ecs-login if you don't have access to the full HPCF service.
Example: Transferring a directory tree between ECGATE onto the Atos HPCF
You may initiate the transfer from ECGATE:
user@ecgb11:~> rsync -avz $SCRATCH/mydataset hpc-login:/scratch/user/
or alternatively from Atos HPCF:
user@aa6-100:~> rsync -avz ecgate:/scratch/group/user/mydataset $SCRATCH/
Both solutions are equivalent, and can be run multiple times. Only new files will be transferred.
You may add the --delete option if you also wish to delete files on the destination that have been removed from the source.
You can use the $HOME environment variable to refer to your files in the rsync command provided this is protected by single quotes to ensure the variable is expanded on the remote host.
For example, to copy a directory from $HOME on ecgate to $HOME on Atos HPCF, initiating the transfer from ecgate, use:
rsync -avz $HOME/mydataset 'hpc-login:$HOME/'
However, the $SCRATCH or $PERM environment variables can only be used to refer to your files on the local host from where you initiate the rsync command as these are not set for use by the rsync command on the remote host.
An alternative option is to use the $HOME variable with pattern substitution. For example, to copy a directory tree from $SCRATCH on ecgate to $SCRATCH on Atos HPCF running the command on ecgate use:
user@ecgb11:~> rsync -avz $SCRATCH/mydataset 'hpc-login:${HOME/home/scratch}/'
or from $PERM on ecgate to $PERM on Atos HPCF running the command on the latter use:
user@aa6-100:~> rsync -avz 'ecgate:${HOME/home/perm}/mydataset' $PERM/
The single quotes are needed here to ensure the $HOME variable takes its value on the remote rather than the local host.
Advanced: High Performance Transfers with bbcp
You may also use a specialised tool called bbcp for best transfer rates. It is available on Atos HPCF, as well as Reading Based platforms Cray HPCF and ECGATE. This tool is not as flexible as rsync when it comes to updating existing or partial copies, but it should be quicker when doing a one-off transfer.
For example, if you wanted to transfer a directory called mydataset in your SCRATCH in Reading, you could initiate the transfer from ECGATE:
user@ecgb11:~> bbcp -rp -s 10 -P 2 $SCRATCH/mydataset hpc-login:/scratch/user/
or alternatively from Atos HPCF:
user@aa6-100:~> bbcp -rp -s 10 -P 2 ecgate:/scratch/group/user/mydataset $SCRATCH/
The options above would perform a recursive copy, preserving file permissions and using 10 parallel streams. It would also report progress every 2 seconds.
You may find all the details in the bbcp official documentation.
Copying softlinks
bbcp will not copy soft links, so if you are copying an entire directory structure that contains them, you may need to copy them over at a second stage with another tool like rsync.