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EMF PSI

The storage systems used by the Electron Microscopy Facility at PSI (EMF) are mounted on the Merlin 7 login nodes. You can copy files from the EMF storage to your home or project directory on Merlin 7, or transfer them from Merlin 7 to your local computer.

Within Merlin 7

The EMF files are accessible through the /emf mount on the Merlin 7 cluster. However, the files are not stored on Merlin 7; the mount provides access to files that remain on the EMF storage system.

Before working with the files, copy them to your home directory or project directory on Merlin 7.

rsync

We recommend using rsync to copy files because it preserves file attributes and provides useful information about the transfer.

Run:

Bash
rsync -avAHXS sourcedir/ destdir/

If you need to change the group ownership of the copied files, use:

Bash
rsync -avAHXS --chown=:$GROUP_NAME sourcedir/ destdir/

Replace $GROUP_NAME with the name of the group that should own the files.

Note

The trailing / in sourcedir/ is significant. It means that the contents of sourcedir are copied to destdir, rather than the directory itself.

cp

Alternatively, you can use cp:

Bash
cp -r sourcedir/ destdir/

From Merlin 7 to your local machine

You can transfer files from Merlin 7 to your local computer using rsync, scp, or a graphical application such as FileZilla.

rsync

rsync is recommended for transferring large amounts of data or for transfers that may need to be resumed.

For example:

Bash
rsync -avAHXS $USER@login001.merlin7.psi.ch:/data/project/general/myproject/ ~/localdata/

scp

For a simple recursive copy, you can use scp:

Bash
scp -r $USER@login001.merlin7.psi.ch:/data/project/general/myproject/ ~/localdata/

FileZilla

You can also use FileZilla to transfer files between your local computer and Merlin 7.

Open FileZilla and create a connection to Merlin 7 using the following settings:

Setting Value
Host login001.merlin7.psi.ch or login002.merlin7.psi.ch
Username Your Merlin 7 username
Password Your Merlin 7 password
Port 22
Protocol SFTP - SSH File Transfer Protocol

Once connected, the files on Merlin 7 will be displayed in the Remote site panel.

You can transfer files between your computer and Merlin 7 by dragging them between the Remote site and Local site panels. Alternatively, right-click a file or directory and select Download or Upload.

Tip

To improve file transfer speeds, increase the maximum number of simultaneous transfers in FileZilla:

  1. Open Edit > Settings.
  2. Select Transfers.
  3. Under Maximum simultaneous transfers, set Maximum simultaneous transfers to 10.
  4. Click OK to save the changes.