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ScopeM ETH Zurich

This article explains how to transfer data remotely between the ETH Zurich ScopeM facility and Merlin 7 using the SFTP (SSH File Transfer Protocol).

Using NoMachine

One of the easiest ways to transfer files using SFTP is through NoMachine and FileZilla.

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 the value to 10.
  4. Click OK to save the changes.

1. Connect to Merlin 7

Connect to Merlin 7 using NoMachine.

2. Open FileZilla

Open FileZilla either by clicking the FileZilla icon or by running the following command in a terminal: filezilla

3. Connect to the ScopeM endpoint

In FileZilla, enter the ScopeM SFTP endpoint in the connection fields:

  • Host: sftp://scopem-krios1data.ethz.ch
  • Username: Your ScopeM username
  • Password: Your ScopeM password
  • Port: 5007

Click Quickconnect to establish the connection.

Once connected, your files on the ScopeM endpoint will be displayed in the Remote site panel.

You can transfer files between ScopeM 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.

NoMachine session

File transfers can continue after you close the NoMachine window, as long as the NoMachine session itself remains active. Do not terminate the NoMachine session until the transfer has completed.

Using the terminal

ScopeM endpoints can also be accessed directly from a Merlin 7 login node using sftp.

Interactive SFTP session

Connect to a ScopeM endpoint with:

Bash
sftp -P 5007 <username>@scopem-krios1data.ethz.ch

If you encounter an error such as "Too many authentication failures", force SFTP to use password authentication:

Bash
sftp -o PubkeyAuthentication=no -o PreferredAuthentications=password -P 5007 <username>@scopem-krios1data.ethz.ch

Enter your password when prompted.

Once connected, use the get command to download files or directories. For example:

Text Only
sftp> get -r home/P1

Fetching home/P1/ to P1
Retrieving home/P1
Retrieving home/P1/J1

The -r option recursively downloads the specified directory and its contents.

Download a directory directly

You can also specify the remote path directly on the command line:

Bash
sftp -r -P 5007 <username>@scopem-krios1data.ethz.ch:home/P1 ./

You will be prompted for your password:

Text Only
<username>@scopem-krios1data.ethz.ch's password:

Connected to scopem-krios1data.ethz.ch.

Fetching /home/P1/ to ./P1
Retrieving /home/P1
Retrieving /home/P1/J1

Configure SSH for easier access

If you frequently transfer data from ScopeM, you can simplify the connection by adding the ScopeM endpoints to your SSH configuration file:

Text Only
$HOME/.ssh/config

For example:

Text Only
Host krios1 krios2 krios3
    HostName scopem-%hdata.ethz.ch

Host scopem-krios*data.ethz.ch
    Port 5007

Host *.ethz.ch
    User <username>

With this configuration, the hostname, port, and username do not need to be specified for every connection.

For example, instead of:

Bash
sftp -r -P 5007 <username>@scopem-krios1data.ethz.ch:home/P1 ./

you can use:

Bash
sftp -r krios1:home/P1 ./

SSH configuration

Adjust the User entry in $HOME/.ssh/config to match your username.