Uppsala Multidisciplinary Center for Advanced Computational Science

Grus user guide

PREREQUISITES

If you have received a NGI delivery and only want to transfer the data to your SNIC-SENS project on Bianca, please follow our Deliver guide instead.

In order to  access the Grus delivery service you need:

1. To be connected to SUNET (Swedish University Computer Network).

Grus contains sensitive data and the access is restricted to SUNET. If you require access to Grus from outside of SUNET, please contact support@uppmax.uu.se. For a list of SUNET members, please see this link:

https://www.sunet.se/sunets-nat/anslutna/

2. An UPPMAX account.

3. An accepted SNIC common user agreement in SUPR.

4. You need to be a member of the delivery project on SUPR.

Finally, note that it will take some time before changes in SUPR are reflected everywhere. For example if the PI adds you as a member of the delivery project, it may take an hour until you are able to log in.

1. Set up 2 factor authentication

Follow the instuctions in Setting up two factor authetication.

Note that this is a second factor specific for UPPMAX. You may have set up two factor authentication for other sites (e.g. SUPR), but you can not use codes from that second factor for authenticating to UPPMAX.

Make sure you enter the correct code! The code you use on Grus is the one labeled UPPMAX, highlighted in green below.


2. Login

Note that Grus only supports connections with sftp. If you connect with regular ssh you will be disconnected directly after authentication.

Recommended: Using a graphical connection:

The easiest way to get your data is to start a graphical Filezilla instance, either on your own computer or on the login node of the cluster you want to transfer your data to. If you want to start FileZilla graphically on a login node, you need to have a graphical connection. This can be achieved either by using ThinLinc or by connecting to the login node with X11-forwarding enabled. To use X11-forwarding you can add the -Y flag to your ordinary ssh command when connecting to UPPMAX. This requires you to have a X-server installed on your own computer to be able to take care of the graphics that will be sent. If you have a Mac you can install XQuartz and Windows users can use MobaXterm.

$ ssh -Y <username>@<cluster>.uppmax.uu.se

For example

$ ssh -Y myuser@rackham.uppmax.uu.se

Once this is done, you start Filezilla by simply typing the command "filezilla". This will open a graphical Filezilla window. To connect to Grus from FileZilla you need to click on File and then Site Manager. Inside the Site Manager you can add a New Site, call it Grus and then make sure you enter the connection details as outlined below.

Host: grus.uppmax.uu.se
Port: 22
Protocol: SFTP
Logon Type: Ask for password
User name: <username>-<projid>

Note that you do not have to enter the password at this stage. That comes later.

OBS! Make sure User is your normal UPPMAX username followed by a hyphen '-' and then the name of your delivery project. For example, 'user-delivery123456'.

In the end it should look like the following:

When you click on connect, you will be prompted for a password. The password is your normal UPPMAX password directly followed by the six digit code from your Authenticator application.

For example, if my password is "secret" and my six digit code at this moment is "287463" the password becomes "secret287463".

Once connected you should see the files on Grus on the right hand side of the Filezilla windows and the files on the computer you are running Filezilla on on the left side. You can now "drag and drop" files either way to upload and download files.

Advanced usage example 1: Using the standard sftp client

The other way to transfer files involve running SFTP on the command line and type all the commands yourself. This is only recommended for advanced users and only if X11-forwarding for some reason is unavailable. You start off by connecting to Grus using the sftp program.

$ sftp <username>-<projid>@grus.uppmax.uu.se
Ex.
$ sftp myuser-delivery999999@grus.uppmax.uu.se

As password you use your normal UPPMAX password directly followed by
the six digits from the second factor application from step 1.

Ex. if your password is "VerySecret" and the second factor code is 123 456 you would type VerySecret123456 as the password in this step.

Once connected you will have to type the sftp commands to upload/download files. Have a look at the Basic SFTP commands guide to get started with it.

Advanced usage example 2: Using lftp
Another possibility is to use lftp (a file transfer client that supports different protocol, sftp among them).

$ lftp sftp://<username>-<projid>@grus.uppmax.uu.se/
Password:
cd ok, cwd=/
lftp <username>-<projid>@grus.uppmax.uu.se:/>

lftp has a mirror command which can be used to download an entire directory tree, 

mirror datadir local_copy_of_datadir

will download datadir into local_copy_of_datadir.